diff --git a/bids_prov/afni/afni_parser.py b/bids_prov/afni/afni_parser.py
index d1ab9a7a6..64524e9d7 100644
--- a/bids_prov/afni/afni_parser.py
+++ b/bids_prov/afni/afni_parser.py
@@ -7,8 +7,11 @@
from itertools import chain
from bids_prov.fsl.fsl_parser import get_entities
-from bids_prov.utils import get_default_graph, CONTEXT_URL, get_id, label_mapping, compute_sha_256_entity, \
+from bids_prov.utils import (
+ get_default_graph, CONTEXT_URL, label_mapping, compute_sha_256_entity,
+ get_activity_urn, get_agent_urn, get_entity_urn, make_alnum, get_uuid,
writing_jsonld
+ )
# regex to catch inputs
# in `cp /fsl/5.0/doc/fsl.css .files no_ext 5.0` --> only `.files` should match
@@ -117,12 +120,12 @@ def build_records(commands_block: list, agent_id: str, verbose: bool = False):
for (block, cmd) in commands_block:
cmd_s = re.split(" |=", cmd)
- a_name = cmd_s[0]
+ activity_name = cmd_s[0]
cmd_args_remain = cmd_s[1:]
inputs = []
outputs = []
function_in_description_functions = False
- command_name_end = os.path.split(a_name)[1]
+ command_name_end = os.path.split(activity_name)[1]
for df in description_functions:
if df["Name"] == command_name_end:
@@ -182,7 +185,7 @@ def build_records(commands_block: list, agent_id: str, verbose: bool = False):
outputs = list(chain(*(attributes.pop(k)
for k in attributes.keys() & OUTPUT_TAGS)))
entity_names = [_ for _ in re.findall(
- INPUT_RE, cmd_without_attributes[len(a_name):])]
+ INPUT_RE, cmd_without_attributes[len(activity_name):])]
if entity_names and entity_names[0] in cmd_without_attributes:
outputs.append(entity_names[-1])
@@ -190,19 +193,24 @@ def build_records(commands_block: list, agent_id: str, verbose: bool = False):
inputs.append(entity_names[0])
# the file name and possible extension
- label = f"{os.path.split(a_name)[1]}"
-
+ activity_label = label_mapping(
+ f'{os.path.split(activity_name)[1]}',
+ 'afni/afni_labels.json')
activity = {
- "@id": f"urn:{get_id()}",
- "Label": label_mapping(label, "afni/afni_labels.json"),
- "AssociatedWith": "urn:" + agent_id,
+ "@id": get_activity_urn(activity_label),
+ "Label": activity_label,
+ "AssociatedWith": agent_id,
"Command": cmd,
"Parameters": param_dic,
"Used": list(),
}
for input_path in inputs:
- input_id = f"urn:{get_id()}" # def format_id
+ # Deal with not human readable paths
+ if not make_alnum(input_path):
+ input_id = 'urn:uuid:' + get_uuid()
+ else:
+ input_id = get_entity_urn(input_path)
existing_input = next(
(entity for entity in records["Entities"] if entity["AtLocation"] == input_path), None)
@@ -223,9 +231,13 @@ def build_records(commands_block: list, agent_id: str, verbose: bool = False):
activity["Used"] = sorted(set(activity["Used"]))
for output_path in outputs:
+ if not make_alnum(output_path):
+ output_id = 'urn:uuid:' + get_uuid()
+ else:
+ output_id = get_entity_urn(output_path)
records["Entities"].append(
{
- "@id": f"urn:{get_id()}",
+ "@id": output_id,
"Label": os.path.split(output_path)[1],
"AtLocation": output_path,
"GeneratedBy": activity["@id"],
@@ -272,7 +284,7 @@ def gather_multiline(input_file: str) -> list:
def readlines(input_file: str) -> list:
"""
- gather multiline command split by \ separator
+ Read lines form an input file and return the list of commands it contains
Parameters
----------
@@ -363,7 +375,7 @@ def fusion_activities(activities, label):
command += activity["Command"] + "; "
return {
- "@id": f"urn:{get_id()}",
+ "@id": get_activity_urn(label),
"Label": label,
"AssociatedWith": activities[0]["AssociatedWith"],
"Command": command,
@@ -454,7 +466,8 @@ def afni_to_bids_prov(filename: str, context_url=CONTEXT_URL, output_file=None,
"""
commands_block = readlines(filename)
- graph, agent_id = get_default_graph(label="AFNI", context_url=context_url, soft_ver=soft_ver)
+ graph, agent_id = get_default_graph(
+ soft_label="AFNI", context_url=context_url, soft_version=soft_ver)
records, bloc_act = build_records(commands_block, agent_id, verbose=verbose)
graph["Records"].update(records)
diff --git a/bids_prov/afni/description_functions.json b/bids_prov/afni/description_functions.json
index 69a958a5f..7effe5113 100644
--- a/bids_prov/afni/description_functions.json
+++ b/bids_prov/afni/description_functions.json
@@ -76,7 +76,7 @@
"GeneratedBy": ["-prefix"]
},
{"Name": "3dAllineate",
- "Used": ["-base", "-input", "-1Dmatrix_apply"],
+ "Used": ["-base", "-input", "-1Dmatrix_apply", "-master"],
"GeneratedBy": ["-prefix"]
},
{"Name": "3dTstat",
@@ -115,7 +115,7 @@
"GeneratedBy" : ["-x1D"]
},
{"Name": "3dmaskave",
- "Used" : [2,3],
+ "Used" : ["-mask", 2,3],
"GeneratedBy" : [">"]
},
{"Name": "3dTnorm",
diff --git a/bids_prov/fsl/description_functions.json b/bids_prov/fsl/description_functions.json
index 672c20ed4..e4e87dcfb 100644
--- a/bids_prov/fsl/description_functions.json
+++ b/bids_prov/fsl/description_functions.json
@@ -8,7 +8,7 @@
"Name": "fslmaths",
"Used": [0, "-add","-sub","-mul","-div","-rem","-mas","-max","-min","-seed","-restart","-save"],
"GeneratedBy": [1],
- "ParametersValue" : ["-dt", "-odt","-thr","-thrp","-thrP","-uthr","-uthrp","-uthrP",
+ "ParametersValue" : ["-dt", "-odt","-thr","-thrp","-thrP","-uthr","-uthrp","-uthrP", "-bptf",
{
"Name": "-grid",
"Index": ["0:2"]
@@ -78,7 +78,7 @@
{
"Name": "cluster",
"Used": ["-i", "-c"],
- "GeneratedBy": ["-o", "--othresh", "--olmax", "--olmaxim", "--osize", "--omax", "--omean", "--opvals", "-c", "--cope", "-x","--xfm", "--stdvol", "--warpvol"]
+ "GeneratedBy": ["-o", "--othresh", "--olmax", "--olmaxim", "--osize", "--omax", "--omean", "--opvals", "-c", "--cope", "-x","--xfm", "--stdvol", "--warpvol", ">"]
},
{
"Name": "echo",
diff --git a/bids_prov/fsl/fsl_parser.py b/bids_prov/fsl/fsl_parser.py
index 29315854d..2f8ce0fa3 100644
--- a/bids_prov/fsl/fsl_parser.py
+++ b/bids_prov/fsl/fsl_parser.py
@@ -8,8 +8,11 @@
from bs4 import BeautifulSoup
-from bids_prov.utils import get_default_graph, CONTEXT_URL, get_id, label_mapping, compute_sha_256_entity, \
+from bids_prov.utils import (
+ get_default_graph, CONTEXT_URL, label_mapping, compute_sha_256_entity,
+ get_activity_urn, get_agent_urn, get_entity_urn, make_alnum, get_uuid,
writing_jsonld
+ )
# regex to catch inputs
# in `cp /fsl/5.0/doc/fsl.css .files no_ext 5.0` --> only `.files` should match
@@ -250,7 +253,7 @@ def _get_entities_from_kwarg(entities, opts, parse_kwarg):
value = []
for (arg, val) in opts._get_kwargs():
# print("\n--arg, val", type(arg), type(val), arg, val)
- if param.split("-")[1] == arg:
+ if param.strip('-') == arg:
# print("\n----arg select", type(arg), arg)
if val != None:
# print("\n------val != None", type(val), val)
@@ -388,14 +391,14 @@ def get_entities(cmd_s, parameters):
if "GeneratedBy" in parameters:
outputs.extend(_get_arg(parameters["GeneratedBy"], arg_rest))
- # print("\n\n inputs", inputs)
+ # print("\n\n inputs", inputs)
# print("\n\n outputs", outputs)
# print("\n\n params", params)
return inputs, outputs, params
-def build_records(groups: Mapping[str, List[str]], agent_id: str):
+def build_records(groups: Mapping[str, List[str]], agent_id: str, verbose: bool = False):
"""
Build the `records` field for the final .jsonld file,
from commands lines grouped by stage (e.g. `Registration`, `Post-stats`)
@@ -420,8 +423,11 @@ def build_records(groups: Mapping[str, List[str]], agent_id: str):
for cmd in v:
# process to remove + and - in pngappend command
cmd = cmd.replace(" + ", " ").replace(" - ", " ")
+ # remove multiple spaces
+ cmd = ' '.join(cmd.split())
+ # split according to the following chars " ", "|", and "="
cmd_s = re.split(" |=", cmd)
- a_name = cmd_s[0]
+ activity_name = cmd_s[0]
inputs = []
outputs = []
@@ -430,7 +436,7 @@ def build_records(groups: Mapping[str, List[str]], agent_id: str):
function_in_description_functions = False
- command_name_end = os.path.split(a_name)[1]
+ command_name_end = os.path.split(activity_name)[1]
for df in description_functions:
if df["Name"] == command_name_end:
description_of_command = df
@@ -439,7 +445,15 @@ def build_records(groups: Mapping[str, List[str]], agent_id: str):
cmd_s[1:], description_of_command)
break
+ if verbose:
+ print("CMD", cmd)
+ print('-> inputs: ', inputs)
+ print('<- outputs: ', outputs)
+ print(" others args :", *parameters)
+
if function_in_description_functions is False:
+ print(f"-> {command_name_end} : Not present in description_functions")
+
# if the function is not in our description file, the process is based on regex
attributes = defaultdict(list)
@@ -457,9 +471,9 @@ def build_records(groups: Mapping[str, List[str]], agent_id: str):
outputs = list(chain(*(attributes.pop(k)
for k in attributes.keys() & OUTPUT_TAGS)))
entity_names = [_ for _ in re.findall(
- INPUT_RE, cmd_without_attributes[len(a_name):])]
+ INPUT_RE, cmd_without_attributes[len(activity_name):])]
- # # cmd_conf = get_closest_config(a_name) # with the module boutiques
+ # # cmd_conf = get_closest_config(activity_name) # with the module boutiques
# cmd_conf = None # None because boutiques is not used at this time
# # if cmd_conf:
# # pos_args = filter(lambda e: not e.startswith("-"), cmd_s) # TODO use "-key value" mappings
@@ -471,13 +485,14 @@ def build_records(groups: Mapping[str, List[str]], agent_id: str):
if len(entity_names) > 1:
inputs.append(entity_names[0])
- # the file name and possible extension
- label = f"{os.path.split(a_name)[1]}"
-
- a = {
- "@id": f"urn:{get_id()}",
- "Label": label_mapping(label, "fsl/fsl_labels.json"),
- "AssociatedWith": "urn:" + agent_id,
+ # Create activity label & record
+ activity_label = label_mapping(
+ f'{os.path.split(activity_name)[1]}',
+ 'fsl/fsl_labels.json')
+ activity = {
+ "@id": get_activity_urn(activity_label),
+ "Label": activity_label,
+ "AssociatedWith": agent_id,
"Command": cmd,
# "attributes": [
# {k: v if len(v) > 1 else v[0]} for k, v in attributes.items()
@@ -487,37 +502,47 @@ def build_records(groups: Mapping[str, List[str]], agent_id: str):
for input_path in inputs:
# input_name = input_path.replace("/", "_") # TODO
- input_id = f"urn:{get_id()}" # def format_id
+ if not make_alnum(input_path):
+ input_id = 'urn:uuid:' + get_uuid()
+ else:
+ input_id = get_entity_urn(input_path)
existing_input = next(
- (entity for entity in records["Entities"] if entity["AtLocation"] == input_path), None)
+ (e for e in records["Entities"] if e["AtLocation"] == input_path), None)
if existing_input is None:
- e = {
+ entity = {
"@id": input_id,
"Label": os.path.split(input_path)[1],
"AtLocation": input_path,
}
- records["Entities"].append(e)
- a["Used"].append(input_id)
+ records["Entities"].append(entity)
+ activity["Used"].append(input_id)
else:
- a["Used"].append(existing_input["@id"])
+ activity["Used"].append(existing_input["@id"])
# Order does not matter and then makes sense to include only unique values
- a["Used"] = sorted(set(a["Used"]))
+ activity["Used"] = sorted(set(activity["Used"]))
for output_path in outputs:
# output_name = output_path.replace("/", "_") # TODO
+ if not make_alnum(output_path):
+ output_id = 'urn:uuid:' + get_uuid()
+ else:
+ output_id = get_entity_urn(output_path)
+
records["Entities"].append(
{
- "@id": f"urn:{get_id()}",
+ "@id": output_id,
"Label": os.path.split(output_path)[1],
"AtLocation": output_path,
- "GeneratedBy": a["@id"],
+ "GeneratedBy": activity["@id"],
# "derivedFrom": input_id,
}
)
- records["Activities"].append(a)
+ records["Activities"].append(activity)
+ if verbose:
+ print('-------------------------')
return dict(records)
@@ -525,10 +550,10 @@ def fsl_to_bids_prov(filename: str, context_url=CONTEXT_URL, output_file=None,
soft_ver="xxx", indent=2, verbose=False) -> bool: # TODO : add fsl version
graph, agent_id = get_default_graph(
- label="FSL", context_url=context_url, soft_ver=soft_ver)
+ soft_label="FSL", context_url=context_url, soft_version=soft_ver)
lines = readlines(filename)
- records = build_records(lines, agent_id)
+ records = build_records(lines, agent_id, verbose)
graph["Records"].update(records)
compute_sha_256_entity(graph["Records"]["Entities"])
diff --git a/bids_prov/spm/spm_parser.py b/bids_prov/spm/spm_parser.py
index 7306192cb..1d6018eec 100644
--- a/bids_prov/spm/spm_parser.py
+++ b/bids_prov/spm/spm_parser.py
@@ -5,8 +5,11 @@
from typing import List, Dict, Generator
from bids_prov.spm import spm_config as conf
-from bids_prov.utils import get_id, get_default_graph, CONTEXT_URL, label_mapping, compute_sha_256_entity, \
+from bids_prov.utils import (
+ get_uuid, get_default_graph, CONTEXT_URL, label_mapping, compute_sha_256_entity,
+ get_activity_urn, get_agent_urn, get_entity_urn,
writing_jsonld
+ )
def format_activity_name(activity_name: str) -> str:
@@ -38,7 +41,7 @@ def get_input_entity(right: str) -> List[dict]:
# called if left has no parameter AND right match with conf.PATH_REGEX and with conf.FILE_REGEX, example :
'matlabbatch{4}.spm.stats.fmri_spec.sess.multi = {
- '/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};"
+ 'ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};"
Parameters
----------
@@ -61,11 +64,12 @@ def get_input_entity(right: str) -> List[dict]:
file_location = re.sub(r"\,1", "", file_drop_quotes) # ds000052/RESULTS/Sub01/con_0001.nii
entity_label_short = "_".join(file_location.split("/")[-2:]) # Sub01_con_0001.nii
entity = {
- "@id": "urn:" + get_id(),
+ "@id": get_entity_urn(
+ "/"+"/".join(file_location.strip("/").split("/")[1:]),
+ file_location.strip("/").split("/")[0]),
"Label": label_mapping(entity_label_short, "spm/spm_activity_labels.json"),
"AtLocation": file_location
}
-
entities.append(entity)
return entities
@@ -170,9 +174,9 @@ def get_entities_from_ext_config(conf_dic: dict, activity_name: str, activity_id
# activity_id), None)
for output in conf_dic[activity]['outputs']:
name = conf_dic[activity]['name']
- entity = {"@id": "urn:" + get_id(),
+ entity = {"@id": get_entity_urn(output),
"Label": label_mapping(name, "spm/spm_activity_labels.json"),
- "Atlocation": output,
+ "AtLocation": output,
"GeneratedBy": activity_id,
}
output_entities.append(entity)
@@ -217,7 +221,7 @@ def find_output_id_from_closest(closest_activity: dict, records: dict) -> str:
Returns
-------
- output_id : entity id, if such one has been generated by the closest activity, else new id
+ output_id : entity id, if such one has been generated by the closest activity, else new id
"""
for entity in records["Entities"]:
if "GeneratedBy" in entity:
@@ -225,7 +229,7 @@ def find_output_id_from_closest(closest_activity: dict, records: dict) -> str:
output_id = entity["@id"]
break
else:
- output_id = "urn:" + get_id()
+ output_id = 'urn:uuid:' + get_uuid()
# output_id = next(
# (entity["@id"] for entity in records["Entities"]
# if parts[-1] == entity["Label"] and entity["GeneratedBy"] == closest_activity["@id"]
@@ -309,11 +313,12 @@ def get_records(task_groups: dict, agent_id: str, verbose=False) -> dict:
command_prefix = command_prefix[:-1]
command += '\n'.join([command_prefix + c for c in end_line_list])
- activity_id = "urn:" + get_id()
+ activity_label = format_activity_name(common_prefix_act)
+ activity_id = get_activity_urn(activity_label)
activity = {"@id": activity_id,
- "Label": format_activity_name(common_prefix_act),
+ "Label": activity_label,
"Used": list(),
- "AssociatedWith": "urn:" + agent_id,
+ "AssociatedWith": agent_id,
"Command": command
}
@@ -350,7 +355,9 @@ def get_records(task_groups: dict, agent_id: str, verbose=False) -> dict:
for idx, entity in enumerate(output_ext_entities):
input_ent = find_entity_from_id(output_id, records["Entities"])
entity['Label'] = f"{entity['Label']}{str(idx + 1)}"
- entity['AtLocation'] = f"c{str(idx + 1)}{input_ent['Label']}"
+ new_at_location = f"c{str(idx + 1)}{input_ent['Label']}"
+ entity['AtLocation'] = new_at_location
+ entity['@id'] = get_entity_urn(new_at_location)
add_ext_entity = 1
# TO DO whatif multiple
@@ -427,7 +434,8 @@ def spm_to_bids_prov(filename: str, context_url=CONTEXT_URL, output_file=None, s
If true, nothing is written in memory because the existing file (if it exists) contains the same content.
"""
- graph, agent_id = get_default_graph(label="SPM", context_url=context_url, soft_ver=spm_ver)
+ graph, agent_id = get_default_graph(
+ soft_label='SPM', context_url=context_url, soft_version=spm_ver)
lines = readlines(filename)
tasks = group_lines(lines) # same as list(lines) to expand generator
records = get_records(tasks, agent_id, verbose=verbose)
diff --git a/bids_prov/tests/test_spm_parser.py b/bids_prov/tests/test_spm_parser.py
index 91298f8d0..65683ecc9 100644
--- a/bids_prov/tests/test_spm_parser.py
+++ b/bids_prov/tests/test_spm_parser.py
@@ -90,11 +90,10 @@ def test_get_input_entity():
right = "{'ds011/sub-01/func/sub-01_task-tonecounting_bold_trunctest.nii.gz'};"
# entity label : sub-01_task-tonecounting_bold.nii.gz
entities = [{
- "@id": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "@id": "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold_trunctest.nii.gz",
"Label": "func_sub-01_task-tonecounting_bold_trunctest.nii.gz",
"AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold_trunctest.nii.gz"
}]
- init_random_state()
right_entity = get_input_entity(right)[0]
assert right_entity == entities[0]
diff --git a/bids_prov/tests/test_utils.py b/bids_prov/tests/test_utils.py
index 7e61aedd0..6ef07eb7e 100644
--- a/bids_prov/tests/test_utils.py
+++ b/bids_prov/tests/test_utils.py
@@ -5,13 +5,16 @@
import json
import hashlib
-from bids_prov.utils import get_id, get_default_graph, CONTEXT_URL, label_mapping, get_sha256
+from bids_prov.utils import (
+ get_uuid, get_random_string, get_rrid, make_alnum,
+ get_activity_urn, get_agent_urn, get_entity_urn,
+ get_default_graph, CONTEXT_URL, label_mapping, get_sha256
+ )
from unittest.mock import mock_open, patch
-
-def test_get_id():
+def test_get_uuid():
# Test that the function returns a valid UUID string
- result = get_id()
+ result = get_uuid()
assert isinstance(result, str)
assert isinstance(uuid.UUID(result), uuid.UUID)
@@ -19,30 +22,78 @@ def test_get_id():
assert uuid.UUID(result).version == 4
# Test that the function returns a different ID each time it's called
- id1 = get_id()
- id2 = get_id()
+ id1 = get_uuid()
+ id2 = get_uuid()
assert id1 != id2
+def test_get_random_string():
+ # Test that the function returns a random string
+ result = get_random_string()
+ assert isinstance(result, str)
+ assert len(result) == 8
+ assert result.isalnum()
+ assert len(get_random_string(5)) == 5
+ assert result != get_random_string()
+
+def test_get_rrid():
+ # Test that the function returns a RRID string
+ result = get_rrid('FSL')
+ assert 'RRID:' in result
+ assert isinstance(result, str)
+ assert result != get_rrid('SPM')
+
+ # Test the the function returns None if the software is not referenced
+ assert get_rrid('unreferenced_software') is None
+
+def test_make_alnum():
+ # Test that the function that removes all non alphanumeric chars from a string
+ assert make_alnum('¨^$£$êµ*ad45@') == 'ad45'
+ assert make_alnum('\\//:!§.;,?[]()}{}') == ''
+ assert make_alnum('ezeasdsa45ADA5sdas') == 'ezeasdsa45ADA5sdas'
+
+def test_get_activity_urn():
+ # Test that the function that returns URNs for activities
+ assert 'urn:spm-' in get_activity_urn('SPM')
+ assert len(get_activity_urn('SPM')) == 16
+ assert 'urn:spmv1242-' in get_activity_urn('SPM v. 1242355')
+ assert len(get_activity_urn('SPM v. 1242355')) == 21
+
+def test_get_agent_urn():
+ # Test that the function that returns URNs for agents
+ assert 'urn:bet-' in get_agent_urn('BET')
+ assert len(get_agent_urn('BET')) == 16
+ assert 'urn:movefile-' in get_agent_urn('Move file')
+ assert len(get_agent_urn('SPM v. 1242355')) == 21
+
+def test_get_entity_urn():
+ # Test that the function that returns URNs for entities
+ assert get_entity_urn('') == 'bids::'
+ assert get_entity_urn('sub-001/func/T1.nii') == 'bids::sub-001/func/T1.nii'
+ assert get_entity_urn('T1.nii') == 'bids::T1.nii'
+ assert get_entity_urn('', 'ds04031') == 'bids:ds04031:'
+ assert get_entity_urn('sub-001/func/T1.nii', 'ds04031') == 'bids:ds04031:sub-001/func/T1.nii'
def test_get_default_graph():
- label = "SPM"
context_url = "http://example.com/context"
spm_ver = "v1.0"
# Test the default arguments
+ label = 'SPM'
graph, agent_id = get_default_graph(label)
assert graph["@context"] == CONTEXT_URL
assert graph["Records"]["Software"][0]["Label"] == label
+ assert graph["Records"]["Software"][0]["AltIdentifier"] == 'RRID:SCR_007037'
assert agent_id is not None
# Test custom arguments
- graph, agent_id = get_default_graph(label, context_url, spm_ver)
+ label = 'Nipype'
+ graph, agent_id = get_default_graph('Nipype', spm_ver, context_url)
assert graph["@context"] == context_url
assert graph["Records"]["Software"][0]["Label"] == label
assert graph["Records"]["Software"][0]["Version"] == spm_ver
+ assert 'AltIdentifier' not in graph["Records"]["Software"][0]
assert agent_id is not None
-
def test_label_mapping():
label = "label1"
mapping_json = {"label1": "mapped_label1", "label2": "mapped_label2"}
diff --git a/bids_prov/utils.py b/bids_prov/utils.py
index 3e57116a2..38eed7bcf 100644
--- a/bids_prov/utils.py
+++ b/bids_prov/utils.py
@@ -2,38 +2,149 @@
import json
import os
import random
+import string
import shutil
import uuid
+from rfc3986 import normalize_uri
from typing import Mapping, Union, Tuple
import re
CONTEXT_URL = "https://raw.githubusercontent.com/bids-standard/BEP028_BIDSprov/master/context.json"
+SOFTWARE_RRIDS = {
+ 'AFNI': 'RRID:SCR_005927',
+ 'FSL': 'RRID:SCR_002823',
+ 'SPM': 'RRID:SCR_007037'
+ }
-
-def get_id():
+def get_uuid() -> str:
return str(uuid.UUID(int=random.getrandbits(128), version=4))
+def get_random_string(length: str = 8) -> str:
+ """ Return a random string of a given length.
+ The string may contain uppercase letters,
+ lowercase letters, and digits.
+
+ Parameters
+ ----------
+ length : length of the output string
+
+ Returns
+ -------
+ str : a random string
+ """
+ return ''.join(random.choices(
+ string.ascii_uppercase + string.ascii_lowercase + string.digits, k=length))
+
+def get_rrid(soft_label: str):
+ """ Return the RRID (see: https://rrid.site/about/Getting%20Started) for a software
+
+ Parameters
+ ----------
+ soft_label : the label of the software (e.g.: FSL, SPM, etc.)
+
+ Returns
+ -------
+ str : the RRID of the software
+ or None if the software is not referenced in SOFTWARE_RRIDS
+ """
+ if soft_label in SOFTWARE_RRIDS:
+ return SOFTWARE_RRIDS[soft_label]
+
+ return None
+
+def make_alnum(input_string: str) -> str:
+ """ Remove all non alphanumeric form a string
+
+ Parameters
+ ----------
+ input_string : string to make alphanumeric
+
+ Returns
+ -------
+ str : input string with all non alphanumeric removed
+ """
+ return re.sub(re.compile(r'[^a-zA-Z0-9]'), '', input_string)
+
+def get_activity_urn(label: str) -> str:
+ """ Return a randomly generated yet human readable URN for a bids prov Activity
+
+ Parameters
+ ----------
+ label : the label of the Activity
-def get_default_graph(label: str, context_url: str = CONTEXT_URL, soft_ver: str = "dev", ) \
+ Returns
+ -------
+ str : a new URN for the Activity
+ """
+ return f'urn:{make_alnum(label)[:8].lower()}-{get_random_string()}'
+
+def get_agent_urn(label: str) -> str:
+ """ Return a randomly generated yet human readable URN for a bids prov Agent
+
+ Parameters
+ ----------
+ label : the label of the Agent
+
+ Returns
+ -------
+ str : a new URN for the Agent
+ """
+ return f'urn:{make_alnum(label)[:8].lower()}-{get_random_string()}'
+
+def get_entity_urn(label: str, dataset: str = '') -> str:
+ """ Return a URN for a bids prov Entity, based on a given label and the
+ id of the BIDS dataset.
+
+ Parameters
+ ----------
+ label : the label of the entity
+ dataset : id of the BIDS dataset
+
+ Returns
+ -------
+ str : a new URN for the entity
+ """
+ return f'bids:{dataset}:{normalize_uri(label)}'
+
+def get_default_graph(soft_label: str, soft_version: str = "dev", context_url: str = CONTEXT_URL) \
-> Tuple[Mapping[str, Union[str, Mapping]], str]: # TODO Dict instead of Mapping , see parser graph["Records"].update
- agent_id = get_id()
+ """ Return the base graph for a bids prov file
+
+ Parameters
+ ----------
+ soft_label : the label of the software generating the provenance tracks (e.g.: FSL, SPM, etc.)
+ soft_version : the version of the software generating the provenance tracks
+ context_url : the url to the json context
+
+ Returns
+ -------
+ tuple :
+ mapping : the base graph
+ str : the id generated for the software
+ """
+ agent_id = get_agent_urn(soft_label)
+ software_record = {
+ "@id": "urn:" + agent_id,
+ "@type": "prov:SoftwareAgent",
+ "Label": soft_label,
+ "Version": soft_version
+ }
+
+ agent_rrid = get_rrid(soft_label)
+ if agent_rrid is not None:
+ software_record["AltIdentifier"] = get_rrid(soft_label)
+
return {
- "@context": context_url,
- "BIDSProvVersion": "dev", # TODO ?
- "Records": {
- "Software": [
- {
- "@id": "urn:" + agent_id,
- "RRID": "RRID:SCR_007037",
- "@type": "prov:SoftwareAgent",
- "Label": label,
- "Version": soft_ver
- }
- ],
- "Activities": [],
- "Entities": [],
- },
- }, agent_id
+ "@context": context_url,
+ "BIDSProvVersion": "dev",
+ "Records": {
+ "Software": [
+ software_record
+ ],
+ "Activities": [],
+ "Entities": [],
+ },
+ }, agent_id
def label_mapping(label: str, mapping_filename: str) -> str:
diff --git a/dev-requirements.txt b/dev-requirements.txt
index b812267c4..04123e1b7 100644
--- a/dev-requirements.txt
+++ b/dev-requirements.txt
@@ -11,4 +11,5 @@ black
pre-commit
rdflib
boutiques
-markdownify
\ No newline at end of file
+markdownify
+rfc3986
\ No newline at end of file
diff --git a/examples/from_parsers/afni/afni_alt_onesided_proc.jsonld b/examples/from_parsers/afni/afni_alt_onesided_proc.jsonld
index 2a503147f..db99f7d53 100644
--- a/examples/from_parsers/afni/afni_alt_onesided_proc.jsonld
+++ b/examples/from_parsers/afni/afni_alt_onesided_proc.jsonld
@@ -4,578 +4,581 @@
"Records": {
"Software": [
{
- "@id": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:afni-Gro6QPto",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
- "Version": "afni24"
+ "Version": "afni24",
+ "AltIdentifier": "RRID:SCR_005927"
}
],
"Activities": [
{
- "@id": "urn:3f372617-f0ba-4f3a-86f0-ce2ea6ec39c1",
+ "@id": "urn:makedire-SqYwHN3W",
"Label": "Make directory",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "mkdir $output_dir",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:732242fd-a890-4e32-9297-9bfcbbeb508f",
+ "@id": "urn:makedire-QxnJipKo",
"Label": "Make directory",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "mkdir $output_dir/stimuli",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:e8af30f7-c70b-43bf-a4d0-b50f658c6762",
+ "@id": "urn:cp-HUFM8Z9b",
"Label": "cp",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "cp ./afni_one_sided_t_test/tone_counting_onset_times.txt ./afni_one_sided_t_test/tone_counting_probe_duration.txt $output_dir/stimuli",
"Parameters": {},
"Used": [
- "urn:cecf4f4e-5ba8-4780-90ce-f798e6c648e7",
- "urn:deeda8b2-3927-47d6-8375-d0341e4f6f2a"
+ "bids::afni_one_sided_t_test/tone_counting_onset_times.txt",
+ "bids::afni_one_sided_t_test/tone_counting_probe_duration.txt"
]
},
{
- "@id": "urn:293a9acc-2652-48ff-842a-2f9da1b4ba07",
+ "@id": "urn:3dcopy-l2qGknLF",
"Label": "3dcopy",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w",
"Parameters": {},
"Used": [
- "urn:467c0714-a9fb-4797-aa59-c1698d242349"
+ "bids::sub-01_T1w.nii.gz"
]
},
{
- "@id": "urn:071d1481-5649-48e9-9846-6a921f7ea79c",
+ "@id": "urn:3dtcat-2fMcNxfG",
"Label": "3dTcat",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Parameters": {},
"Used": [
- "urn:daa4ed3c-3454-4ae4-8628-7225154d1eb0"
+ "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'"
]
},
{
- "@id": "urn:e57b37e7-704b-4d09-af2e-ab42fd8cfe33",
+ "@id": "urn:3dtoutco-yFRBtHgF",
"Label": "3dToutcount",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D",
"Parameters": {},
"Used": [
- "urn:a40f9ca3-df62-492c-982a-3add9b872a76"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:5d3ffd11-a23c-4698-a32d-c48296ce3859",
+ "@id": "urn:cat-dqhcebkF",
"Label": "cat",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "cat outcount.r*.1D > outcount_rall.1D",
"Parameters": {},
"Used": [
- "urn:bf3ba33a-183c-44e2-9d66-a3582e62fe86"
+ "bids::outcount.r*.1D"
]
},
{
- "@id": "urn:9fc62455-73dd-4732-8555-2a83319f69e3",
+ "@id": "urn:3dtshift-dO16EIrj",
"Label": "3dTshift",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig",
"Parameters": {},
"Used": [
- "urn:a40f9ca3-df62-492c-982a-3add9b872a76"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:4754665a-16eb-480f-bfcd-88b9d170d65a",
+ "@id": "urn:alignepi-Br6aVj6Q",
"Label": "align_epi_anat.py",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off",
"Parameters": {},
"Used": [
- "urn:29663157-072a-468b-9e47-921f47d9e875",
- "urn:afaaa713-1d26-4313-a970-3feebd8700eb"
+ "bids::pb01.$subj.r01.tshift+orig",
+ "bids::sub-01_T1w+orig"
]
},
{
- "@id": "urn:2b1a7ae1-af74-4c55-b949-3d417afdf260",
+ "@id": "urn:autotlrc-SLmdPYCT",
"Label": "@auto_tlrc",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss",
"Parameters": {},
"Used": [
- "urn:4f3d0144-7485-4165-a2fe-005b88ebf5e6",
- "urn:6aedf88b-6fe2-45d4-b5b7-28bf7c208071"
+ "bids::TT_N27+tlrc",
+ "bids::sub-01_T1w_ns+orig"
]
},
{
- "@id": "urn:41a204e9-1848-4df7-93a1-c30b986f3042",
+ "@id": "urn:catmatve-8kR6WPCJ",
"Label": "cat_matvec",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D",
"Parameters": {},
"Used": [
- "urn:73011544-3c7b-40fc-a4e2-4875797a05ab"
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:7d32a82f-24af-4bee-91b0-02ee1102c9f5",
+ "@id": "urn:3dvolreg-MO2QPl4S",
"Label": "3dvolreg",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig",
"Parameters": {},
"Used": [
- "urn:70ffec24-924a-4cd7-844c-044fb416aad9"
+ "bids::pb01.$subj.r$run.tshift+orig"
]
},
{
- "@id": "urn:0552d4c0-6c50-45cc-bcbb-d0fff1a58c2e",
+ "@id": "urn:3dcalc-vWik6uf0",
"Label": "3dcalc",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1",
"Parameters": {},
"Used": [
- "urn:70ffec24-924a-4cd7-844c-044fb416aad9"
+ "bids::pb01.$subj.r$run.tshift+orig"
]
},
{
- "@id": "urn:0af4a5a4-304f-4649-87b3-1dc04d628fed",
+ "@id": "urn:catmatve-WX7hvT4l",
"Label": "cat_matvec",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D",
"Parameters": {},
"Used": [
- "urn:73011544-3c7b-40fc-a4e2-4875797a05ab"
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:06728249-4ffc-4603-b140-7caa08e743c2",
+ "@id": "urn:3dalline-P5dVQGMq",
"Label": "3dAllineate",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run",
"Parameters": {},
"Used": [
- "urn:190b6895-634d-4cd9-9869-84a4418e0b03",
- "urn:70ffec24-924a-4cd7-844c-044fb416aad9",
- "urn:81b4feac-9606-47d8-8017-e256fb9fb699"
+ "bids::mat.r$run.warp.aff12.1D",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:4012b491-3ae3-4848-8074-bfa332f439e7",
+ "@id": "urn:3dalline-IQbhXwPW",
"Label": "3dAllineate",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run",
"Parameters": {},
"Used": [
- "urn:190b6895-634d-4cd9-9869-84a4418e0b03",
- "urn:81b4feac-9606-47d8-8017-e256fb9fb699",
- "urn:ae1ca939-9a9a-4d62-b535-cafd3fa44a68"
+ "bids::mat.r$run.warp.aff12.1D",
+ "bids::rm.epi.all1+orig",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:bdc3428f-9888-480f-abf0-64468fa52057",
+ "@id": "urn:3dtstat-aHNJsJpN",
"Label": "3dTstat",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc",
"Parameters": {},
"Used": [
- "urn:2882c8ed-c1db-4ef4-8981-d39df13b5080"
+ "bids::rm.epi.1.r$run+tlrc"
]
},
{
- "@id": "urn:3eafcf21-6255-4ba7-bd80-78455dd0f901",
+ "@id": "urn:cat-ooV5oiCZ",
"Label": "cat",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "cat dfile.r*.1D > dfile_rall.1D",
"Parameters": {},
"Used": [
- "urn:8dbbbca1-8bc2-4b0e-a357-1e05f5c0fc1f"
+ "bids::dfile.r*.1D"
]
},
{
- "@id": "urn:0813e30b-9cdc-415d-b3cd-0645ea508097",
+ "@id": "urn:3dcopy-Qd51Dq5h",
"Label": "3dcopy",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents",
"Parameters": {},
"Used": [
- "urn:6deda758-ef02-498f-a4a6-535b3f4fb043"
+ "bids::rm.epi.min.r01+tlrc"
]
},
{
- "@id": "urn:21411b96-1a6e-4640-8ea1-69e64343c162",
+ "@id": "urn:3dcalc-F1a82z5E",
"Label": "3dcalc",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg",
"Parameters": {},
"Used": [
- "urn:7caddf4f-423b-4db3-b628-cbac240104b3",
- "urn:edb1bdc5-b136-41ad-8df7-ac98335d54b7"
+ "bids::mask_epi_extents+tlrc",
+ "bids::rm.epi.nomask.r$run+tlrc"
]
},
{
- "@id": "urn:1b3ad86b-c8fb-4714-8d00-bafd6168d6ca",
+ "@id": "urn:3dcopy-xSIXkAbw",
"Label": "3dcopy",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj",
"Parameters": {},
"Used": [
- "urn:81b4feac-9606-47d8-8017-e256fb9fb699"
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:cefc4a69-2580-432a-9712-462d38e98ed3",
+ "@id": "urn:3dalline-egS8PqoA",
"Label": "3dAllineate",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped",
"Parameters": {},
"Used": [
- "urn:7d32da7c-f063-4104-9d88-ae97dd8e5608"
+ "bids::anat_final.$subj+tlrc",
+ "bids::warp.anat.Xat.1D"
]
},
{
- "@id": "urn:d1ea45e7-a812-4de4-9c30-1ec9a59e9d41",
+ "@id": "urn:3dmerge-9O9531Yb",
"Label": "3dmerge",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc",
"Parameters": {},
"Used": [
- "urn:986f8c11-eedf-404b-bea2-fad45a7d6986",
- "urn:b405b370-8eaa-48b0-92c3-fcbba8236113"
+ "bids::pb02.$subj.r$run.volreg+tlrc",
+ "bids::pb03.$subj.r$run.blur"
]
},
{
- "@id": "urn:77e850b5-6812-461e-93f0-580c0bd99f98",
+ "@id": "urn:3dautoma-V6BI7yr8",
"Label": "3dAutomask",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:529e73e1-7848-46e1-b58f-24e6441cdb1e"
+ "bids::pb03.$subj.r$run.blur+tlrc"
]
},
{
- "@id": "urn:a443387d-ae1c-47b0-be9f-f85b0fd90438",
+ "@id": "urn:3dmaskto-gzb3Ebjx",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:118fb4ec-dde5-416b-aba9-4dad18c4c6ed",
+ "@id": "urn:3dresamp-aq8ZMB1d",
"Label": "3dresample",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat",
"Parameters": {},
"Used": [
- "urn:81b4feac-9606-47d8-8017-e256fb9fb699",
- "urn:a5389e7d-d431-43bb-8d2c-c68cdfdd10fe"
+ "bids::full_mask.$subj+tlrc",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:0b7c6124-4e20-4583-ad3f-b7cacb34ed43",
+ "@id": "urn:3dmaskto-YgHNOP1P",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj",
"Parameters": {},
"Used": [
- "urn:e2e35562-610f-4238-bbea-f339229b4f33"
+ "bids::rm.resam.anat+tlrc"
]
},
{
- "@id": "urn:dd4cd79c-c8c5-4f25-b7fd-0fe1731c5694",
+ "@id": "urn:3dabover-F1iBpqow",
"Label": "3dABoverlap",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt",
"Parameters": {},
"Used": [
- "urn:0519e719-8734-4119-b7e1-c2ae7ecb72ab",
- "urn:457d391d-f8af-4766-94cd-9b534bda02f2"
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee"
]
},
{
- "@id": "urn:97e65b94-ae5f-4f1f-8829-877b3f883ff4",
+ "@id": "urn:3ddot-aNumrLXq",
"Label": "3ddot",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt",
"Parameters": {},
"Used": [
- "urn:0519e719-8734-4119-b7e1-c2ae7ecb72ab",
- "urn:457d391d-f8af-4766-94cd-9b534bda02f2"
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee"
]
},
{
- "@id": "urn:5bb8508a-eda5-4365-81fb-999ffd24853e",
+ "@id": "urn:3dresamp-XlduVezT",
"Label": "3dresample",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc",
"Parameters": {},
"Used": [
- "urn:1f98c4b0-daf2-4e68-9c91-1148e6a5e140",
- "urn:a5389e7d-d431-43bb-8d2c-c68cdfdd10fe"
+ "bids::/Users/u1591557/abin/TT_N27+tlrc",
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:4830f327-2309-4954-8099-23d6077d7c00",
+ "@id": "urn:3dmaskto-KnI1R4hJ",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group",
"Parameters": {},
"Used": [
- "urn:c4c118f0-ce74-41f3-910b-79f9f4d747eb"
+ "bids::rm.resam.group+tlrc"
]
},
{
- "@id": "urn:e61bbb8d-d5d3-4835-958e-c7de860c6474",
+ "@id": "urn:3dtstat-gqenW7Kx",
"Label": "3dTstat",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:529e73e1-7848-46e1-b58f-24e6441cdb1e"
+ "bids::pb03.$subj.r$run.blur+tlrc"
]
},
{
- "@id": "urn:99fdddd9-cb59-44fc-a275-ee3393b74160",
+ "@id": "urn:3dcalc-BfEIk4TY",
"Label": "3dcalc",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale",
"Parameters": {},
"Used": [
- "urn:529e73e1-7848-46e1-b58f-24e6441cdb1e",
- "urn:7caddf4f-423b-4db3-b628-cbac240104b3",
- "urn:f8b35d61-6b39-4d1e-b9e8-e8a0f7c1bf73"
+ "bids::mask_epi_extents+tlrc",
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::rm.mean_r$run+tlrc"
]
},
{
- "@id": "urn:f95a770c-8509-4d92-9064-08ba635398ef",
+ "@id": "urn:1dtoolpy-dlVV0iVy",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D",
"Parameters": {},
"Used": [
- "urn:7ceb1b7b-507f-432b-a8ee-af9cc600339d"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:ca967613-3f22-4861-9331-8475dc0dffaa",
+ "@id": "urn:1dtoolpy-9aAS3KMx",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D",
"Parameters": {},
"Used": [
- "urn:7ceb1b7b-507f-432b-a8ee-af9cc600339d"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:9a9266f3-afad-4b3d-8fe4-000dacd8c70e",
+ "@id": "urn:1dtoolpy-H0OYkGwb",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}",
"Parameters": {},
"Used": [
- "urn:7ceb1b7b-507f-432b-a8ee-af9cc600339d"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:e63e06d1-3992-44fd-b5a6-fd0d6c86aeaf",
+ "@id": "urn:3ddeconv-vvEyyOkM",
"Label": "3dDeconvolve",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj",
"Parameters": {},
"Used": [
- "urn:130b200a-a004-4ac6-917b-fae4be88252d"
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD"
]
},
{
- "@id": "urn:33d94269-b0ee-4b88-b5fc-dd8b5f68ea2d",
+ "@id": "urn:1dtoolpy-huXhI1mz",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt",
"Parameters": {},
"Used": [
- "urn:b7d21574-2f03-409f-b7d5-363bb4297b36"
+ "bids::X.xmat.1D"
]
},
{
- "@id": "urn:ae7558b3-c12b-4858-b7d2-b1fd79149b23",
+ "@id": "urn:3dtcat-FuFiO3Gd",
"Label": "3dTcat",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD",
"Parameters": {},
"Used": [
- "urn:130b200a-a004-4ac6-917b-fae4be88252d"
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD"
]
},
{
- "@id": "urn:75ff7e84-a2f8-4fcd-9c17-97f92cfcec40",
+ "@id": "urn:3dtstat-dXEp8W3V",
"Label": "3dTstat",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:d1e1cda7-db65-4013-a6e5-eff822140f17"
+ "bids::all_runs.$subj+tlrc%22[$ktrs]%22"
]
},
{
- "@id": "urn:0e3d9bab-2776-4009-8c33-f64c88a586c0",
+ "@id": "urn:3dtstat-Qc8wnCbA",
"Label": "3dTstat",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:4e86443f-aeb9-467a-87cd-921d8561e79d"
+ "bids::errts.$%7Bsubj%7D+tlrc%22[$ktrs]%22"
]
},
{
- "@id": "urn:bd40b1fe-f58d-4f57-abba-63275e76d0c1",
+ "@id": "urn:3dcalc-DXPGfw54",
"Label": "3dcalc",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj",
"Parameters": {},
"Used": [
- "urn:a5389e7d-d431-43bb-8d2c-c68cdfdd10fe",
- "urn:c512daa6-81d5-4f4b-b599-ad2406137f3c",
- "urn:ffbf1f1d-cc38-47b8-a1a2-c0242ca8e8f8"
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.noise.all+tlrc",
+ "bids::rm.signal.all+tlrc"
]
},
{
- "@id": "urn:9749c11a-671c-4c79-9951-10d84f2c77a6",
+ "@id": "urn:3dtnorm-aL7aVzi7",
"Label": "3dTnorm",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc",
"Parameters": {},
"Used": [
- "urn:cff0d752-9ae5-4404-92c9-6fff79dcd286"
+ "bids::errts.$%7Bsubj%7D+tlrc"
]
},
{
- "@id": "urn:a28a1432-8e3d-4d39-9cf9-e6acda7ca2fc",
+ "@id": "urn:3dmaskav-r6J6hrSP",
"Label": "3dmaskave",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D",
"Parameters": {},
- "Used": []
+ "Used": [
+ "bids::full_mask.$subj+tlrc"
+ ]
},
{
- "@id": "urn:1c42556b-6ea5-40c5-ba7f-d049ffbfac3c",
+ "@id": "urn:3dtstat-SK7HPnMN",
"Label": "3dTstat",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D",
"Parameters": {},
"Used": [
- "urn:deec3fb9-4e28-4d7c-8a47-599403e4edcd"
+ "bids::out.gcor.1D"
]
},
{
- "@id": "urn:331280a9-cad6-443e-8ec0-0bd032dec1f7",
+ "@id": "urn:3dcalc-AtoT3iN7",
"Label": "3dcalc",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP",
"Parameters": {},
"Used": [
- "urn:859bef03-d16d-49d0-95d7-526e5a3b3e9d",
- "urn:bd25383b-d975-4195-831d-bb521d441d8b"
+ "bids::gmean.errts.unit.1D",
+ "bids::rm.errts.unit+tlrc"
]
},
{
- "@id": "urn:fd23797b-703e-44e6-9ce0-93a6c6659007",
+ "@id": "urn:3dtstat-OyyA0af6",
"Label": "3dTstat",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc",
"Parameters": {},
"Used": [
- "urn:cf72bf6d-c398-4e69-9a8d-dbd8c530a31e"
+ "bids::rm.DP+tlrc"
]
},
{
- "@id": "urn:0f2a2124-3de2-4554-af3f-3833d2222dae",
+ "@id": "urn:1dcat-cOD2csn8",
"Label": "1dcat",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D",
"Parameters": {},
"Used": [
- "urn:8adb28e5-349d-4f53-8b18-4ed3975fae39"
+ "bids::X.nocensor.xmat.1D'[3]'"
]
},
{
- "@id": "urn:14a31446-8871-49fa-b1e0-e00260791d2c",
+ "@id": "urn:1dcat-66f4THnB",
"Label": "1dcat",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D",
"Parameters": {},
"Used": [
- "urn:fc6df78f-dcf6-493f-9d17-9b7821a4991b"
+ "bids::X.nocensor.xmat.1D'[4]'"
]
},
{
- "@id": "urn:f3a1b8eb-becf-4260-8526-cd7f14a93549",
+ "@id": "urn:3dtstat-8UaSUhxA",
"Label": "3dTstat",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"",
"Parameters": {},
"Used": [
- "urn:94f1e1b4-8e76-41fb-9f3b-d60517272174"
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:8e28756c-7915-4747-a230-d16d1b31fd66",
+ "@id": "urn:1dcat-VP7bb6XX",
"Label": "1dcat",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D",
"Parameters": {},
"Used": [
- "urn:94f1e1b4-8e76-41fb-9f3b-d60517272174"
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:1f3ccb95-5c68-4eda-a0e2-23aef8d5c592",
+ "@id": "urn:3dfwhmx-YOrRfjvt",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D",
"Parameters": {},
"Used": [
- "urn:a5389e7d-d431-43bb-8d2c-c68cdfdd10fe"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:194a0e78-c788-4530-b7c0-0155f909d523",
+ "@id": "urn:3dfwhmx-d666scW1",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D",
"Parameters": {},
"Used": [
- "urn:a5389e7d-d431-43bb-8d2c-c68cdfdd10fe"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:33ed9bcb-6059-4783-88f7-1aa00fe0a5c0",
+ "@id": "urn:3dclusts-duYWBtRe",
"Label": "3dClustSim",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim",
"Parameters": {},
"Used": [
- "urn:a5389e7d-d431-43bb-8d2c-c68cdfdd10fe"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:47ff32c1-ea81-41eb-aa5c-9e0cecfb40ce",
+ "@id": "urn:genepire-sz6pO5DZ",
"Label": "gen_epi_review.py",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD",
"Parameters": {},
"Used": [
- "urn:c09831f3-2daa-4d46-8cc2-8d3a6d13e061"
+ "bids::pb00.$subj.r*.tcat+orig.HEAD"
]
},
{
- "@id": "urn:a0828193-6c5d-4073-910f-4d6ef6b19f1a",
+ "@id": "urn:genssrev-50k1KCS5",
"Label": "gen_ss_review_scripts.py",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:afni-Gro6QPto",
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@@ -586,22 +589,22 @@
],
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{
- "@id": "urn:4a800646-417a-4105-bc31-99944567ceb1",
+ "@id": "bids::$output_dir",
"Label": "$output_dir",
"AtLocation": "$output_dir",
- "GeneratedBy": "urn:3f372617-f0ba-4f3a-86f0-ce2ea6ec39c1",
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{
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"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:732242fd-a890-4e32-9297-9bfcbbeb508f"
+ "GeneratedBy": "urn:makedire-QxnJipKo"
},
{
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+ "@id": "bids::afni_one_sided_t_test/tone_counting_onset_times.txt",
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"digest": {
@@ -609,7 +612,7 @@
}
},
{
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@@ -617,13 +620,13 @@
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"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:e8af30f7-c70b-43bf-a4d0-b50f658c6762"
+ "GeneratedBy": "urn:cp-HUFM8Z9b"
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@@ -631,13 +634,13 @@
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"AtLocation": "$output_dir/sub-01_T1w",
- "GeneratedBy": "urn:293a9acc-2652-48ff-842a-2f9da1b4ba07"
+ "GeneratedBy": "urn:3dcopy-l2qGknLF"
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{
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@@ -645,13 +648,13 @@
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"AtLocation": "$output_dir/pb00.$subj.r01.tcat",
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+ "GeneratedBy": "urn:3dtcat-2fMcNxfG"
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{
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"digest": {
@@ -659,16 +662,16 @@
}
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"AtLocation": "outcount.r$run.1D",
- "GeneratedBy": "urn:e57b37e7-704b-4d09-af2e-ab42fd8cfe33",
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{
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@@ -676,25 +679,25 @@
}
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{
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"AtLocation": "outcount_rall.1D",
- "GeneratedBy": "urn:5d3ffd11-a23c-4698-a32d-c48296ce3859",
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+ "@id": "bids::pb01.$subj.r$run.tshift",
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"AtLocation": "pb01.$subj.r$run.tshift",
- "GeneratedBy": "urn:9fc62455-73dd-4732-8555-2a83319f69e3",
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{
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"digest": {
@@ -702,7 +705,7 @@
}
},
{
- "@id": "urn:afaaa713-1d26-4313-a970-3feebd8700eb",
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"AtLocation": "pb01.$subj.r01.tshift+orig",
"digest": {
@@ -710,16 +713,16 @@
}
},
{
- "@id": "urn:6cd92a40-17cd-479a-9600-66c386988190",
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"Label": "_al_junk",
"AtLocation": "_al_junk",
- "GeneratedBy": "urn:4754665a-16eb-480f-bfcd-88b9d170d65a",
+ "GeneratedBy": "urn:alignepi-Br6aVj6Q",
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{
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+ "@id": "bids::TT_N27+tlrc",
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"AtLocation": "TT_N27+tlrc",
"digest": {
@@ -727,7 +730,7 @@
}
},
{
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+ "@id": "bids::sub-01_T1w_ns+orig",
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"AtLocation": "sub-01_T1w_ns+orig",
"digest": {
@@ -735,7 +738,7 @@
}
},
{
- "@id": "urn:73011544-3c7b-40fc-a4e2-4875797a05ab",
+ "@id": "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc::WARP_DATA",
"digest": {
@@ -743,16 +746,16 @@
}
},
{
- "@id": "urn:7d32da7c-f063-4104-9d88-ae97dd8e5608",
+ "@id": "bids::warp.anat.Xat.1D",
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"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:41a204e9-1848-4df7-93a1-c30b986f3042",
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{
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"AtLocation": "pb01.$subj.r$run.tshift+orig",
"digest": {
@@ -760,34 +763,34 @@
}
},
{
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"AtLocation": "mat.r$run.vr.aff12.1D",
- "GeneratedBy": "urn:7d32a82f-24af-4bee-91b0-02ee1102c9f5",
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{
- "@id": "urn:5b08b56f-4377-43f7-b896-5416f06b36b1",
+ "@id": "bids::rm.epi.all1",
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"AtLocation": "rm.epi.all1",
- "GeneratedBy": "urn:0552d4c0-6c50-45cc-bcbb-d0fff1a58c2e",
+ "GeneratedBy": "urn:3dcalc-vWik6uf0",
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{
- "@id": "urn:190b6895-634d-4cd9-9869-84a4418e0b03",
+ "@id": "bids::mat.r$run.warp.aff12.1D",
"Label": "mat.r$run.warp.aff12.1D",
"AtLocation": "mat.r$run.warp.aff12.1D",
- "GeneratedBy": "urn:0af4a5a4-304f-4649-87b3-1dc04d628fed",
+ "GeneratedBy": "urn:catmatve-WX7hvT4l",
"digest": {
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}
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{
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+ "@id": "bids::sub-01_T1w_ns+tlrc",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc",
"digest": {
@@ -795,16 +798,16 @@
}
},
{
- "@id": "urn:c663425b-256d-4ff3-b4d9-a89d08feeac8",
+ "@id": "bids::rm.epi.nomask.r$run",
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"AtLocation": "rm.epi.nomask.r$run",
- "GeneratedBy": "urn:06728249-4ffc-4603-b140-7caa08e743c2",
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{
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"digest": {
@@ -812,16 +815,16 @@
}
},
{
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+ "@id": "bids::rm.epi.1.r$run",
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"AtLocation": "rm.epi.1.r$run",
- "GeneratedBy": "urn:4012b491-3ae3-4848-8074-bfa332f439e7",
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{
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"digest": {
@@ -829,16 +832,16 @@
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},
{
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"AtLocation": "rm.epi.min.r$run",
- "GeneratedBy": "urn:bdc3428f-9888-480f-abf0-64468fa52057",
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{
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"digest": {
@@ -846,16 +849,16 @@
}
},
{
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- "GeneratedBy": "urn:3eafcf21-6255-4ba7-bd80-78455dd0f901",
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{
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"digest": {
@@ -863,16 +866,16 @@
}
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{
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- "GeneratedBy": "urn:0813e30b-9cdc-415d-b3cd-0645ea508097",
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{
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@@ -880,7 +883,7 @@
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{
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"digest": {
@@ -888,34 +891,42 @@
}
},
{
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- "GeneratedBy": "urn:21411b96-1a6e-4640-8ea1-69e64343c162",
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{
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"AtLocation": "anat_final.$subj",
- "GeneratedBy": "urn:1b3ad86b-c8fb-4714-8d00-bafd6168d6ca",
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{
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- "GeneratedBy": "urn:cefc4a69-2580-432a-9712-462d38e98ed3",
+ "GeneratedBy": "urn:3dalline-egS8PqoA",
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@@ -923,7 +934,7 @@
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{
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@@ -931,7 +942,7 @@
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{
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@@ -939,25 +950,25 @@
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{
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- "GeneratedBy": "urn:77e850b5-6812-461e-93f0-580c0bd99f98",
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{
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- "GeneratedBy": "urn:a443387d-ae1c-47b0-be9f-f85b0fd90438",
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{
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"digest": {
@@ -965,16 +976,16 @@
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{
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- "GeneratedBy": "urn:118fb4ec-dde5-416b-aba9-4dad18c4c6ed",
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{
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"digest": {
@@ -982,16 +993,16 @@
}
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{
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"AtLocation": "mask_anat.$subj",
- "GeneratedBy": "urn:0b7c6124-4e20-4583-ad3f-b7cacb34ed43",
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{
- "@id": "urn:0519e719-8734-4119-b7e1-c2ae7ecb72ab",
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"digest": {
@@ -999,7 +1010,7 @@
}
},
{
- "@id": "urn:457d391d-f8af-4766-94cd-9b534bda02f2",
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@@ -1007,7 +1018,7 @@
}
},
{
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+ "@id": "bids::/Users/u1591557/abin/TT_N27+tlrc",
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"digest": {
@@ -1015,16 +1026,16 @@
}
},
{
- "@id": "urn:555d9d1b-ef9d-4724-b97a-1be35882ee1e",
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- "GeneratedBy": "urn:5bb8508a-eda5-4365-81fb-999ffd24853e",
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}
},
{
- "@id": "urn:c4c118f0-ce74-41f3-910b-79f9f4d747eb",
+ "@id": "bids::rm.resam.group+tlrc",
"Label": "rm.resam.group",
"AtLocation": "rm.resam.group+tlrc",
"digest": {
@@ -1032,25 +1043,25 @@
}
},
{
- "@id": "urn:375c91f6-f7c7-4879-8f95-2a01b4bf1ac9",
+ "@id": "bids::mask_group",
"Label": "mask_group",
"AtLocation": "mask_group",
- "GeneratedBy": "urn:4830f327-2309-4954-8099-23d6077d7c00",
+ "GeneratedBy": "urn:3dmaskto-KnI1R4hJ",
"digest": {
"sha256": "d7093b26470ded8d7e939359017b18d28a2da4c6bb702c1183df20bca614f949"
}
},
{
- "@id": "urn:5703fe98-7035-4267-bfc4-7fb711d4a477",
+ "@id": "bids::rm.mean_r$run",
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"AtLocation": "rm.mean_r$run",
- "GeneratedBy": "urn:e61bbb8d-d5d3-4835-958e-c7de860c6474",
+ "GeneratedBy": "urn:3dtstat-gqenW7Kx",
"digest": {
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}
},
{
- "@id": "urn:f8b35d61-6b39-4d1e-b9e8-e8a0f7c1bf73",
+ "@id": "bids::rm.mean_r$run+tlrc",
"Label": "rm.mean_r$run",
"AtLocation": "rm.mean_r$run+tlrc",
"digest": {
@@ -1058,34 +1069,34 @@
}
},
{
- "@id": "urn:3e95a2cf-79dd-411b-b72b-84eadc9f6529",
+ "@id": "bids::pb04.$subj.r$run.scale",
"Label": "pb04.$subj.r$run.scale",
"AtLocation": "pb04.$subj.r$run.scale",
- "GeneratedBy": "urn:99fdddd9-cb59-44fc-a275-ee3393b74160",
+ "GeneratedBy": "urn:3dcalc-BfEIk4TY",
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}
},
{
- "@id": "urn:d99020da-414e-4667-b1f4-695e3c5c3f4b",
+ "@id": "bids::motion_demean.1D",
"Label": "motion_demean.1D",
"AtLocation": "motion_demean.1D",
- "GeneratedBy": "urn:f95a770c-8509-4d92-9064-08ba635398ef",
+ "GeneratedBy": "urn:1dtoolpy-dlVV0iVy",
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}
},
{
- "@id": "urn:308fe337-072b-4704-8cdd-117d8eea1928",
+ "@id": "bids::motion_deriv.1D",
"Label": "motion_deriv.1D",
"AtLocation": "motion_deriv.1D",
- "GeneratedBy": "urn:ca967613-3f22-4861-9331-8475dc0dffaa",
+ "GeneratedBy": "urn:1dtoolpy-9aAS3KMx",
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"sha256": "47185bf319e91642ad6f2a396a43fc9f8db7b82f2a9aef326bfe4a955120038b"
}
},
{
- "@id": "urn:130b200a-a004-4ac6-917b-fae4be88252d",
+ "@id": "bids::pb04.$subj.r*.scale+tlrc.HEAD",
"Label": "pb04.$subj.r*.scale",
"AtLocation": "pb04.$subj.r*.scale+tlrc.HEAD",
"digest": {
@@ -1093,25 +1104,25 @@
}
},
{
- "@id": "urn:b7d21574-2f03-409f-b7d5-363bb4297b36",
+ "@id": "bids::X.xmat.1D",
"Label": "X.xmat.1D",
"AtLocation": "X.xmat.1D",
- "GeneratedBy": "urn:e63e06d1-3992-44fd-b5a6-fd0d6c86aeaf",
+ "GeneratedBy": "urn:3ddeconv-vvEyyOkM",
"digest": {
"sha256": "cdbd4f4edf6fa02a9d7fcf9a3e593893438e9279c9523fbb6993630a83ad5162"
}
},
{
- "@id": "urn:0cc0ab94-4f84-4683-baea-d3e0d4183a7a",
+ "@id": "bids::all_runs.$subj",
"Label": "all_runs.$subj",
"AtLocation": "all_runs.$subj",
- "GeneratedBy": "urn:ae7558b3-c12b-4858-b7d2-b1fd79149b23",
+ "GeneratedBy": "urn:3dtcat-FuFiO3Gd",
"digest": {
"sha256": "bcf27fc2e339e751d0ea9bba931674c21fd9d434ff411330f4df55f872a8cc7e"
}
},
{
- "@id": "urn:d1e1cda7-db65-4013-a6e5-eff822140f17",
+ "@id": "bids::all_runs.$subj+tlrc%22[$ktrs]%22",
"Label": "all_runs.$subj",
"AtLocation": "all_runs.$subj+tlrc\"[$ktrs]\"",
"digest": {
@@ -1119,16 +1130,16 @@
}
},
{
- "@id": "urn:4e0d8bea-e775-47bd-b9b7-3e7d46641b11",
+ "@id": "bids::rm.signal.all",
"Label": "rm.signal.all",
"AtLocation": "rm.signal.all",
- "GeneratedBy": "urn:75ff7e84-a2f8-4fcd-9c17-97f92cfcec40",
+ "GeneratedBy": "urn:3dtstat-dXEp8W3V",
"digest": {
"sha256": "bda68a16c0afd5e55d4d7415c8c959e61a9aad7898dd456b0f3bb597363dde31"
}
},
{
- "@id": "urn:4e86443f-aeb9-467a-87cd-921d8561e79d",
+ "@id": "bids::errts.$%7Bsubj%7D+tlrc%22[$ktrs]%22",
"Label": "errts.${subj}",
"AtLocation": "errts.${subj}+tlrc\"[$ktrs]\"",
"digest": {
@@ -1136,16 +1147,16 @@
}
},
{
- "@id": "urn:4bbba145-a298-46fc-9d71-59ec7c739744",
+ "@id": "bids::rm.noise.all",
"Label": "rm.noise.all",
"AtLocation": "rm.noise.all",
- "GeneratedBy": "urn:0e3d9bab-2776-4009-8c33-f64c88a586c0",
+ "GeneratedBy": "urn:3dtstat-Qc8wnCbA",
"digest": {
"sha256": "431314eb75d086ce08373b3a374427969e89414c4a2d607e449c1f6485c547af"
}
},
{
- "@id": "urn:ffbf1f1d-cc38-47b8-a1a2-c0242ca8e8f8",
+ "@id": "bids::rm.signal.all+tlrc",
"Label": "rm.signal.all",
"AtLocation": "rm.signal.all+tlrc",
"digest": {
@@ -1153,7 +1164,7 @@
}
},
{
- "@id": "urn:c512daa6-81d5-4f4b-b599-ad2406137f3c",
+ "@id": "bids::rm.noise.all+tlrc",
"Label": "rm.noise.all",
"AtLocation": "rm.noise.all+tlrc",
"digest": {
@@ -1161,16 +1172,16 @@
}
},
{
- "@id": "urn:dd2a855c-e782-42f5-ba65-a3a396a789de",
+ "@id": "bids::TSNR.$subj",
"Label": "TSNR.$subj",
"AtLocation": "TSNR.$subj",
- "GeneratedBy": "urn:bd40b1fe-f58d-4f57-abba-63275e76d0c1",
+ "GeneratedBy": "urn:3dcalc-DXPGfw54",
"digest": {
"sha256": "303f183145a1e295686c08335d3b70753777cf0fa0b3f9628cf8de5471359a00"
}
},
{
- "@id": "urn:cff0d752-9ae5-4404-92c9-6fff79dcd286",
+ "@id": "bids::errts.$%7Bsubj%7D+tlrc",
"Label": "errts.${subj}",
"AtLocation": "errts.${subj}+tlrc",
"digest": {
@@ -1178,25 +1189,25 @@
}
},
{
- "@id": "urn:3f1fbed3-59f6-40e0-ad6f-8bda59adde98",
+ "@id": "bids::rm.errts.unit",
"Label": "rm.errts.unit",
"AtLocation": "rm.errts.unit",
- "GeneratedBy": "urn:9749c11a-671c-4c79-9951-10d84f2c77a6",
+ "GeneratedBy": "urn:3dtnorm-aL7aVzi7",
"digest": {
"sha256": "03b570ad773a00f51ab7e6cdedfebdeca45f5356de0c25f9e3be44d7bf2c7151"
}
},
{
- "@id": "urn:859bef03-d16d-49d0-95d7-526e5a3b3e9d",
+ "@id": "bids::gmean.errts.unit.1D",
"Label": "gmean.errts.unit.1D",
"AtLocation": "gmean.errts.unit.1D",
- "GeneratedBy": "urn:a28a1432-8e3d-4d39-9cf9-e6acda7ca2fc",
+ "GeneratedBy": "urn:3dmaskav-r6J6hrSP",
"digest": {
"sha256": "a35a66cce2e2d487762823c197ca1edc450a9887f46f125826b69c5021662f95"
}
},
{
- "@id": "urn:deec3fb9-4e28-4d7c-8a47-599403e4edcd",
+ "@id": "bids::out.gcor.1D",
"Label": "out.gcor.1D",
"AtLocation": "out.gcor.1D",
"digest": {
@@ -1204,16 +1215,16 @@
}
},
{
- "@id": "urn:4cef8fb6-2bfe-4c0e-85b8-4020e5ea01e3",
+ "@id": "urn:uuid:3a91568f-3bee-4245-9cdc-fd2740c30039",
"Label": "-",
"AtLocation": "-",
- "GeneratedBy": "urn:1c42556b-6ea5-40c5-ba7f-d049ffbfac3c",
+ "GeneratedBy": "urn:3dtstat-SK7HPnMN",
"digest": {
"sha256": "dac304c9f20899ca1ef5aa403e565345fd0ff4ed80c35f82007c9b03a68292b3"
}
},
{
- "@id": "urn:bd25383b-d975-4195-831d-bb521d441d8b",
+ "@id": "bids::rm.errts.unit+tlrc",
"Label": "rm.errts.unit",
"AtLocation": "rm.errts.unit+tlrc",
"digest": {
@@ -1221,16 +1232,16 @@
}
},
{
- "@id": "urn:62cef0cc-1cb3-4d9b-b110-a01298294d4b",
+ "@id": "bids::rm.DP",
"Label": "rm.DP",
"AtLocation": "rm.DP",
- "GeneratedBy": "urn:331280a9-cad6-443e-8ec0-0bd032dec1f7",
+ "GeneratedBy": "urn:3dcalc-AtoT3iN7",
"digest": {
"sha256": "06a0bfbc609c1a06ecf93c479a3288d2911c7f5f3e93cf49c5d26f721c2035ed"
}
},
{
- "@id": "urn:cf72bf6d-c398-4e69-9a8d-dbd8c530a31e",
+ "@id": "bids::rm.DP+tlrc",
"Label": "rm.DP",
"AtLocation": "rm.DP+tlrc",
"digest": {
@@ -1238,16 +1249,16 @@
}
},
{
- "@id": "urn:8b99d805-d291-4e91-b46b-a85013a83cfb",
+ "@id": "bids::corr_brain",
"Label": "corr_brain",
"AtLocation": "corr_brain",
- "GeneratedBy": "urn:fd23797b-703e-44e6-9ce0-93a6c6659007",
+ "GeneratedBy": "urn:3dtstat-OyyA0af6",
"digest": {
"sha256": "74e3aeae0da338b871ab5dc9e8859a4e81fcf1b3c0042cd22fe337eb7baf5eae"
}
},
{
- "@id": "urn:8adb28e5-349d-4f53-8b18-4ed3975fae39",
+ "@id": "bids::X.nocensor.xmat.1D'[3]'",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D'[3]'",
"digest": {
@@ -1255,16 +1266,16 @@
}
},
{
- "@id": "urn:9686bceb-c078-427b-bb3f-d03889dc3a4d",
+ "@id": "bids::ideal_tone_counting.1D",
"Label": "ideal_tone_counting.1D",
"AtLocation": "ideal_tone_counting.1D",
- "GeneratedBy": "urn:0f2a2124-3de2-4554-af3f-3833d2222dae",
+ "GeneratedBy": "urn:1dcat-cOD2csn8",
"digest": {
"sha256": "9bb1cabac5ce7ca19dffa5cd6336a9bf82d362fea2ce9341978406e421b5333c"
}
},
{
- "@id": "urn:fc6df78f-dcf6-493f-9d17-9b7821a4991b",
+ "@id": "bids::X.nocensor.xmat.1D'[4]'",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D'[4]'",
"digest": {
@@ -1272,16 +1283,16 @@
}
},
{
- "@id": "urn:1e71f56b-d494-46ce-ba1b-e6e6a05abd1f",
+ "@id": "bids::ideal_probe.1D",
"Label": "ideal_probe.1D",
"AtLocation": "ideal_probe.1D",
- "GeneratedBy": "urn:14a31446-8871-49fa-b1e0-e00260791d2c",
+ "GeneratedBy": "urn:1dcat-66f4THnB",
"digest": {
"sha256": "705d93afa8b6ded9f4f572db3f967b54e9906942669af51dd8287a9863bb4288"
}
},
{
- "@id": "urn:94f1e1b4-8e76-41fb-9f3b-d60517272174",
+ "@id": "bids::X.nocensor.xmat.1D%22[$reg_cols]%22",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D\"[$reg_cols]\"",
"digest": {
@@ -1289,52 +1300,52 @@
}
},
{
- "@id": "urn:f331cbfd-e6cb-4474-b9d2-f5093b12b4b7",
+ "@id": "bids::sum_ideal.1D",
"Label": "sum_ideal.1D",
"AtLocation": "sum_ideal.1D",
- "GeneratedBy": "urn:f3a1b8eb-becf-4260-8526-cd7f14a93549",
+ "GeneratedBy": "urn:3dtstat-8UaSUhxA",
"digest": {
"sha256": "b2dccadcd84b2d26ec9685c4d1846baf2f11b867f31c36a08748d1c85467b01a"
}
},
{
- "@id": "urn:e350024b-aa85-47b7-a4a4-239310870a5f",
+ "@id": "bids::X.stim.xmat.1D",
"Label": "X.stim.xmat.1D",
"AtLocation": "X.stim.xmat.1D",
- "GeneratedBy": "urn:8e28756c-7915-4747-a230-d16d1b31fd66",
+ "GeneratedBy": "urn:1dcat-VP7bb6XX",
"digest": {
"sha256": "7c61b2f4bbb9eb0cecb19f81faa3a79b94d547b7fb4087ed18e368619e0004e6"
}
},
{
- "@id": "urn:7be1cf76-746a-42a3-aa4f-a4ae45ef4735",
+ "@id": "bids::blur.epits.1D",
"Label": "blur.epits.1D",
"AtLocation": "blur.epits.1D",
- "GeneratedBy": "urn:1f3ccb95-5c68-4eda-a0e2-23aef8d5c592",
+ "GeneratedBy": "urn:3dfwhmx-YOrRfjvt",
"digest": {
"sha256": "623e70a42214e56babc1f1dca156e0b11ba09865dbd6ca9549d54ca2fc601515"
}
},
{
- "@id": "urn:c04a985a-03ce-4123-916b-52f1738c5371",
+ "@id": "bids::blur.errts.1D",
"Label": "blur.errts.1D",
"AtLocation": "blur.errts.1D",
- "GeneratedBy": "urn:194a0e78-c788-4530-b7c0-0155f909d523",
+ "GeneratedBy": "urn:3dfwhmx-d666scW1",
"digest": {
"sha256": "73969700079b5d3275536ac7eaf0e17571d7e74ec49553b6940f90d5718fc800"
}
},
{
- "@id": "urn:ef22e358-c84a-4ca8-b3e2-005482fd2886",
+ "@id": "bids::ClustSim",
"Label": "ClustSim",
"AtLocation": "ClustSim",
- "GeneratedBy": "urn:33ed9bcb-6059-4783-88f7-1aa00fe0a5c0",
+ "GeneratedBy": "urn:3dclusts-duYWBtRe",
"digest": {
"sha256": "2e0cdba2c91902ba12d742a39cb20df66cfd705ba8de767fbf68aae8eb65c6f0"
}
},
{
- "@id": "urn:c09831f3-2daa-4d46-8cc2-8d3a6d13e061",
+ "@id": "bids::pb00.$subj.r*.tcat+orig.HEAD",
"Label": "pb00.$subj.r*.tcat",
"AtLocation": "pb00.$subj.r*.tcat+orig.HEAD",
"digest": {
@@ -1342,10 +1353,10 @@
}
},
{
- "@id": "urn:307ab064-d2fc-4591-bb45-46dd57cf2d2d",
+ "@id": "bids::-exit0",
"Label": "-exit0",
"AtLocation": "-exit0",
- "GeneratedBy": "urn:a0828193-6c5d-4073-910f-4d6ef6b19f1a",
+ "GeneratedBy": "urn:genssrev-50k1KCS5",
"digest": {
"sha256": "871a4d3513ed2924cbb10c1c15a196eac4a46a05bdcc248e3bcdb23327b3ad90"
}
diff --git a/examples/from_parsers/afni/afni_alt_onesided_proc.png b/examples/from_parsers/afni/afni_alt_onesided_proc.png
index e2c50a42a..25de549a8 100644
Binary files a/examples/from_parsers/afni/afni_alt_onesided_proc.png and b/examples/from_parsers/afni/afni_alt_onesided_proc.png differ
diff --git a/examples/from_parsers/afni/afni_alt_onesided_proc_block.jsonld b/examples/from_parsers/afni/afni_alt_onesided_proc_block.jsonld
index 329a0a511..90d10c5e3 100644
--- a/examples/from_parsers/afni/afni_alt_onesided_proc_block.jsonld
+++ b/examples/from_parsers/afni/afni_alt_onesided_proc_block.jsonld
@@ -4,187 +4,189 @@
"Records": {
"Software": [
{
- "@id": "urn:e1c44cbe-f3d0-4f0e-a12c-b3228ede5239",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:afni-CUfM2GF9",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
- "Version": "afni24"
+ "Version": "afni24",
+ "AltIdentifier": "RRID:SCR_005927"
}
],
"Activities": [
{
- "@id": "urn:0f6e1769-0854-4759-a3da-2c830f0e3125",
+ "@id": "urn:autobloc-v8H5Ogxq",
"Label": "auto block: setup",
- "AssociatedWith": "urn:e1c44cbe-f3d0-4f0e-a12c-b3228ede5239",
+ "AssociatedWith": "urn:afni-CUfM2GF9",
"Command": "mkdir $output_dir; mkdir $output_dir/stimuli; cp ./afni_one_sided_t_test/tone_counting_onset_times.txt ./afni_one_sided_t_test/tone_counting_probe_duration.txt $output_dir/stimuli; 3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w; ",
"Used": [
- "urn:0f4d54c0-a22d-4e21-8302-30a73e21a790",
- "urn:4125e09e-1e8f-485f-a75a-200cf5ed26c0",
- "urn:ac5590b1-bd70-4147-b25f-7328029e7372"
+ "bids::afni_one_sided_t_test/tone_counting_onset_times.txt",
+ "bids::afni_one_sided_t_test/tone_counting_probe_duration.txt",
+ "bids::sub-01_T1w.nii.gz"
]
},
{
- "@id": "urn:8c453e99-08d2-4dc0-be26-4e3d7142869f",
+ "@id": "urn:autobloc-X3Kz90HY",
"Label": "auto block: tcat",
- "AssociatedWith": "urn:e1c44cbe-f3d0-4f0e-a12c-b3228ede5239",
+ "AssociatedWith": "urn:afni-CUfM2GF9",
"Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ",
"Used": [
- "urn:228beb26-f70c-48f3-9558-0bd838529fbe"
+ "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'"
]
},
{
- "@id": "urn:937bd6fc-0ed1-424a-bbc8-828824a18e79",
+ "@id": "urn:autobloc-GVYJczpS",
"Label": "auto block: outcount",
- "AssociatedWith": "urn:e1c44cbe-f3d0-4f0e-a12c-b3228ede5239",
+ "AssociatedWith": "urn:afni-CUfM2GF9",
"Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ",
"Used": [
- "urn:a2819925-6bb1-4437-91bb-8750d8d911eb",
- "urn:26ab105c-e2ae-422f-bea8-19180cabf617"
+ "bids::pb00.$subj.r$run.tcat+orig",
+ "bids::outcount.r*.1D"
]
},
{
- "@id": "urn:259ba45e-774a-49f8-857b-82f0fe731dd6",
+ "@id": "urn:tshift-HGyQiLrF",
"Label": "tshift",
- "AssociatedWith": "urn:e1c44cbe-f3d0-4f0e-a12c-b3228ede5239",
+ "AssociatedWith": "urn:afni-CUfM2GF9",
"Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ",
"Used": [
- "urn:a2819925-6bb1-4437-91bb-8750d8d911eb"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:abf735c9-2667-495b-9fa1-321a42d9e42b",
+ "@id": "urn:align-dbfMq7NE",
"Label": "align",
- "AssociatedWith": "urn:e1c44cbe-f3d0-4f0e-a12c-b3228ede5239",
+ "AssociatedWith": "urn:afni-CUfM2GF9",
"Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ",
"Used": [
- "urn:7a5e09c8-074d-47d7-a7e6-7757a3b0002c",
- "urn:fce53e58-532c-4750-882a-d04ef8ea1b35"
+ "bids::pb01.$subj.r01.tshift+orig",
+ "bids::sub-01_T1w+orig"
]
},
{
- "@id": "urn:52ac7507-1b78-451b-8d71-a8134799b096",
+ "@id": "urn:tlrc-RV1CChcN",
"Label": "tlrc",
- "AssociatedWith": "urn:e1c44cbe-f3d0-4f0e-a12c-b3228ede5239",
+ "AssociatedWith": "urn:afni-CUfM2GF9",
"Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ",
"Used": [
- "urn:294250c1-3f20-4e89-9043-505157d79e92",
- "urn:fc85c9c4-03af-41d2-a7d3-5665cd1240cc",
- "urn:b5e0225f-eff0-4e8c-beb9-09e171bbf0a1"
+ "bids::TT_N27+tlrc",
+ "bids::sub-01_T1w_ns+orig",
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:4ba9541e-ec77-485c-bc03-5344cbfa840c",
+ "@id": "urn:volreg-qY8NgHG7",
"Label": "volreg",
- "AssociatedWith": "urn:e1c44cbe-f3d0-4f0e-a12c-b3228ede5239",
+ "AssociatedWith": "urn:afni-CUfM2GF9",
"Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig; 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1; cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D; 3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run; 3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run; 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc; cat dfile.r*.1D > dfile_rall.1D; 3dcopy rm.epi.min.r01+tlrc mask_epi_extents; 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg; 3dcopy sub-01_T1w_ns+tlrc anat_final.$subj; 3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped; ",
"Used": [
- "urn:17f65b7b-4973-4314-93d1-559ab4356cc9",
- "urn:17f65b7b-4973-4314-93d1-559ab4356cc9",
- "urn:b5e0225f-eff0-4e8c-beb9-09e171bbf0a1",
- "urn:17f65b7b-4973-4314-93d1-559ab4356cc9",
- "urn:fbeeaff6-baec-49f5-a079-172e049a9402",
- "urn:2cb625e4-d86b-4d08-8244-67e8ecce7a1a",
- "urn:fbeeaff6-baec-49f5-a079-172e049a9402",
- "urn:106667e2-534d-4083-93fd-ff640a2eb33f",
- "urn:c570a9cb-ff5a-493a-8eb2-a0ef15df96d5",
- "urn:9b6dc0b4-91fd-4b34-9598-11ed55ece512",
- "urn:e6d2ef28-055a-4391-baea-97dd8a9d185e",
- "urn:f6b197d3-067e-40ee-8d6a-f03cda41761e",
- "urn:fbeeaff6-baec-49f5-a079-172e049a9402",
- "urn:00e42115-626f-4d62-82d8-d85d631329e5"
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.epi.all1+orig",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.epi.1.r$run+tlrc",
+ "bids::dfile.r*.1D",
+ "bids::rm.epi.min.r01+tlrc",
+ "bids::mask_epi_extents+tlrc",
+ "bids::rm.epi.nomask.r$run+tlrc",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::anat_final.$subj+tlrc",
+ "bids::warp.anat.Xat.1D"
]
},
{
- "@id": "urn:28ba5f12-1365-4bbb-ab4a-159bd0b33b34",
+ "@id": "urn:blur-2ufpOLNQ",
"Label": "blur",
- "AssociatedWith": "urn:e1c44cbe-f3d0-4f0e-a12c-b3228ede5239",
+ "AssociatedWith": "urn:afni-CUfM2GF9",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc; ",
"Used": [
- "urn:37420101-c925-4820-bf6d-1042ad709005",
- "urn:7c75b9d4-e136-4ed6-b193-472e6a391505"
+ "bids::pb02.$subj.r$run.volreg+tlrc",
+ "bids::pb03.$subj.r$run.blur"
]
},
{
- "@id": "urn:c6a0afd0-daa5-4243-aa57-e91e9b546865",
+ "@id": "urn:mask-YfQVxxPi",
"Label": "mask",
- "AssociatedWith": "urn:e1c44cbe-f3d0-4f0e-a12c-b3228ede5239",
+ "AssociatedWith": "urn:afni-CUfM2GF9",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc; 3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj; 3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj; 3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt; 3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt; 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group; ",
"Used": [
- "urn:fc554388-45db-473b-bbeb-5bf07fa85ca2",
- "urn:57ffb538-8bfb-451f-86b0-b0206ccfa026",
- "urn:fbeeaff6-baec-49f5-a079-172e049a9402",
- "urn:8c2d444b-075c-4191-bf34-335cfe698345",
- "urn:55e6156b-c2e4-4d1d-a9a8-a7a9fcf74833",
- "urn:bc3512b9-619b-476c-bc4a-880a9ae12666",
- "urn:55e6156b-c2e4-4d1d-a9a8-a7a9fcf74833",
- "urn:bc3512b9-619b-476c-bc4a-880a9ae12666",
- "urn:57ffb538-8bfb-451f-86b0-b0206ccfa026",
- "urn:e76b0898-df47-4906-9f8a-87374cd4bc62",
- "urn:72363f1e-f5ea-4349-8948-478f8f0659f9"
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.resam.anat+tlrc",
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee",
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee",
+ "bids::/Users/u1591557/abin/TT_N27+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.resam.group+tlrc"
]
},
{
- "@id": "urn:7403f17c-c790-471e-8b6d-55d5650cb385",
+ "@id": "urn:scale-GmmL0l7Q",
"Label": "scale",
- "AssociatedWith": "urn:e1c44cbe-f3d0-4f0e-a12c-b3228ede5239",
+ "AssociatedWith": "urn:afni-CUfM2GF9",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc; 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale; ",
"Used": [
- "urn:fc554388-45db-473b-bbeb-5bf07fa85ca2",
- "urn:d50db812-375c-4601-92d1-9324de903322",
- "urn:f6b197d3-067e-40ee-8d6a-f03cda41761e",
- "urn:fc554388-45db-473b-bbeb-5bf07fa85ca2"
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::mask_epi_extents+tlrc",
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::rm.mean_r$run+tlrc"
]
},
{
- "@id": "urn:e276d06e-84be-4349-8afb-33c503367cc2",
+ "@id": "urn:regress-JwuObKc8",
"Label": "regress",
- "AssociatedWith": "urn:e1c44cbe-f3d0-4f0e-a12c-b3228ede5239",
+ "AssociatedWith": "urn:afni-CUfM2GF9",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}; 3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj; 1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt; 3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD; 3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"; 3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"; 3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj; 3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc; 3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D; 3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D; 3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP; 3dTstat -sum -prefix corr_brain rm.DP+tlrc; 1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D; 1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D; 3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"; 1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D; ",
"Used": [
- "urn:8fa0af1f-38fc-4157-81f5-a87d031deb90",
- "urn:8fa0af1f-38fc-4157-81f5-a87d031deb90",
- "urn:8fa0af1f-38fc-4157-81f5-a87d031deb90",
- "urn:15e916d5-27d4-444d-a43d-e713ae6026bc",
- "urn:15e916d5-27d4-444d-a43d-e713ae6026bc",
- "urn:5207d313-7a90-44e0-8017-473f8c0516b2",
- "urn:bbed6eaf-912f-44a5-ad69-bcdd07b5611c",
- "urn:57ffb538-8bfb-451f-86b0-b0206ccfa026",
- "urn:6e005855-789f-4ce9-8fe7-417db70629cc",
- "urn:9bf6596d-5bb9-4781-8357-feaaccd82518",
- "urn:743b2c7e-35e5-4c6b-84e1-4c69ba55c9d8",
- "urn:8172d375-1bc3-425a-b82f-2e1c215b9f7c",
- "urn:ec4e23f3-d608-4e76-b1d0-afb393f4f5af",
- "urn:2b061de6-9339-4873-b556-40feb2d7bb4f",
- "urn:cefdfa11-917c-4d55-870b-b181f657575f",
- "urn:998920fc-bc8a-4ead-aac5-a44e39b2a4c0",
- "urn:439259c5-7d95-4c8d-83ab-ab595ec441a1",
- "urn:439259c5-7d95-4c8d-83ab-ab595ec441a1"
+ "bids::dfile_rall.1D",
+ "bids::dfile_rall.1D",
+ "bids::dfile_rall.1D",
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD",
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD",
+ "bids::all_runs.$subj+tlrc%22[$ktrs]%22",
+ "bids::errts.$%7Bsubj%7D+tlrc%22[$ktrs]%22",
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.noise.all+tlrc",
+ "bids::rm.signal.all+tlrc",
+ "bids::errts.$%7Bsubj%7D+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::out.gcor.1D",
+ "bids::rm.errts.unit+tlrc",
+ "bids::rm.DP+tlrc",
+ "bids::X.nocensor.xmat.1D'[3]'",
+ "bids::X.nocensor.xmat.1D'[4]'",
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22",
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:a8be1d24-6de4-45b2-92ad-dc44be445319",
+ "@id": "urn:bluresti-QW19fifr",
"Label": "blur estimation",
- "AssociatedWith": "urn:e1c44cbe-f3d0-4f0e-a12c-b3228ede5239",
+ "AssociatedWith": "urn:afni-CUfM2GF9",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D; 3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D; 3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim; ",
"Used": [
- "urn:57ffb538-8bfb-451f-86b0-b0206ccfa026",
- "urn:57ffb538-8bfb-451f-86b0-b0206ccfa026",
- "urn:57ffb538-8bfb-451f-86b0-b0206ccfa026"
+ "bids::full_mask.$subj+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:8c4107d0-f88c-4a4c-9357-6e1e19ad1201",
+ "@id": "urn:autobloc-44jc0p9G",
"Label": "auto block: generate review scripts",
- "AssociatedWith": "urn:e1c44cbe-f3d0-4f0e-a12c-b3228ede5239",
+ "AssociatedWith": "urn:afni-CUfM2GF9",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD; gen_ss_review_scripts.py -mot_limit 0.3 -exit0; ",
"Used": [
- "urn:97a56b57-4ac3-43c8-a6e1-bf20b58206dd"
+ "bids::pb00.$subj.r*.tcat+orig.HEAD"
]
}
],
"Entities": [
{
- "@id": "urn:4125e09e-1e8f-485f-a75a-200cf5ed26c0",
+ "@id": "bids::afni_one_sided_t_test/tone_counting_onset_times.txt",
"Label": "tone_counting_onset_times.txt",
"AtLocation": "./afni_one_sided_t_test/tone_counting_onset_times.txt",
"digest": {
@@ -192,7 +194,7 @@
}
},
{
- "@id": "urn:0f4d54c0-a22d-4e21-8302-30a73e21a790",
+ "@id": "bids::afni_one_sided_t_test/tone_counting_probe_duration.txt",
"Label": "tone_counting_probe_duration.txt",
"AtLocation": "./afni_one_sided_t_test/tone_counting_probe_duration.txt",
"digest": {
@@ -200,7 +202,7 @@
}
},
{
- "@id": "urn:ac5590b1-bd70-4147-b25f-7328029e7372",
+ "@id": "bids::sub-01_T1w.nii.gz",
"Label": "sub-01_T1w.nii.gz",
"AtLocation": "sub-01_T1w.nii.gz",
"digest": {
@@ -208,34 +210,34 @@
}
},
{
- "@id": "urn:8eebfcaf-f179-4ce4-83df-6d852735775d",
+ "@id": "bids::$output_dir",
"Label": "$output_dir",
"AtLocation": "$output_dir",
- "GeneratedBy": "urn:0f6e1769-0854-4759-a3da-2c830f0e3125",
+ "GeneratedBy": "urn:autobloc-v8H5Ogxq",
"digest": {
"sha256": "9fa4c635e6533ddf2fed54295920052818d948c3ffe97bc753bd7336b453f8cb"
}
},
{
- "@id": "urn:ce469927-3e7f-4362-b6fc-0cca4d0aa043",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:0f6e1769-0854-4759-a3da-2c830f0e3125"
+ "GeneratedBy": "urn:autobloc-v8H5Ogxq"
},
{
- "@id": "urn:64845e67-36b3-45b7-a4bb-2e3a3460a920",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:0f6e1769-0854-4759-a3da-2c830f0e3125"
+ "GeneratedBy": "urn:autobloc-v8H5Ogxq"
},
{
- "@id": "urn:08d57a05-4f66-4823-85e2-c934a8c15fa0",
+ "@id": "bids::$output_dir/sub-01_T1w",
"Label": "sub-01_T1w",
"AtLocation": "$output_dir/sub-01_T1w",
- "GeneratedBy": "urn:0f6e1769-0854-4759-a3da-2c830f0e3125"
+ "GeneratedBy": "urn:autobloc-v8H5Ogxq"
},
{
- "@id": "urn:228beb26-f70c-48f3-9558-0bd838529fbe",
+ "@id": "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Label": "sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"digest": {
@@ -243,13 +245,13 @@
}
},
{
- "@id": "urn:468ccc66-cf3f-46b5-8d4b-e7e23acd6202",
+ "@id": "bids::$output_dir/pb00.$subj.r01.tcat",
"Label": "pb00.$subj.r01.tcat",
"AtLocation": "$output_dir/pb00.$subj.r01.tcat",
- "GeneratedBy": "urn:8c453e99-08d2-4dc0-be26-4e3d7142869f"
+ "GeneratedBy": "urn:autobloc-X3Kz90HY"
},
{
- "@id": "urn:a2819925-6bb1-4437-91bb-8750d8d911eb",
+ "@id": "bids::pb00.$subj.r$run.tcat+orig",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -257,7 +259,7 @@
}
},
{
- "@id": "urn:26ab105c-e2ae-422f-bea8-19180cabf617",
+ "@id": "bids::outcount.r*.1D",
"Label": "outcount.r*.1D",
"AtLocation": "outcount.r*.1D",
"digest": {
@@ -265,25 +267,25 @@
}
},
{
- "@id": "urn:7ce0ef63-f223-435e-8607-3e688090e616",
+ "@id": "bids::outcount.r$run.1D",
"Label": "outcount.r$run.1D",
"AtLocation": "outcount.r$run.1D",
- "GeneratedBy": "urn:937bd6fc-0ed1-424a-bbc8-828824a18e79",
+ "GeneratedBy": "urn:autobloc-GVYJczpS",
"digest": {
"sha256": "63d9f539e5470badc625d557109f68bc4eecbb02ca2667483739d52f95e5d0dd"
}
},
{
- "@id": "urn:bb0d45ca-b60f-4985-b5c1-879a7474c556",
+ "@id": "bids::outcount_rall.1D",
"Label": "outcount_rall.1D",
"AtLocation": "outcount_rall.1D",
- "GeneratedBy": "urn:937bd6fc-0ed1-424a-bbc8-828824a18e79",
+ "GeneratedBy": "urn:autobloc-GVYJczpS",
"digest": {
"sha256": "cb887fd5e4d5e9acb3a24820d0f7a62ed38a5ffb0fdedd373440ac0219fb186a"
}
},
{
- "@id": "urn:a2819925-6bb1-4437-91bb-8750d8d911eb",
+ "@id": "bids::pb00.$subj.r$run.tcat+orig",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -291,16 +293,16 @@
}
},
{
- "@id": "urn:a7f23811-e909-45a2-9551-846e81269793",
+ "@id": "bids::pb01.$subj.r$run.tshift",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift",
- "GeneratedBy": "urn:259ba45e-774a-49f8-857b-82f0fe731dd6",
+ "GeneratedBy": "urn:tshift-HGyQiLrF",
"digest": {
"sha256": "c6bf01cea8d2eac1d7a866f80b865c6e7d4b4e012dbb63d480ac9a8551162d72"
}
},
{
- "@id": "urn:7a5e09c8-074d-47d7-a7e6-7757a3b0002c",
+ "@id": "bids::sub-01_T1w+orig",
"Label": "sub-01_T1w",
"AtLocation": "sub-01_T1w+orig",
"digest": {
@@ -308,7 +310,7 @@
}
},
{
- "@id": "urn:fce53e58-532c-4750-882a-d04ef8ea1b35",
+ "@id": "bids::pb01.$subj.r01.tshift+orig",
"Label": "pb01.$subj.r01.tshift",
"AtLocation": "pb01.$subj.r01.tshift+orig",
"digest": {
@@ -316,16 +318,16 @@
}
},
{
- "@id": "urn:8a892058-4a73-4e1e-91a1-50996c954677",
+ "@id": "bids::_al_junk",
"Label": "_al_junk",
"AtLocation": "_al_junk",
- "GeneratedBy": "urn:abf735c9-2667-495b-9fa1-321a42d9e42b",
+ "GeneratedBy": "urn:align-dbfMq7NE",
"digest": {
"sha256": "bd785a075a4c6446e1e54de9e628913f7f1c814e86b69a9fbfe933209e6d37b5"
}
},
{
- "@id": "urn:fc85c9c4-03af-41d2-a7d3-5665cd1240cc",
+ "@id": "bids::TT_N27+tlrc",
"Label": "TT_N27",
"AtLocation": "TT_N27+tlrc",
"digest": {
@@ -333,7 +335,7 @@
}
},
{
- "@id": "urn:294250c1-3f20-4e89-9043-505157d79e92",
+ "@id": "bids::sub-01_T1w_ns+orig",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+orig",
"digest": {
@@ -341,7 +343,7 @@
}
},
{
- "@id": "urn:b5e0225f-eff0-4e8c-beb9-09e171bbf0a1",
+ "@id": "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc::WARP_DATA",
"digest": {
@@ -349,16 +351,16 @@
}
},
{
- "@id": "urn:00e42115-626f-4d62-82d8-d85d631329e5",
+ "@id": "bids::warp.anat.Xat.1D",
"Label": "warp.anat.Xat.1D",
"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:52ac7507-1b78-451b-8d71-a8134799b096",
+ "GeneratedBy": "urn:tlrc-RV1CChcN",
"digest": {
"sha256": "800633fb5b4e9be64078bc181c4d5510ffb73fc5cccaf364c7fb6a294aa06728"
}
},
{
- "@id": "urn:b5e0225f-eff0-4e8c-beb9-09e171bbf0a1",
+ "@id": "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc::WARP_DATA",
"digest": {
@@ -366,16 +368,16 @@
}
},
{
- "@id": "urn:00e42115-626f-4d62-82d8-d85d631329e5",
+ "@id": "bids::warp.anat.Xat.1D",
"Label": "warp.anat.Xat.1D",
"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:52ac7507-1b78-451b-8d71-a8134799b096",
+ "GeneratedBy": "urn:tlrc-RV1CChcN",
"digest": {
"sha256": "800633fb5b4e9be64078bc181c4d5510ffb73fc5cccaf364c7fb6a294aa06728"
}
},
{
- "@id": "urn:17f65b7b-4973-4314-93d1-559ab4356cc9",
+ "@id": "bids::pb01.$subj.r$run.tshift+orig",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift+orig",
"digest": {
@@ -383,7 +385,7 @@
}
},
{
- "@id": "urn:fbeeaff6-baec-49f5-a079-172e049a9402",
+ "@id": "bids::sub-01_T1w_ns+tlrc",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc",
"digest": {
@@ -391,7 +393,7 @@
}
},
{
- "@id": "urn:2cb625e4-d86b-4d08-8244-67e8ecce7a1a",
+ "@id": "bids::rm.epi.all1+orig",
"Label": "rm.epi.all1",
"AtLocation": "rm.epi.all1+orig",
"digest": {
@@ -399,7 +401,7 @@
}
},
{
- "@id": "urn:106667e2-534d-4083-93fd-ff640a2eb33f",
+ "@id": "bids::rm.epi.1.r$run+tlrc",
"Label": "rm.epi.1.r$run",
"AtLocation": "rm.epi.1.r$run+tlrc",
"digest": {
@@ -407,7 +409,7 @@
}
},
{
- "@id": "urn:c570a9cb-ff5a-493a-8eb2-a0ef15df96d5",
+ "@id": "bids::dfile.r*.1D",
"Label": "dfile.r*.1D",
"AtLocation": "dfile.r*.1D",
"digest": {
@@ -415,7 +417,7 @@
}
},
{
- "@id": "urn:9b6dc0b4-91fd-4b34-9598-11ed55ece512",
+ "@id": "bids::rm.epi.min.r01+tlrc",
"Label": "rm.epi.min.r01",
"AtLocation": "rm.epi.min.r01+tlrc",
"digest": {
@@ -423,7 +425,7 @@
}
},
{
- "@id": "urn:e6d2ef28-055a-4391-baea-97dd8a9d185e",
+ "@id": "bids::rm.epi.nomask.r$run+tlrc",
"Label": "rm.epi.nomask.r$run",
"AtLocation": "rm.epi.nomask.r$run+tlrc",
"digest": {
@@ -431,7 +433,7 @@
}
},
{
- "@id": "urn:f6b197d3-067e-40ee-8d6a-f03cda41761e",
+ "@id": "bids::mask_epi_extents+tlrc",
"Label": "mask_epi_extents",
"AtLocation": "mask_epi_extents+tlrc",
"digest": {
@@ -439,97 +441,105 @@
}
},
{
- "@id": "urn:350a0778-9254-4176-9a33-a0818269567c",
+ "@id": "bids::anat_final.$subj+tlrc",
+ "Label": "anat_final.$subj",
+ "AtLocation": "anat_final.$subj+tlrc",
+ "digest": {
+ "sha256": "94eb1853614cc085b22772c011f119f6a0ad7ec06cba2850587762e7f1a6eae6"
+ }
+ },
+ {
+ "@id": "bids::mat.r$run.vr.aff12.1D",
"Label": "mat.r$run.vr.aff12.1D",
"AtLocation": "mat.r$run.vr.aff12.1D",
- "GeneratedBy": "urn:4ba9541e-ec77-485c-bc03-5344cbfa840c",
+ "GeneratedBy": "urn:volreg-qY8NgHG7",
"digest": {
"sha256": "2e6e6c2ce8089cfa3c6e11dc72fca0cc8497f7a55faae2ced402de4867466c91"
}
},
{
- "@id": "urn:6bd7080e-f014-4aed-a37b-116bf21a0b17",
+ "@id": "bids::rm.epi.all1",
"Label": "rm.epi.all1",
"AtLocation": "rm.epi.all1",
- "GeneratedBy": "urn:4ba9541e-ec77-485c-bc03-5344cbfa840c",
+ "GeneratedBy": "urn:volreg-qY8NgHG7",
"digest": {
"sha256": "1023e3c16cecdbdc73ea456bcf33c2e5bb4f1e07094b73d29022d651e5fa3f85"
}
},
{
- "@id": "urn:0e1ad22b-a9db-4107-bc9a-94a8f1d8d404",
+ "@id": "bids::rm.epi.nomask.r$run",
"Label": "rm.epi.nomask.r$run",
"AtLocation": "rm.epi.nomask.r$run",
- "GeneratedBy": "urn:4ba9541e-ec77-485c-bc03-5344cbfa840c",
+ "GeneratedBy": "urn:volreg-qY8NgHG7",
"digest": {
"sha256": "03d6cba0426c5545e350e6b63a19b0e46f8dfa2223fd08691753e8914a479e36"
}
},
{
- "@id": "urn:35d52516-0a10-4bef-a288-ddee2d54b063",
+ "@id": "bids::rm.epi.1.r$run",
"Label": "rm.epi.1.r$run",
"AtLocation": "rm.epi.1.r$run",
- "GeneratedBy": "urn:4ba9541e-ec77-485c-bc03-5344cbfa840c",
+ "GeneratedBy": "urn:volreg-qY8NgHG7",
"digest": {
"sha256": "b1b9128c103ea246625db1a35e6f474a221ca6c1105a30df38aefdc4d5421e84"
}
},
{
- "@id": "urn:ec4094f9-34b6-47e6-b779-1afe82137825",
+ "@id": "bids::rm.epi.min.r$run",
"Label": "rm.epi.min.r$run",
"AtLocation": "rm.epi.min.r$run",
- "GeneratedBy": "urn:4ba9541e-ec77-485c-bc03-5344cbfa840c",
+ "GeneratedBy": "urn:volreg-qY8NgHG7",
"digest": {
"sha256": "b4418a96ddbbf25afdfd01ed0506ddebe009011ba18aed10137f994260fd1a66"
}
},
{
- "@id": "urn:8fa0af1f-38fc-4157-81f5-a87d031deb90",
+ "@id": "bids::dfile_rall.1D",
"Label": "dfile_rall.1D",
"AtLocation": "dfile_rall.1D",
- "GeneratedBy": "urn:4ba9541e-ec77-485c-bc03-5344cbfa840c",
+ "GeneratedBy": "urn:volreg-qY8NgHG7",
"digest": {
"sha256": "011e7296870a1ac7e15377fb0d529ed68710bb16b138bef6aeb6c645f437dcf2"
}
},
{
- "@id": "urn:6a2cef36-9e48-44a3-ab46-7ceccdf60d22",
+ "@id": "bids::mask_epi_extents",
"Label": "mask_epi_extents",
"AtLocation": "mask_epi_extents",
- "GeneratedBy": "urn:4ba9541e-ec77-485c-bc03-5344cbfa840c",
+ "GeneratedBy": "urn:volreg-qY8NgHG7",
"digest": {
"sha256": "a69dd71209516ec24e2b3364072ed54adff16619459b1c369866210ec642e987"
}
},
{
- "@id": "urn:313bfacd-6dd9-4444-b67c-630818383b51",
+ "@id": "bids::pb02.$subj.r$run.volreg",
"Label": "pb02.$subj.r$run.volreg",
"AtLocation": "pb02.$subj.r$run.volreg",
- "GeneratedBy": "urn:4ba9541e-ec77-485c-bc03-5344cbfa840c",
+ "GeneratedBy": "urn:volreg-qY8NgHG7",
"digest": {
"sha256": "8821927190ac1b3f8f9d9a5ec74f6468ae6c1cb736e58e5de2cdbe3543d5cc0c"
}
},
{
- "@id": "urn:8b46cfac-0abd-4e71-8513-693452ceb539",
+ "@id": "bids::anat_final.$subj",
"Label": "anat_final.$subj",
"AtLocation": "anat_final.$subj",
- "GeneratedBy": "urn:4ba9541e-ec77-485c-bc03-5344cbfa840c",
+ "GeneratedBy": "urn:volreg-qY8NgHG7",
"digest": {
"sha256": "69b750d004bdba337de0b4ffa683bd92bc8f34b854d320327839ad264b28c4c5"
}
},
{
- "@id": "urn:45ed5b05-f663-4362-8890-1d1a3ff488fc",
+ "@id": "bids::anat_w_skull_warped",
"Label": "anat_w_skull_warped",
"AtLocation": "anat_w_skull_warped",
- "GeneratedBy": "urn:4ba9541e-ec77-485c-bc03-5344cbfa840c",
+ "GeneratedBy": "urn:volreg-qY8NgHG7",
"digest": {
"sha256": "462fdb8cd2b882e250fee3c6adb7acf0b0b9a9edb3e1cadf9d45d16180871105"
}
},
{
- "@id": "urn:7c75b9d4-e136-4ed6-b193-472e6a391505",
+ "@id": "bids::pb03.$subj.r$run.blur",
"Label": "pb03.$subj.r$run.blur",
"AtLocation": "pb03.$subj.r$run.blur",
"digest": {
@@ -537,7 +547,7 @@
}
},
{
- "@id": "urn:37420101-c925-4820-bf6d-1042ad709005",
+ "@id": "bids::pb02.$subj.r$run.volreg+tlrc",
"Label": "pb02.$subj.r$run.volreg",
"AtLocation": "pb02.$subj.r$run.volreg+tlrc",
"digest": {
@@ -545,7 +555,7 @@
}
},
{
- "@id": "urn:fbeeaff6-baec-49f5-a079-172e049a9402",
+ "@id": "bids::sub-01_T1w_ns+tlrc",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc",
"digest": {
@@ -553,7 +563,7 @@
}
},
{
- "@id": "urn:fc554388-45db-473b-bbeb-5bf07fa85ca2",
+ "@id": "bids::pb03.$subj.r$run.blur+tlrc",
"Label": "pb03.$subj.r$run.blur",
"AtLocation": "pb03.$subj.r$run.blur+tlrc",
"digest": {
@@ -561,7 +571,7 @@
}
},
{
- "@id": "urn:57ffb538-8bfb-451f-86b0-b0206ccfa026",
+ "@id": "bids::full_mask.$subj+tlrc",
"Label": "full_mask.$subj",
"AtLocation": "full_mask.$subj+tlrc",
"digest": {
@@ -569,7 +579,7 @@
}
},
{
- "@id": "urn:8c2d444b-075c-4191-bf34-335cfe698345",
+ "@id": "bids::rm.resam.anat+tlrc",
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"AtLocation": "rm.resam.anat+tlrc",
"digest": {
@@ -577,7 +587,7 @@
}
},
{
- "@id": "urn:55e6156b-c2e4-4d1d-a9a8-a7a9fcf74833",
+ "@id": "bids::mask_anat.$subj+tlrc",
"Label": "mask_anat.$subj",
"AtLocation": "mask_anat.$subj+tlrc",
"digest": {
@@ -585,7 +595,7 @@
}
},
{
- "@id": "urn:bc3512b9-619b-476c-bc4a-880a9ae12666",
+ "@id": "bids::tee",
"Label": "tee",
"AtLocation": "tee",
"digest": {
@@ -593,7 +603,7 @@
}
},
{
- "@id": "urn:e76b0898-df47-4906-9f8a-87374cd4bc62",
+ "@id": "bids::/Users/u1591557/abin/TT_N27+tlrc",
"Label": "TT_N27",
"AtLocation": "/Users/u1591557/abin/TT_N27+tlrc",
"digest": {
@@ -601,7 +611,7 @@
}
},
{
- "@id": "urn:72363f1e-f5ea-4349-8948-478f8f0659f9",
+ "@id": "bids::rm.resam.group+tlrc",
"Label": "rm.resam.group",
"AtLocation": "rm.resam.group+tlrc",
"digest": {
@@ -609,61 +619,61 @@
}
},
{
- "@id": "urn:14d3eb5f-0a80-4c8f-a914-3dab7a4616ac",
+ "@id": "bids::rm.mask_r$run",
"Label": "rm.mask_r$run",
"AtLocation": "rm.mask_r$run",
- "GeneratedBy": "urn:c6a0afd0-daa5-4243-aa57-e91e9b546865",
+ "GeneratedBy": "urn:mask-YfQVxxPi",
"digest": {
"sha256": "d251275ec819884fd84596da3fa356f3d83709d66170c45ad73c2f14ee830b35"
}
},
{
- "@id": "urn:961fa567-caf3-4ed8-ae75-dda92e3ba9d3",
+ "@id": "bids::full_mask.$subj",
"Label": "full_mask.$subj",
"AtLocation": "full_mask.$subj",
- "GeneratedBy": "urn:c6a0afd0-daa5-4243-aa57-e91e9b546865",
+ "GeneratedBy": "urn:mask-YfQVxxPi",
"digest": {
"sha256": "02da8c6ed741c00cb6ccb8da25bf6ca853afb9100b992c854209afde9e30918f"
}
},
{
- "@id": "urn:09ffacab-5b4d-4357-8cdb-8251000e16ad",
+ "@id": "bids::rm.resam.anat",
"Label": "rm.resam.anat",
"AtLocation": "rm.resam.anat",
- "GeneratedBy": "urn:c6a0afd0-daa5-4243-aa57-e91e9b546865",
+ "GeneratedBy": "urn:mask-YfQVxxPi",
"digest": {
"sha256": "fe716d2bdbce773476ef264f2cd990f7114d7f2d7245c0cbeb10e8abc7feff9b"
}
},
{
- "@id": "urn:54492869-0fc2-40ba-aa88-313a046b2166",
+ "@id": "bids::mask_anat.$subj",
"Label": "mask_anat.$subj",
"AtLocation": "mask_anat.$subj",
- "GeneratedBy": "urn:c6a0afd0-daa5-4243-aa57-e91e9b546865",
+ "GeneratedBy": "urn:mask-YfQVxxPi",
"digest": {
"sha256": "d3f1becfb7c7d234361e002cc34c3ca5b5333640259f572993b773f6973f0e98"
}
},
{
- "@id": "urn:80d150d5-a203-4fe1-8f28-78b7983e99d0",
+ "@id": "bids::rm.resam.group",
"Label": "rm.resam.group",
"AtLocation": "./rm.resam.group",
- "GeneratedBy": "urn:c6a0afd0-daa5-4243-aa57-e91e9b546865",
+ "GeneratedBy": "urn:mask-YfQVxxPi",
"digest": {
"sha256": "79e954aee237a244a2498f6f7811a10a1c4508563eebd38000c13f2c145942c9"
}
},
{
- "@id": "urn:bddb6f19-ed2e-4865-8afa-11983eb5244a",
+ "@id": "bids::mask_group",
"Label": "mask_group",
"AtLocation": "mask_group",
- "GeneratedBy": "urn:c6a0afd0-daa5-4243-aa57-e91e9b546865",
+ "GeneratedBy": "urn:mask-YfQVxxPi",
"digest": {
"sha256": "d7093b26470ded8d7e939359017b18d28a2da4c6bb702c1183df20bca614f949"
}
},
{
- "@id": "urn:f6b197d3-067e-40ee-8d6a-f03cda41761e",
+ "@id": "bids::mask_epi_extents+tlrc",
"Label": "mask_epi_extents",
"AtLocation": "mask_epi_extents+tlrc",
"digest": {
@@ -671,7 +681,7 @@
}
},
{
- "@id": "urn:fc554388-45db-473b-bbeb-5bf07fa85ca2",
+ "@id": "bids::pb03.$subj.r$run.blur+tlrc",
"Label": "pb03.$subj.r$run.blur",
"AtLocation": "pb03.$subj.r$run.blur+tlrc",
"digest": {
@@ -679,7 +689,7 @@
}
},
{
- "@id": "urn:d50db812-375c-4601-92d1-9324de903322",
+ "@id": "bids::rm.mean_r$run+tlrc",
"Label": "rm.mean_r$run",
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"digest": {
@@ -687,34 +697,34 @@
}
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{
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"AtLocation": "rm.mean_r$run",
- "GeneratedBy": "urn:7403f17c-c790-471e-8b6d-55d5650cb385",
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- "GeneratedBy": "urn:7403f17c-c790-471e-8b6d-55d5650cb385",
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@@ -722,7 +732,7 @@
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"digest": {
@@ -730,7 +740,7 @@
}
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{
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@@ -738,7 +748,7 @@
}
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{
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@@ -746,7 +756,7 @@
}
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{
- "@id": "urn:9bf6596d-5bb9-4781-8357-feaaccd82518",
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@@ -754,7 +764,7 @@
}
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{
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@@ -762,7 +772,7 @@
}
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@@ -770,7 +780,7 @@
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@@ -778,7 +788,7 @@
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@@ -786,7 +796,7 @@
}
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{
- "@id": "urn:2b061de6-9339-4873-b556-40feb2d7bb4f",
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@@ -794,7 +804,7 @@
}
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{
- "@id": "urn:cefdfa11-917c-4d55-870b-b181f657575f",
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@@ -802,7 +812,7 @@
}
},
{
- "@id": "urn:998920fc-bc8a-4ead-aac5-a44e39b2a4c0",
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"digest": {
@@ -810,7 +820,7 @@
}
},
{
- "@id": "urn:439259c5-7d95-4c8d-83ab-ab595ec441a1",
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@@ -818,133 +828,133 @@
}
},
{
- "@id": "urn:f53f6f1c-8fa1-475d-9785-20fc21be0b8c",
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"Label": "motion_demean.1D",
"AtLocation": "motion_demean.1D",
- "GeneratedBy": "urn:e276d06e-84be-4349-8afb-33c503367cc2",
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{
- "@id": "urn:f6107a2d-78b5-439e-b2ef-d8f01818384d",
+ "@id": "bids::motion_deriv.1D",
"Label": "motion_deriv.1D",
"AtLocation": "motion_deriv.1D",
- "GeneratedBy": "urn:e276d06e-84be-4349-8afb-33c503367cc2",
+ "GeneratedBy": "urn:regress-JwuObKc8",
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"sha256": "47185bf319e91642ad6f2a396a43fc9f8db7b82f2a9aef326bfe4a955120038b"
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{
- "@id": "urn:500d3a9d-69cc-460b-a355-9dab472abdae",
+ "@id": "bids::all_runs.$subj",
"Label": "all_runs.$subj",
"AtLocation": "all_runs.$subj",
- "GeneratedBy": "urn:e276d06e-84be-4349-8afb-33c503367cc2",
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{
- "@id": "urn:fa0a32dc-6a13-4287-bbb8-fe661c397d52",
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"Label": "rm.signal.all",
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{
- "@id": "urn:a8f31dff-dfb2-4aaa-b8ed-c8d3cdf1b2b5",
+ "@id": "bids::rm.noise.all",
"Label": "rm.noise.all",
"AtLocation": "rm.noise.all",
- "GeneratedBy": "urn:e276d06e-84be-4349-8afb-33c503367cc2",
+ "GeneratedBy": "urn:regress-JwuObKc8",
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},
{
- "@id": "urn:d3c5145f-774b-428e-834c-b7c6f59a6035",
+ "@id": "bids::TSNR.$subj",
"Label": "TSNR.$subj",
"AtLocation": "TSNR.$subj",
- "GeneratedBy": "urn:e276d06e-84be-4349-8afb-33c503367cc2",
+ "GeneratedBy": "urn:regress-JwuObKc8",
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},
{
- "@id": "urn:ff71fdd3-6130-454c-bb60-6e05689951d0",
+ "@id": "bids::rm.errts.unit",
"Label": "rm.errts.unit",
"AtLocation": "rm.errts.unit",
- "GeneratedBy": "urn:e276d06e-84be-4349-8afb-33c503367cc2",
+ "GeneratedBy": "urn:regress-JwuObKc8",
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},
{
- "@id": "urn:c45aa579-f1e2-43b7-88c6-ac3538101b48",
+ "@id": "urn:uuid:bcdad7b0-1900-445e-a58d-7cdbd0dd9cfc",
"Label": "-",
"AtLocation": "-",
- "GeneratedBy": "urn:e276d06e-84be-4349-8afb-33c503367cc2",
+ "GeneratedBy": "urn:regress-JwuObKc8",
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}
},
{
- "@id": "urn:d109f03f-2452-4835-ba8c-da09ec89b328",
+ "@id": "bids::rm.DP",
"Label": "rm.DP",
"AtLocation": "rm.DP",
- "GeneratedBy": "urn:e276d06e-84be-4349-8afb-33c503367cc2",
+ "GeneratedBy": "urn:regress-JwuObKc8",
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{
- "@id": "urn:09d9c8f9-372f-4df5-9eec-3925b086aff3",
+ "@id": "bids::corr_brain",
"Label": "corr_brain",
"AtLocation": "corr_brain",
- "GeneratedBy": "urn:e276d06e-84be-4349-8afb-33c503367cc2",
+ "GeneratedBy": "urn:regress-JwuObKc8",
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{
- "@id": "urn:931c0fca-72bc-4596-a994-9a18b2f928b5",
+ "@id": "bids::ideal_tone_counting.1D",
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"AtLocation": "ideal_tone_counting.1D",
- "GeneratedBy": "urn:e276d06e-84be-4349-8afb-33c503367cc2",
+ "GeneratedBy": "urn:regress-JwuObKc8",
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},
{
- "@id": "urn:c13342ec-7aed-4f95-904a-ce7f33f1f427",
+ "@id": "bids::ideal_probe.1D",
"Label": "ideal_probe.1D",
"AtLocation": "ideal_probe.1D",
- "GeneratedBy": "urn:e276d06e-84be-4349-8afb-33c503367cc2",
+ "GeneratedBy": "urn:regress-JwuObKc8",
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},
{
- "@id": "urn:390eec17-c797-4abc-82ba-6403ead30662",
+ "@id": "bids::sum_ideal.1D",
"Label": "sum_ideal.1D",
"AtLocation": "sum_ideal.1D",
- "GeneratedBy": "urn:e276d06e-84be-4349-8afb-33c503367cc2",
+ "GeneratedBy": "urn:regress-JwuObKc8",
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{
- "@id": "urn:8100e5db-f870-49c9-a8db-fdbc87ef7e8e",
+ "@id": "bids::X.stim.xmat.1D",
"Label": "X.stim.xmat.1D",
"AtLocation": "X.stim.xmat.1D",
- "GeneratedBy": "urn:e276d06e-84be-4349-8afb-33c503367cc2",
+ "GeneratedBy": "urn:regress-JwuObKc8",
"digest": {
"sha256": "7c61b2f4bbb9eb0cecb19f81faa3a79b94d547b7fb4087ed18e368619e0004e6"
}
},
{
- "@id": "urn:57ffb538-8bfb-451f-86b0-b0206ccfa026",
+ "@id": "bids::full_mask.$subj+tlrc",
"Label": "full_mask.$subj",
"AtLocation": "full_mask.$subj+tlrc",
"digest": {
@@ -952,34 +962,34 @@
}
},
{
- "@id": "urn:b4155dba-057b-4b8a-9925-1c3911333ee4",
+ "@id": "bids::blur.epits.1D",
"Label": "blur.epits.1D",
"AtLocation": "blur.epits.1D",
- "GeneratedBy": "urn:a8be1d24-6de4-45b2-92ad-dc44be445319",
+ "GeneratedBy": "urn:bluresti-QW19fifr",
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"sha256": "623e70a42214e56babc1f1dca156e0b11ba09865dbd6ca9549d54ca2fc601515"
}
},
{
- "@id": "urn:a5922a6e-ff4b-4d99-bd5b-9fd777cf45c8",
+ "@id": "bids::blur.errts.1D",
"Label": "blur.errts.1D",
"AtLocation": "blur.errts.1D",
- "GeneratedBy": "urn:a8be1d24-6de4-45b2-92ad-dc44be445319",
+ "GeneratedBy": "urn:bluresti-QW19fifr",
"digest": {
"sha256": "73969700079b5d3275536ac7eaf0e17571d7e74ec49553b6940f90d5718fc800"
}
},
{
- "@id": "urn:efb6bea3-87da-4cb4-a5d6-bafb6ac600a2",
+ "@id": "bids::ClustSim",
"Label": "ClustSim",
"AtLocation": "ClustSim",
- "GeneratedBy": "urn:a8be1d24-6de4-45b2-92ad-dc44be445319",
+ "GeneratedBy": "urn:bluresti-QW19fifr",
"digest": {
"sha256": "2e0cdba2c91902ba12d742a39cb20df66cfd705ba8de767fbf68aae8eb65c6f0"
}
},
{
- "@id": "urn:97a56b57-4ac3-43c8-a6e1-bf20b58206dd",
+ "@id": "bids::pb00.$subj.r*.tcat+orig.HEAD",
"Label": "pb00.$subj.r*.tcat",
"AtLocation": "pb00.$subj.r*.tcat+orig.HEAD",
"digest": {
@@ -987,10 +997,10 @@
}
},
{
- "@id": "urn:01813183-0b7e-4d7a-9d01-a64ac607b9d1",
+ "@id": "bids::-exit0",
"Label": "-exit0",
"AtLocation": "-exit0",
- "GeneratedBy": "urn:8c4107d0-f88c-4a4c-9357-6e1e19ad1201",
+ "GeneratedBy": "urn:autobloc-44jc0p9G",
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diff --git a/examples/from_parsers/afni/afni_alt_onesided_proc_block.png b/examples/from_parsers/afni/afni_alt_onesided_proc_block.png
index 606ba50a0..f7742fd75 100644
Binary files a/examples/from_parsers/afni/afni_alt_onesided_proc_block.png and b/examples/from_parsers/afni/afni_alt_onesided_proc_block.png differ
diff --git a/examples/from_parsers/afni/afni_bi_sided_t_test_proc.jsonld b/examples/from_parsers/afni/afni_bi_sided_t_test_proc.jsonld
index 4bada318e..cc5b78098 100644
--- a/examples/from_parsers/afni/afni_bi_sided_t_test_proc.jsonld
+++ b/examples/from_parsers/afni/afni_bi_sided_t_test_proc.jsonld
@@ -4,578 +4,581 @@
"Records": {
"Software": [
{
- "@id": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:afni-txVAU8vU",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
- "Version": "afni24"
+ "Version": "afni24",
+ "AltIdentifier": "RRID:SCR_005927"
}
],
"Activities": [
{
- "@id": "urn:c9fd7c76-2ae4-45b3-878b-40d9bad11085",
+ "@id": "urn:makedire-0Fti9SVV",
"Label": "Make directory",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "mkdir $output_dir",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:1bdaaef0-7042-4734-8cfd-098e9962a533",
+ "@id": "urn:makedire-bcLbDmzU",
"Label": "Make directory",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "mkdir $output_dir/stimuli",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:95c94be2-273b-4c7d-8a39-1ce112181183",
+ "@id": "urn:cp-b7zqj7dm",
"Label": "cp",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "cp ./afni_bi_sided_t_test/tone_counting_onset_times.txt ./afni_bi_sided_t_test/tone_counting_probe_duration.txt $output_dir/stimuli",
"Parameters": {},
"Used": [
- "urn:69fcfb15-c77c-40c4-a487-3ad726504cfb",
- "urn:d448379e-f728-47d2-9567-f7ba106cd541"
+ "bids::afni_bi_sided_t_test/tone_counting_onset_times.txt",
+ "bids::afni_bi_sided_t_test/tone_counting_probe_duration.txt"
]
},
{
- "@id": "urn:ab4d3e7f-fd6c-4189-a5dd-b726f1e3eaab",
+ "@id": "urn:3dcopy-2WaosrZR",
"Label": "3dcopy",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w",
"Parameters": {},
"Used": [
- "urn:3d997e80-8feb-4949-9ca6-5f2e3bd68fc6"
+ "bids::sub-01_T1w.nii.gz"
]
},
{
- "@id": "urn:3e718433-e2b5-434d-a596-249413698da1",
+ "@id": "urn:3dtcat-vsgPEg41",
"Label": "3dTcat",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Parameters": {},
"Used": [
- "urn:916a0919-3412-4ed1-b4b5-ea6838d333b7"
+ "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'"
]
},
{
- "@id": "urn:918fcb03-359d-488c-bb96-5b75f21afc6b",
+ "@id": "urn:3dtoutco-ua12ThWL",
"Label": "3dToutcount",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D",
"Parameters": {},
"Used": [
- "urn:f8a81771-0ea9-47d0-8c3e-b3482efcb7a4"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:e36979a0-f0bf-44cd-aadc-8b80d1ca6d10",
+ "@id": "urn:cat-eN68PKM4",
"Label": "cat",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "cat outcount.r*.1D > outcount_rall.1D",
"Parameters": {},
"Used": [
- "urn:1e927d75-77b7-4b4e-baef-e3ee46d7b843"
+ "bids::outcount.r*.1D"
]
},
{
- "@id": "urn:5bbeda84-ea59-4602-8539-b4825125464d",
+ "@id": "urn:3dtshift-Uz9V0GCp",
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- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig",
"Parameters": {},
"Used": [
- "urn:f8a81771-0ea9-47d0-8c3e-b3482efcb7a4"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:fe69b019-583c-4c4e-a2c3-63b4d352a94c",
+ "@id": "urn:alignepi-TOfxbivF",
"Label": "align_epi_anat.py",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off",
"Parameters": {},
"Used": [
- "urn:06372779-6792-4e37-84d1-cd68357b7aed",
- "urn:6b2dccb0-069c-4d61-91cb-9885fcb4a556"
+ "bids::pb01.$subj.r01.tshift+orig",
+ "bids::sub-01_T1w+orig"
]
},
{
- "@id": "urn:34938128-0ef3-4618-8817-c35f21e124a4",
+ "@id": "urn:autotlrc-fCMHL5Be",
"Label": "@auto_tlrc",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss",
"Parameters": {},
"Used": [
- "urn:19459e8e-1991-490b-b90f-a18c3dc7528b",
- "urn:39ea58bb-83ea-4c9e-8050-7adcf255c33d"
+ "bids::TT_N27+tlrc",
+ "bids::sub-01_T1w_ns+orig"
]
},
{
- "@id": "urn:1dcfe420-527d-4cc2-8411-9c1433b5fdff",
+ "@id": "urn:catmatve-EA5f1njv",
"Label": "cat_matvec",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D",
"Parameters": {},
"Used": [
- "urn:3b785f19-73bf-4c34-a038-7a9b4396a169"
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:9514e444-af9c-4649-b1e3-f2b7371e2ff3",
+ "@id": "urn:3dvolreg-AMq9LYqj",
"Label": "3dvolreg",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig",
"Parameters": {},
"Used": [
- "urn:70787460-c0e9-4624-a974-df03ea059fd7"
+ "bids::pb01.$subj.r$run.tshift+orig"
]
},
{
- "@id": "urn:bbdd547f-1200-4863-9dda-efa4d1e55184",
+ "@id": "urn:3dcalc-tCPpupxx",
"Label": "3dcalc",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1",
"Parameters": {},
"Used": [
- "urn:70787460-c0e9-4624-a974-df03ea059fd7"
+ "bids::pb01.$subj.r$run.tshift+orig"
]
},
{
- "@id": "urn:0c6b3aeb-06f8-4e6b-b3ed-88acdbf9e0e6",
+ "@id": "urn:catmatve-ASEHsX2B",
"Label": "cat_matvec",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D",
"Parameters": {},
"Used": [
- "urn:3b785f19-73bf-4c34-a038-7a9b4396a169"
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:cfc270b2-011d-4313-9bf2-42cf99099862",
+ "@id": "urn:3dalline-c8Wq1xUb",
"Label": "3dAllineate",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run",
"Parameters": {},
"Used": [
- "urn:63697e02-287b-45a2-bb20-41e265601261",
- "urn:70787460-c0e9-4624-a974-df03ea059fd7",
- "urn:eb67c517-fe9a-4f7c-b7b0-36247be03247"
+ "bids::mat.r$run.warp.aff12.1D",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:eba38419-a546-4321-8e0a-8f3a41271a29",
+ "@id": "urn:3dalline-vga6PrVm",
"Label": "3dAllineate",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run",
"Parameters": {},
"Used": [
- "urn:63697e02-287b-45a2-bb20-41e265601261",
- "urn:bcdad7b0-1900-445e-a58d-7cdbd0dd9cfc",
- "urn:eb67c517-fe9a-4f7c-b7b0-36247be03247"
+ "bids::mat.r$run.warp.aff12.1D",
+ "bids::rm.epi.all1+orig",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:e8191e7e-8505-4e9d-afc8-41e2324eb4dc",
+ "@id": "urn:3dtstat-u3xfjqu5",
"Label": "3dTstat",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc",
"Parameters": {},
"Used": [
- "urn:53f02519-829b-4f61-9838-40048b816257"
+ "bids::rm.epi.1.r$run+tlrc"
]
},
{
- "@id": "urn:8dc8374c-cbe1-47f8-9d6a-39ae8a5ebb34",
+ "@id": "urn:cat-BB7nFSIT",
"Label": "cat",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "cat dfile.r*.1D > dfile_rall.1D",
"Parameters": {},
"Used": [
- "urn:df826b1c-74a5-4f67-be42-d15657ccada8"
+ "bids::dfile.r*.1D"
]
},
{
- "@id": "urn:c6aa20f8-dfc4-434c-b06e-e6740edb0f2e",
+ "@id": "urn:3dcopy-ItJcDYQh",
"Label": "3dcopy",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents",
"Parameters": {},
"Used": [
- "urn:5ec304ae-9211-417c-9b97-ef828474c68b"
+ "bids::rm.epi.min.r01+tlrc"
]
},
{
- "@id": "urn:cdeffd5b-2823-49f0-9667-028119716d19",
+ "@id": "urn:3dcalc-QNV69JtD",
"Label": "3dcalc",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg",
"Parameters": {},
"Used": [
- "urn:15230b74-4ca6-46fd-b1af-f3fc88d9eaae",
- "urn:d2bdd17d-7e8f-4856-b026-90a880f4ba20"
+ "bids::mask_epi_extents+tlrc",
+ "bids::rm.epi.nomask.r$run+tlrc"
]
},
{
- "@id": "urn:a878b257-a9ba-4bcb-bec8-cff004db2580",
+ "@id": "urn:3dcopy-TwtrebDo",
"Label": "3dcopy",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj",
"Parameters": {},
"Used": [
- "urn:63697e02-287b-45a2-bb20-41e265601261"
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:0d96712d-754c-4811-b72f-475acab451eb",
+ "@id": "urn:3dalline-nXJQxFlv",
"Label": "3dAllineate",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped",
"Parameters": {},
"Used": [
- "urn:bdf545f3-a058-4328-9ee9-0e77526c0c60"
+ "bids::anat_final.$subj+tlrc",
+ "bids::warp.anat.Xat.1D"
]
},
{
- "@id": "urn:2b5a4047-ae13-4ad8-a91e-4bbedd00ee70",
+ "@id": "urn:3dmerge-uXqNQnGf",
"Label": "3dmerge",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc",
"Parameters": {},
"Used": [
- "urn:ad783a8d-3eff-4062-aaaa-b0da2153285b",
- "urn:c0c5482a-7a18-4535-99df-1f2f4b42155f"
+ "bids::pb02.$subj.r$run.volreg+tlrc",
+ "bids::pb03.$subj.r$run.blur"
]
},
{
- "@id": "urn:ba73f7d7-f70a-4503-aafa-a70b10d74b93",
+ "@id": "urn:3dautoma-qCCyx8G0",
"Label": "3dAutomask",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:ecb6bbdc-7c07-4bf7-aab1-114ab87660c3"
+ "bids::pb03.$subj.r$run.blur+tlrc"
]
},
{
- "@id": "urn:300db58b-407a-44d5-a5bc-4ae178718157",
+ "@id": "urn:3dmaskto-jiLWLBrG",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:5b0ca4be-398b-4a17-bcfd-4979613d6409",
+ "@id": "urn:3dresamp-FwzGbJVc",
"Label": "3dresample",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat",
"Parameters": {},
"Used": [
- "urn:1e21013c-20db-4252-9699-71e73b1cfd0e",
- "urn:63697e02-287b-45a2-bb20-41e265601261"
+ "bids::full_mask.$subj+tlrc",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:c5da5238-d255-4788-8c65-a97fbad74c2e",
+ "@id": "urn:3dmaskto-RVcsMKcS",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj",
"Parameters": {},
"Used": [
- "urn:c0b2dc25-6399-41b4-8c90-2115b9a9c877"
+ "bids::rm.resam.anat+tlrc"
]
},
{
- "@id": "urn:298d54e4-1c6b-48c3-94f7-7d82fa1b91b7",
+ "@id": "urn:3dabover-OJyxHobE",
"Label": "3dABoverlap",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt",
"Parameters": {},
"Used": [
- "urn:110ea3e4-213d-4c0f-b3d4-095ffe94e454",
- "urn:9cc3040c-923c-4223-bcdc-65e44e3724df"
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee"
]
},
{
- "@id": "urn:afb793a2-e11b-40df-bbab-7c55f13dce6f",
+ "@id": "urn:3ddot-E9GgrurE",
"Label": "3ddot",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt",
"Parameters": {},
"Used": [
- "urn:110ea3e4-213d-4c0f-b3d4-095ffe94e454",
- "urn:9cc3040c-923c-4223-bcdc-65e44e3724df"
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee"
]
},
{
- "@id": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "@id": "urn:3dresamp-XGsxOkPW",
"Label": "3dresample",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc",
"Parameters": {},
"Used": [
- "urn:1e21013c-20db-4252-9699-71e73b1cfd0e",
- "urn:c63f6bf6-7480-414e-a8fb-7a1c37996839"
+ "bids::/Users/u1591557/abin/TT_N27+tlrc",
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:9c4e2e74-846d-4682-a86d-4fa43b9361c7",
+ "@id": "urn:3dmaskto-LUJAYzmp",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group",
"Parameters": {},
"Used": [
- "urn:b052d775-addc-449b-a406-368acd0aaa97"
+ "bids::rm.resam.group+tlrc"
]
},
{
- "@id": "urn:fd503d11-d2f7-4355-8724-cf332ba8f69b",
+ "@id": "urn:3dtstat-cKPGlKpB",
"Label": "3dTstat",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:ecb6bbdc-7c07-4bf7-aab1-114ab87660c3"
+ "bids::pb03.$subj.r$run.blur+tlrc"
]
},
{
- "@id": "urn:92e806a1-588a-400a-8267-1d331938bd79",
+ "@id": "urn:3dcalc-tPKcNwoc",
"Label": "3dcalc",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale",
"Parameters": {},
"Used": [
- "urn:746a6f07-d57a-4b68-884b-13ab76184159",
- "urn:d2bdd17d-7e8f-4856-b026-90a880f4ba20",
- "urn:ecb6bbdc-7c07-4bf7-aab1-114ab87660c3"
+ "bids::mask_epi_extents+tlrc",
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::rm.mean_r$run+tlrc"
]
},
{
- "@id": "urn:24c48049-423b-4f4a-a68b-63c3d0593e99",
+ "@id": "urn:1dtoolpy-hvoaibny",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D",
"Parameters": {},
"Used": [
- "urn:938163b7-bf0d-40c8-8a24-9c77029d9a41"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:78b84e7b-706b-4025-b3d4-5ef478ebf581",
+ "@id": "urn:1dtoolpy-v7BEH6Xe",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D",
"Parameters": {},
"Used": [
- "urn:938163b7-bf0d-40c8-8a24-9c77029d9a41"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:eabf2d58-12bc-4264-9a14-841b35d36c2e",
+ "@id": "urn:1dtoolpy-bcpmMe0c",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}",
"Parameters": {},
"Used": [
- "urn:938163b7-bf0d-40c8-8a24-9c77029d9a41"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:dd7c30e9-086f-4453-b4e0-cfd2dd378337",
+ "@id": "urn:3ddeconv-cRZYLlEP",
"Label": "3dDeconvolve",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj",
"Parameters": {},
"Used": [
- "urn:51fd66c2-887c-4586-9153-c4330b011c21"
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD"
]
},
{
- "@id": "urn:86fd4be2-654d-4f6d-8dcf-1c8eaf851151",
+ "@id": "urn:1dtoolpy-AyaX1uPn",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt",
"Parameters": {},
"Used": [
- "urn:c92f09a2-3673-461a-b213-7e6e77ae9127"
+ "bids::X.xmat.1D"
]
},
{
- "@id": "urn:f8cbfb50-209b-45f0-af1c-cb1e8654524f",
+ "@id": "urn:3dtcat-RWGfnPWP",
"Label": "3dTcat",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD",
"Parameters": {},
"Used": [
- "urn:51fd66c2-887c-4586-9153-c4330b011c21"
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD"
]
},
{
- "@id": "urn:cda9ebcc-abd5-4d2a-b0dc-3b2680aa1967",
+ "@id": "urn:3dtstat-q51vxYT3",
"Label": "3dTstat",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:40b50dc9-2f0a-4a54-8f74-308039d60ecd"
+ "bids::all_runs.$subj+tlrc%22[$ktrs]%22"
]
},
{
- "@id": "urn:af761f7e-80af-4622-bb60-411065c9e5d1",
+ "@id": "urn:3dtstat-8sPDnE0L",
"Label": "3dTstat",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:4ce7cdba-5a0b-4246-8ee3-840b44f92bf6"
+ "bids::errts.$%7Bsubj%7D+tlrc%22[$ktrs]%22"
]
},
{
- "@id": "urn:e6aad8a6-9056-4e8e-b591-ba2a4094b8a0",
+ "@id": "urn:3dcalc-RGwLKWHE",
"Label": "3dcalc",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj",
"Parameters": {},
"Used": [
- "urn:1e21013c-20db-4252-9699-71e73b1cfd0e",
- "urn:80fcdacd-a0b4-41a5-a625-30221b6d3350",
- "urn:92d99567-2e04-4755-84bf-14cd9ef1de78"
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.noise.all+tlrc",
+ "bids::rm.signal.all+tlrc"
]
},
{
- "@id": "urn:c073483a-c70c-494e-bc37-5a2327064f06",
+ "@id": "urn:3dtnorm-4ZPKtBfb",
"Label": "3dTnorm",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc",
"Parameters": {},
"Used": [
- "urn:9b4436bc-3b0f-4b8f-ba17-18aac004a520"
+ "bids::errts.$%7Bsubj%7D+tlrc"
]
},
{
- "@id": "urn:e6b65e1a-fafb-4bb5-965e-f7a176a560ff",
+ "@id": "urn:3dmaskav-hV4DuJDG",
"Label": "3dmaskave",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D",
"Parameters": {},
- "Used": []
+ "Used": [
+ "bids::full_mask.$subj+tlrc"
+ ]
},
{
- "@id": "urn:80f381a3-fcaa-49fb-885e-4debddb8a786",
+ "@id": "urn:3dtstat-QdOKIy3R",
"Label": "3dTstat",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D",
"Parameters": {},
"Used": [
- "urn:2a93e9d8-8d47-40af-8bcf-eaf983b9add1"
+ "bids::out.gcor.1D"
]
},
{
- "@id": "urn:c879c188-eaba-4d99-a76b-7031e921db86",
+ "@id": "urn:3dcalc-04jOYgES",
"Label": "3dcalc",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP",
"Parameters": {},
"Used": [
- "urn:1da351b2-5bea-4433-a57f-1ed0437d697f",
- "urn:f8678749-7602-488a-9d3a-8f2490d6f419"
+ "bids::gmean.errts.unit.1D",
+ "bids::rm.errts.unit+tlrc"
]
},
{
- "@id": "urn:075b19d7-cccb-49e7-a9c8-4a0abc906eab",
+ "@id": "urn:3dtstat-GsOJRmrW",
"Label": "3dTstat",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc",
"Parameters": {},
"Used": [
- "urn:25fc6c6e-026b-4ab5-b54f-ab765a104838"
+ "bids::rm.DP+tlrc"
]
},
{
- "@id": "urn:d48a8eec-56b1-4aa8-af22-922fc27586e6",
+ "@id": "urn:1dcat-XCdniniz",
"Label": "1dcat",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D",
"Parameters": {},
"Used": [
- "urn:604a1e3b-15de-497b-a525-ca9bd99f2a09"
+ "bids::X.nocensor.xmat.1D'[3]'"
]
},
{
- "@id": "urn:c504956f-4b7b-4992-abbd-46b5fc4f8a21",
+ "@id": "urn:1dcat-1e0KL3UX",
"Label": "1dcat",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D",
"Parameters": {},
"Used": [
- "urn:4b941985-5a56-41fe-bdf5-274158f7437c"
+ "bids::X.nocensor.xmat.1D'[4]'"
]
},
{
- "@id": "urn:d749afb2-7262-4434-9504-06cb313cac64",
+ "@id": "urn:3dtstat-HjsESDaO",
"Label": "3dTstat",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"",
"Parameters": {},
"Used": [
- "urn:a92420ab-a033-4844-a6f7-39500db2e482"
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:a04f7934-f7bc-4170-b2eb-5c6c732b5848",
+ "@id": "urn:1dcat-kqae8pGw",
"Label": "1dcat",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D",
"Parameters": {},
"Used": [
- "urn:a92420ab-a033-4844-a6f7-39500db2e482"
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:314e11c6-9e73-48fd-80b8-5255796a06d1",
+ "@id": "urn:3dfwhmx-c2Id8xz4",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D",
"Parameters": {},
"Used": [
- "urn:1e21013c-20db-4252-9699-71e73b1cfd0e"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:a6811528-b35b-46f8-8c64-c27db6cc51f3",
+ "@id": "urn:3dfwhmx-1pDteEI5",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D",
"Parameters": {},
"Used": [
- "urn:1e21013c-20db-4252-9699-71e73b1cfd0e"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:b1798fa5-41c3-4c32-af33-ba038526e4b9",
+ "@id": "urn:3dclusts-ANy7O8lb",
"Label": "3dClustSim",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim",
"Parameters": {},
"Used": [
- "urn:1e21013c-20db-4252-9699-71e73b1cfd0e"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:f1ad28d0-6c5d-4619-ac2a-c7f4bee41ea6",
+ "@id": "urn:genepire-eciHyYWL",
"Label": "gen_epi_review.py",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD",
"Parameters": {},
"Used": [
- "urn:fb2855e1-e166-43d1-82c1-370fde58b2ce"
+ "bids::pb00.$subj.r*.tcat+orig.HEAD"
]
},
{
- "@id": "urn:cc3659dd-8933-41f9-b132-b2a64e91ffaf",
+ "@id": "urn:genssrev-Mk4Ku1i2",
"Label": "gen_ss_review_scripts.py",
- "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "AssociatedWith": "urn:afni-txVAU8vU",
"Command": "gen_ss_review_scripts.py -mot_limit 0.3 -exit0",
"Parameters": {
"-mot_limit": "0.3",
@@ -586,22 +589,22 @@
],
"Entities": [
{
- "@id": "urn:b83677f5-b62b-4acd-96b5-716f9da67ac6",
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"Label": "$output_dir",
"AtLocation": "$output_dir",
- "GeneratedBy": "urn:c9fd7c76-2ae4-45b3-878b-40d9bad11085",
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},
{
- "@id": "urn:d09ce11e-697a-4e13-bee2-7628d33893fd",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:1bdaaef0-7042-4734-8cfd-098e9962a533"
+ "GeneratedBy": "urn:makedire-bcLbDmzU"
},
{
- "@id": "urn:69fcfb15-c77c-40c4-a487-3ad726504cfb",
+ "@id": "bids::afni_bi_sided_t_test/tone_counting_onset_times.txt",
"Label": "tone_counting_onset_times.txt",
"AtLocation": "./afni_bi_sided_t_test/tone_counting_onset_times.txt",
"digest": {
@@ -609,7 +612,7 @@
}
},
{
- "@id": "urn:d448379e-f728-47d2-9567-f7ba106cd541",
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"Label": "tone_counting_probe_duration.txt",
"AtLocation": "./afni_bi_sided_t_test/tone_counting_probe_duration.txt",
"digest": {
@@ -617,13 +620,13 @@
}
},
{
- "@id": "urn:0bc910a4-11f0-409b-a806-fc0893a40976",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:95c94be2-273b-4c7d-8a39-1ce112181183"
+ "GeneratedBy": "urn:cp-b7zqj7dm"
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{
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+ "@id": "bids::sub-01_T1w.nii.gz",
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"AtLocation": "sub-01_T1w.nii.gz",
"digest": {
@@ -631,13 +634,13 @@
}
},
{
- "@id": "urn:a1759d55-2299-4ec2-aeb4-4d553b6e6626",
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"Label": "sub-01_T1w",
"AtLocation": "$output_dir/sub-01_T1w",
- "GeneratedBy": "urn:ab4d3e7f-fd6c-4189-a5dd-b726f1e3eaab"
+ "GeneratedBy": "urn:3dcopy-2WaosrZR"
},
{
- "@id": "urn:916a0919-3412-4ed1-b4b5-ea6838d333b7",
+ "@id": "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Label": "sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"digest": {
@@ -645,13 +648,13 @@
}
},
{
- "@id": "urn:9713c577-48d4-4ce2-9732-3e5b2cf78e79",
+ "@id": "bids::$output_dir/pb00.$subj.r01.tcat",
"Label": "pb00.$subj.r01.tcat",
"AtLocation": "$output_dir/pb00.$subj.r01.tcat",
- "GeneratedBy": "urn:3e718433-e2b5-434d-a596-249413698da1"
+ "GeneratedBy": "urn:3dtcat-vsgPEg41"
},
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- "@id": "urn:f8a81771-0ea9-47d0-8c3e-b3482efcb7a4",
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"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -659,16 +662,16 @@
}
},
{
- "@id": "urn:6669d29c-1ab8-456b-a381-2731b50c2173",
+ "@id": "bids::outcount.r$run.1D",
"Label": "outcount.r$run.1D",
"AtLocation": "outcount.r$run.1D",
- "GeneratedBy": "urn:918fcb03-359d-488c-bb96-5b75f21afc6b",
+ "GeneratedBy": "urn:3dtoutco-ua12ThWL",
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{
- "@id": "urn:1e927d75-77b7-4b4e-baef-e3ee46d7b843",
+ "@id": "bids::outcount.r*.1D",
"Label": "outcount.r*.1D",
"AtLocation": "outcount.r*.1D",
"digest": {
@@ -676,25 +679,25 @@
}
},
{
- "@id": "urn:739ed39d-7cda-4f20-a616-6cfacd7eb0ba",
+ "@id": "bids::outcount_rall.1D",
"Label": "outcount_rall.1D",
"AtLocation": "outcount_rall.1D",
- "GeneratedBy": "urn:e36979a0-f0bf-44cd-aadc-8b80d1ca6d10",
+ "GeneratedBy": "urn:cat-eN68PKM4",
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{
- "@id": "urn:bb40fcd5-09a3-4b42-93b4-ed8ed7ee95dd",
+ "@id": "bids::pb01.$subj.r$run.tshift",
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"AtLocation": "pb01.$subj.r$run.tshift",
- "GeneratedBy": "urn:5bbeda84-ea59-4602-8539-b4825125464d",
+ "GeneratedBy": "urn:3dtshift-Uz9V0GCp",
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{
- "@id": "urn:6b2dccb0-069c-4d61-91cb-9885fcb4a556",
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"AtLocation": "sub-01_T1w+orig",
"digest": {
@@ -702,7 +705,7 @@
}
},
{
- "@id": "urn:06372779-6792-4e37-84d1-cd68357b7aed",
+ "@id": "bids::pb01.$subj.r01.tshift+orig",
"Label": "pb01.$subj.r01.tshift",
"AtLocation": "pb01.$subj.r01.tshift+orig",
"digest": {
@@ -710,16 +713,16 @@
}
},
{
- "@id": "urn:47e1138d-c62e-4541-b2d0-585c81198052",
+ "@id": "bids::_al_junk",
"Label": "_al_junk",
"AtLocation": "_al_junk",
- "GeneratedBy": "urn:fe69b019-583c-4c4e-a2c3-63b4d352a94c",
+ "GeneratedBy": "urn:alignepi-TOfxbivF",
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{
- "@id": "urn:19459e8e-1991-490b-b90f-a18c3dc7528b",
+ "@id": "bids::TT_N27+tlrc",
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"AtLocation": "TT_N27+tlrc",
"digest": {
@@ -727,7 +730,7 @@
}
},
{
- "@id": "urn:39ea58bb-83ea-4c9e-8050-7adcf255c33d",
+ "@id": "bids::sub-01_T1w_ns+orig",
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"AtLocation": "sub-01_T1w_ns+orig",
"digest": {
@@ -735,7 +738,7 @@
}
},
{
- "@id": "urn:3b785f19-73bf-4c34-a038-7a9b4396a169",
+ "@id": "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc::WARP_DATA",
"digest": {
@@ -743,16 +746,16 @@
}
},
{
- "@id": "urn:bdf545f3-a058-4328-9ee9-0e77526c0c60",
+ "@id": "bids::warp.anat.Xat.1D",
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"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:1dcfe420-527d-4cc2-8411-9c1433b5fdff",
+ "GeneratedBy": "urn:catmatve-EA5f1njv",
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{
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"AtLocation": "pb01.$subj.r$run.tshift+orig",
"digest": {
@@ -760,34 +763,34 @@
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{
- "@id": "urn:a68a1574-7b09-437f-b75a-2c7214dbf8c6",
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"AtLocation": "mat.r$run.vr.aff12.1D",
- "GeneratedBy": "urn:9514e444-af9c-4649-b1e3-f2b7371e2ff3",
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{
- "@id": "urn:02775417-0217-4d74-8e8a-e0541b4e1a0b",
+ "@id": "bids::rm.epi.all1",
"Label": "rm.epi.all1",
"AtLocation": "rm.epi.all1",
- "GeneratedBy": "urn:bbdd547f-1200-4863-9dda-efa4d1e55184",
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@@ -795,16 +798,16 @@
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@@ -863,16 +866,16 @@
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@@ -880,7 +883,7 @@
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@@ -888,34 +891,42 @@
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@@ -931,7 +942,7 @@
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@@ -939,25 +950,25 @@
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@@ -965,16 +976,16 @@
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@@ -982,16 +993,16 @@
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@@ -999,7 +1010,7 @@
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@@ -1032,25 +1043,25 @@
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@@ -1058,34 +1069,34 @@
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@@ -1093,25 +1104,25 @@
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@@ -1119,16 +1130,16 @@
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@@ -1136,16 +1147,16 @@
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@@ -1153,7 +1164,7 @@
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@@ -1161,16 +1172,16 @@
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@@ -1178,25 +1189,25 @@
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{
- "@id": "urn:2a93e9d8-8d47-40af-8bcf-eaf983b9add1",
+ "@id": "bids::out.gcor.1D",
"Label": "out.gcor.1D",
"AtLocation": "out.gcor.1D",
"digest": {
@@ -1204,16 +1215,16 @@
}
},
{
- "@id": "urn:fa5a7811-b41a-413e-9cb5-a8ed8170aa68",
+ "@id": "urn:uuid:4f2586b4-aacf-4613-877c-dcfbc2fc6bd6",
"Label": "-",
"AtLocation": "-",
- "GeneratedBy": "urn:80f381a3-fcaa-49fb-885e-4debddb8a786",
+ "GeneratedBy": "urn:3dtstat-QdOKIy3R",
"digest": {
"sha256": "dac304c9f20899ca1ef5aa403e565345fd0ff4ed80c35f82007c9b03a68292b3"
}
},
{
- "@id": "urn:f8678749-7602-488a-9d3a-8f2490d6f419",
+ "@id": "bids::rm.errts.unit+tlrc",
"Label": "rm.errts.unit",
"AtLocation": "rm.errts.unit+tlrc",
"digest": {
@@ -1221,16 +1232,16 @@
}
},
{
- "@id": "urn:b1d3f413-1a3f-4a66-8cee-b24bfdb8d5ea",
+ "@id": "bids::rm.DP",
"Label": "rm.DP",
"AtLocation": "rm.DP",
- "GeneratedBy": "urn:c879c188-eaba-4d99-a76b-7031e921db86",
+ "GeneratedBy": "urn:3dcalc-04jOYgES",
"digest": {
"sha256": "06a0bfbc609c1a06ecf93c479a3288d2911c7f5f3e93cf49c5d26f721c2035ed"
}
},
{
- "@id": "urn:25fc6c6e-026b-4ab5-b54f-ab765a104838",
+ "@id": "bids::rm.DP+tlrc",
"Label": "rm.DP",
"AtLocation": "rm.DP+tlrc",
"digest": {
@@ -1238,16 +1249,16 @@
}
},
{
- "@id": "urn:bfc5f78d-f8d3-4eee-8fd5-8835562215ba",
+ "@id": "bids::corr_brain",
"Label": "corr_brain",
"AtLocation": "corr_brain",
- "GeneratedBy": "urn:075b19d7-cccb-49e7-a9c8-4a0abc906eab",
+ "GeneratedBy": "urn:3dtstat-GsOJRmrW",
"digest": {
"sha256": "74e3aeae0da338b871ab5dc9e8859a4e81fcf1b3c0042cd22fe337eb7baf5eae"
}
},
{
- "@id": "urn:604a1e3b-15de-497b-a525-ca9bd99f2a09",
+ "@id": "bids::X.nocensor.xmat.1D'[3]'",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D'[3]'",
"digest": {
@@ -1255,16 +1266,16 @@
}
},
{
- "@id": "urn:7ab095d7-8d81-4df7-aa9f-2167bce867fc",
+ "@id": "bids::ideal_tone_counting.1D",
"Label": "ideal_tone_counting.1D",
"AtLocation": "ideal_tone_counting.1D",
- "GeneratedBy": "urn:d48a8eec-56b1-4aa8-af22-922fc27586e6",
+ "GeneratedBy": "urn:1dcat-XCdniniz",
"digest": {
"sha256": "9bb1cabac5ce7ca19dffa5cd6336a9bf82d362fea2ce9341978406e421b5333c"
}
},
{
- "@id": "urn:4b941985-5a56-41fe-bdf5-274158f7437c",
+ "@id": "bids::X.nocensor.xmat.1D'[4]'",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D'[4]'",
"digest": {
@@ -1272,16 +1283,16 @@
}
},
{
- "@id": "urn:5f12525b-764a-4493-b764-0c8b7057963b",
+ "@id": "bids::ideal_probe.1D",
"Label": "ideal_probe.1D",
"AtLocation": "ideal_probe.1D",
- "GeneratedBy": "urn:c504956f-4b7b-4992-abbd-46b5fc4f8a21",
+ "GeneratedBy": "urn:1dcat-1e0KL3UX",
"digest": {
"sha256": "705d93afa8b6ded9f4f572db3f967b54e9906942669af51dd8287a9863bb4288"
}
},
{
- "@id": "urn:a92420ab-a033-4844-a6f7-39500db2e482",
+ "@id": "bids::X.nocensor.xmat.1D%22[$reg_cols]%22",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D\"[$reg_cols]\"",
"digest": {
@@ -1289,52 +1300,52 @@
}
},
{
- "@id": "urn:ae3b0d12-52f4-48a2-88d4-0678d5f09e99",
+ "@id": "bids::sum_ideal.1D",
"Label": "sum_ideal.1D",
"AtLocation": "sum_ideal.1D",
- "GeneratedBy": "urn:d749afb2-7262-4434-9504-06cb313cac64",
+ "GeneratedBy": "urn:3dtstat-HjsESDaO",
"digest": {
"sha256": "b2dccadcd84b2d26ec9685c4d1846baf2f11b867f31c36a08748d1c85467b01a"
}
},
{
- "@id": "urn:ce793436-f751-49ce-83f6-51ec93dd4b41",
+ "@id": "bids::X.stim.xmat.1D",
"Label": "X.stim.xmat.1D",
"AtLocation": "X.stim.xmat.1D",
- "GeneratedBy": "urn:a04f7934-f7bc-4170-b2eb-5c6c732b5848",
+ "GeneratedBy": "urn:1dcat-kqae8pGw",
"digest": {
"sha256": "7c61b2f4bbb9eb0cecb19f81faa3a79b94d547b7fb4087ed18e368619e0004e6"
}
},
{
- "@id": "urn:4ae332d7-a922-405f-badd-a8bf6db8669f",
+ "@id": "bids::blur.epits.1D",
"Label": "blur.epits.1D",
"AtLocation": "blur.epits.1D",
- "GeneratedBy": "urn:314e11c6-9e73-48fd-80b8-5255796a06d1",
+ "GeneratedBy": "urn:3dfwhmx-c2Id8xz4",
"digest": {
"sha256": "623e70a42214e56babc1f1dca156e0b11ba09865dbd6ca9549d54ca2fc601515"
}
},
{
- "@id": "urn:35b68be2-b883-4bde-9698-c01bc4e682f7",
+ "@id": "bids::blur.errts.1D",
"Label": "blur.errts.1D",
"AtLocation": "blur.errts.1D",
- "GeneratedBy": "urn:a6811528-b35b-46f8-8c64-c27db6cc51f3",
+ "GeneratedBy": "urn:3dfwhmx-1pDteEI5",
"digest": {
"sha256": "73969700079b5d3275536ac7eaf0e17571d7e74ec49553b6940f90d5718fc800"
}
},
{
- "@id": "urn:8547393d-de20-4286-9185-a5e3e8872ec0",
+ "@id": "bids::ClustSim",
"Label": "ClustSim",
"AtLocation": "ClustSim",
- "GeneratedBy": "urn:b1798fa5-41c3-4c32-af33-ba038526e4b9",
+ "GeneratedBy": "urn:3dclusts-ANy7O8lb",
"digest": {
"sha256": "2e0cdba2c91902ba12d742a39cb20df66cfd705ba8de767fbf68aae8eb65c6f0"
}
},
{
- "@id": "urn:fb2855e1-e166-43d1-82c1-370fde58b2ce",
+ "@id": "bids::pb00.$subj.r*.tcat+orig.HEAD",
"Label": "pb00.$subj.r*.tcat",
"AtLocation": "pb00.$subj.r*.tcat+orig.HEAD",
"digest": {
@@ -1342,10 +1353,10 @@
}
},
{
- "@id": "urn:0e8df35d-318a-47ab-aad9-59de5d48e26e",
+ "@id": "bids::-exit0",
"Label": "-exit0",
"AtLocation": "-exit0",
- "GeneratedBy": "urn:cc3659dd-8933-41f9-b132-b2a64e91ffaf",
+ "GeneratedBy": "urn:genssrev-Mk4Ku1i2",
"digest": {
"sha256": "871a4d3513ed2924cbb10c1c15a196eac4a46a05bdcc248e3bcdb23327b3ad90"
}
diff --git a/examples/from_parsers/afni/afni_bi_sided_t_test_proc.png b/examples/from_parsers/afni/afni_bi_sided_t_test_proc.png
index 7ac283a3e..7c0c124e9 100644
Binary files a/examples/from_parsers/afni/afni_bi_sided_t_test_proc.png and b/examples/from_parsers/afni/afni_bi_sided_t_test_proc.png differ
diff --git a/examples/from_parsers/afni/afni_bi_sided_t_test_proc_block.jsonld b/examples/from_parsers/afni/afni_bi_sided_t_test_proc_block.jsonld
index 239bfd62d..ea593d946 100644
--- a/examples/from_parsers/afni/afni_bi_sided_t_test_proc_block.jsonld
+++ b/examples/from_parsers/afni/afni_bi_sided_t_test_proc_block.jsonld
@@ -4,187 +4,189 @@
"Records": {
"Software": [
{
- "@id": "urn:5e24e0c2-394f-49db-9a68-e68d7d5c0b1e",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:afni-3nwbHacO",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
- "Version": "afni24"
+ "Version": "afni24",
+ "AltIdentifier": "RRID:SCR_005927"
}
],
"Activities": [
{
- "@id": "urn:669e1fc0-0ce7-4613-8e8b-08db4a63db9b",
+ "@id": "urn:autobloc-tFuAHJrf",
"Label": "auto block: setup",
- "AssociatedWith": "urn:5e24e0c2-394f-49db-9a68-e68d7d5c0b1e",
+ "AssociatedWith": "urn:afni-3nwbHacO",
"Command": "mkdir $output_dir; mkdir $output_dir/stimuli; cp ./afni_bi_sided_t_test/tone_counting_onset_times.txt ./afni_bi_sided_t_test/tone_counting_probe_duration.txt $output_dir/stimuli; 3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w; ",
"Used": [
- "urn:e5081baa-1acc-4ca1-b4e0-b504d7fed955",
- "urn:ff6a8b57-ac8c-4df4-b617-4b3a0b2bc2b9",
- "urn:3604a5a0-8d0a-446e-aaa0-a81b7138d093"
+ "bids::afni_bi_sided_t_test/tone_counting_onset_times.txt",
+ "bids::afni_bi_sided_t_test/tone_counting_probe_duration.txt",
+ "bids::sub-01_T1w.nii.gz"
]
},
{
- "@id": "urn:5a9fabb2-3b10-40fa-8806-332d6cd96b61",
+ "@id": "urn:autobloc-MwLVnXkn",
"Label": "auto block: tcat",
- "AssociatedWith": "urn:5e24e0c2-394f-49db-9a68-e68d7d5c0b1e",
+ "AssociatedWith": "urn:afni-3nwbHacO",
"Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ",
"Used": [
- "urn:3aa1e7d1-1fae-4173-89a7-0f4c340c28a2"
+ "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'"
]
},
{
- "@id": "urn:68e5f037-ae24-4110-bf68-0f33967fcdb1",
+ "@id": "urn:autobloc-2Iba5XAL",
"Label": "auto block: outcount",
- "AssociatedWith": "urn:5e24e0c2-394f-49db-9a68-e68d7d5c0b1e",
+ "AssociatedWith": "urn:afni-3nwbHacO",
"Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ",
"Used": [
- "urn:e27a29e8-02ac-43cb-8f10-e82b13654dc8",
- "urn:0e2391fb-c48d-4922-b20e-de1d93161959"
+ "bids::pb00.$subj.r$run.tcat+orig",
+ "bids::outcount.r*.1D"
]
},
{
- "@id": "urn:23dc9eac-7e0a-4fb9-8c41-fd286cb8e6d4",
+ "@id": "urn:tshift-J20yUWRy",
"Label": "tshift",
- "AssociatedWith": "urn:5e24e0c2-394f-49db-9a68-e68d7d5c0b1e",
+ "AssociatedWith": "urn:afni-3nwbHacO",
"Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ",
"Used": [
- "urn:e27a29e8-02ac-43cb-8f10-e82b13654dc8"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:e284cc01-ac8b-4ecd-815d-0ca2f933f53d",
+ "@id": "urn:align-Y6FaxgZA",
"Label": "align",
- "AssociatedWith": "urn:5e24e0c2-394f-49db-9a68-e68d7d5c0b1e",
+ "AssociatedWith": "urn:afni-3nwbHacO",
"Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ",
"Used": [
- "urn:d5e3f198-a9c4-4128-a3bc-7636be079ef3",
- "urn:fb3bb527-ace9-4fc0-aa87-c2013e3eec38"
+ "bids::pb01.$subj.r01.tshift+orig",
+ "bids::sub-01_T1w+orig"
]
},
{
- "@id": "urn:f4df6cb7-c701-436a-9430-d2721a0a52a6",
+ "@id": "urn:tlrc-grbWf7H9",
"Label": "tlrc",
- "AssociatedWith": "urn:5e24e0c2-394f-49db-9a68-e68d7d5c0b1e",
+ "AssociatedWith": "urn:afni-3nwbHacO",
"Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ",
"Used": [
- "urn:790edad4-6308-4c2b-9d08-5cf9b9a4a3e9",
- "urn:d6edc215-1f9b-4996-8ac6-215c125316b0",
- "urn:ab38c57b-f9d1-418f-b7da-f63d7457eea2"
+ "bids::TT_N27+tlrc",
+ "bids::sub-01_T1w_ns+orig",
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:55245bd5-e2b9-4e3d-89f6-898175db3b62",
+ "@id": "urn:volreg-M7Va6mGv",
"Label": "volreg",
- "AssociatedWith": "urn:5e24e0c2-394f-49db-9a68-e68d7d5c0b1e",
+ "AssociatedWith": "urn:afni-3nwbHacO",
"Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig; 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1; cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D; 3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run; 3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run; 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc; cat dfile.r*.1D > dfile_rall.1D; 3dcopy rm.epi.min.r01+tlrc mask_epi_extents; 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg; 3dcopy sub-01_T1w_ns+tlrc anat_final.$subj; 3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped; ",
"Used": [
- "urn:049ce5bc-724a-4c47-9d72-b77a52f94361",
- "urn:049ce5bc-724a-4c47-9d72-b77a52f94361",
- "urn:ab38c57b-f9d1-418f-b7da-f63d7457eea2",
- "urn:049ce5bc-724a-4c47-9d72-b77a52f94361",
- "urn:cd986e5e-05c7-43b3-b72a-4808042f2c32",
- "urn:2a874c72-652a-4395-a282-238a0e8df62d",
- "urn:cd986e5e-05c7-43b3-b72a-4808042f2c32",
- "urn:07e15c34-289b-4c89-93b3-2b34fda0c07b",
- "urn:30ce15aa-b1f3-470f-b216-c9bfba4b1af6",
- "urn:8a02b9ac-5f58-42b6-8490-6ca2a3ed4eb9",
- "urn:b2692284-5f1d-4184-8b98-7b75bfd8039b",
- "urn:b7b63411-c4b2-48d7-9f0a-01e2993bd15b",
- "urn:cd986e5e-05c7-43b3-b72a-4808042f2c32",
- "urn:8eabd3c2-aef1-4561-a750-b18b5d99a114"
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.epi.all1+orig",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.epi.1.r$run+tlrc",
+ "bids::dfile.r*.1D",
+ "bids::rm.epi.min.r01+tlrc",
+ "bids::mask_epi_extents+tlrc",
+ "bids::rm.epi.nomask.r$run+tlrc",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::anat_final.$subj+tlrc",
+ "bids::warp.anat.Xat.1D"
]
},
{
- "@id": "urn:2e0f436c-79e9-46a8-b63d-7dfc24beea09",
+ "@id": "urn:blur-KDTQ0s9b",
"Label": "blur",
- "AssociatedWith": "urn:5e24e0c2-394f-49db-9a68-e68d7d5c0b1e",
+ "AssociatedWith": "urn:afni-3nwbHacO",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc; ",
"Used": [
- "urn:55641ff0-5d1d-4ecc-9c94-201c2e014103",
- "urn:61125ce4-0505-4313-a6d8-9dd9309b3597"
+ "bids::pb02.$subj.r$run.volreg+tlrc",
+ "bids::pb03.$subj.r$run.blur"
]
},
{
- "@id": "urn:095fe016-ca8c-4a9d-a138-9274f9d4f80a",
+ "@id": "urn:mask-5kCG03AG",
"Label": "mask",
- "AssociatedWith": "urn:5e24e0c2-394f-49db-9a68-e68d7d5c0b1e",
+ "AssociatedWith": "urn:afni-3nwbHacO",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc; 3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj; 3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj; 3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt; 3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt; 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group; ",
"Used": [
- "urn:122448d3-c878-4554-9aea-fb011671618f",
- "urn:cd986e5e-05c7-43b3-b72a-4808042f2c32",
- "urn:de18d140-2ad9-4fee-826c-495b339dfe68",
- "urn:59b7eaaf-cde7-420b-a100-db32d13e794f",
- "urn:4172ba06-847c-4616-ab77-c3c41b1d787c",
- "urn:9e1850b6-ffea-47ef-8e79-c79113529136",
- "urn:4172ba06-847c-4616-ab77-c3c41b1d787c",
- "urn:9e1850b6-ffea-47ef-8e79-c79113529136",
- "urn:42db81f2-95ce-49f7-a8de-88aa3b7ded4f",
- "urn:de18d140-2ad9-4fee-826c-495b339dfe68",
- "urn:b0346181-d3dd-47ca-80c9-9296654fcf8a"
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.resam.anat+tlrc",
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee",
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee",
+ "bids::/Users/u1591557/abin/TT_N27+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.resam.group+tlrc"
]
},
{
- "@id": "urn:210b7976-e9ae-4243-a954-7f09d63fafe5",
+ "@id": "urn:scale-wdQCkfkN",
"Label": "scale",
- "AssociatedWith": "urn:5e24e0c2-394f-49db-9a68-e68d7d5c0b1e",
+ "AssociatedWith": "urn:afni-3nwbHacO",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc; 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale; ",
"Used": [
- "urn:122448d3-c878-4554-9aea-fb011671618f",
- "urn:122448d3-c878-4554-9aea-fb011671618f",
- "urn:b2692284-5f1d-4184-8b98-7b75bfd8039b",
- "urn:beceec26-7523-46af-b8d7-0f6a297b520d"
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::mask_epi_extents+tlrc",
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::rm.mean_r$run+tlrc"
]
},
{
- "@id": "urn:b5a3c5a4-ab0c-4be4-a61d-2bbfdd0b664b",
+ "@id": "urn:regress-8sCPNBhu",
"Label": "regress",
- "AssociatedWith": "urn:5e24e0c2-394f-49db-9a68-e68d7d5c0b1e",
+ "AssociatedWith": "urn:afni-3nwbHacO",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}; 3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj; 1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt; 3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD; 3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"; 3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"; 3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj; 3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc; 3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D; 3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D; 3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP; 3dTstat -sum -prefix corr_brain rm.DP+tlrc; 1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D; 1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D; 3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"; 1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D; ",
"Used": [
- "urn:7931efc7-71d6-4b0d-a464-dfb77e182541",
- "urn:7931efc7-71d6-4b0d-a464-dfb77e182541",
- "urn:7931efc7-71d6-4b0d-a464-dfb77e182541",
- "urn:ca9401a0-9fb9-4db4-ac56-2dd3abd530ed",
- "urn:ca9401a0-9fb9-4db4-ac56-2dd3abd530ed",
- "urn:499070c6-6176-448b-8cc1-3e736dcbd1d7",
- "urn:7e33bcfc-5cc9-4b7b-a65e-ed61463c35e0",
- "urn:6df1bfc5-ec9b-4942-9652-579daee2b106",
- "urn:aa73830e-3f84-4726-afd9-f26f5c1d4b12",
- "urn:de18d140-2ad9-4fee-826c-495b339dfe68",
- "urn:e2f6c140-b7ba-4df9-910a-ebd2fa54148a",
- "urn:dc20751a-2da6-4559-afab-80dac72ca3f9",
- "urn:7a2f3c98-6954-48a3-88c5-7705eaa93121",
- "urn:b41877d1-5a48-4ad7-8454-3a5389e52fee",
- "urn:5caedbe9-19f3-420e-8d87-f4e20ddbcce3",
- "urn:dc49031c-cf43-4d64-bf8b-afea21e10b55",
- "urn:87c3b7ec-ea9f-4656-83e4-9204d9e52a20",
- "urn:87c3b7ec-ea9f-4656-83e4-9204d9e52a20"
+ "bids::dfile_rall.1D",
+ "bids::dfile_rall.1D",
+ "bids::dfile_rall.1D",
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD",
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD",
+ "bids::all_runs.$subj+tlrc%22[$ktrs]%22",
+ "bids::errts.$%7Bsubj%7D+tlrc%22[$ktrs]%22",
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.noise.all+tlrc",
+ "bids::rm.signal.all+tlrc",
+ "bids::errts.$%7Bsubj%7D+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::out.gcor.1D",
+ "bids::rm.errts.unit+tlrc",
+ "bids::rm.DP+tlrc",
+ "bids::X.nocensor.xmat.1D'[3]'",
+ "bids::X.nocensor.xmat.1D'[4]'",
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22",
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:ad85f4d2-bc86-4eb0-b051-e88d0ec7f05c",
+ "@id": "urn:bluresti-ZYY6Uhpa",
"Label": "blur estimation",
- "AssociatedWith": "urn:5e24e0c2-394f-49db-9a68-e68d7d5c0b1e",
+ "AssociatedWith": "urn:afni-3nwbHacO",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D; 3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D; 3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim; ",
"Used": [
- "urn:de18d140-2ad9-4fee-826c-495b339dfe68",
- "urn:de18d140-2ad9-4fee-826c-495b339dfe68",
- "urn:de18d140-2ad9-4fee-826c-495b339dfe68"
+ "bids::full_mask.$subj+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:e77c0498-1451-4586-9da6-e9057e9481a9",
+ "@id": "urn:autobloc-2YsKSu6y",
"Label": "auto block: generate review scripts",
- "AssociatedWith": "urn:5e24e0c2-394f-49db-9a68-e68d7d5c0b1e",
+ "AssociatedWith": "urn:afni-3nwbHacO",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD; gen_ss_review_scripts.py -mot_limit 0.3 -exit0; ",
"Used": [
- "urn:2eb17bf4-6037-4b2b-8ee3-1b2c53770e8f"
+ "bids::pb00.$subj.r*.tcat+orig.HEAD"
]
}
],
"Entities": [
{
- "@id": "urn:e5081baa-1acc-4ca1-b4e0-b504d7fed955",
+ "@id": "bids::afni_bi_sided_t_test/tone_counting_onset_times.txt",
"Label": "tone_counting_onset_times.txt",
"AtLocation": "./afni_bi_sided_t_test/tone_counting_onset_times.txt",
"digest": {
@@ -192,7 +194,7 @@
}
},
{
- "@id": "urn:ff6a8b57-ac8c-4df4-b617-4b3a0b2bc2b9",
+ "@id": "bids::afni_bi_sided_t_test/tone_counting_probe_duration.txt",
"Label": "tone_counting_probe_duration.txt",
"AtLocation": "./afni_bi_sided_t_test/tone_counting_probe_duration.txt",
"digest": {
@@ -200,7 +202,7 @@
}
},
{
- "@id": "urn:3604a5a0-8d0a-446e-aaa0-a81b7138d093",
+ "@id": "bids::sub-01_T1w.nii.gz",
"Label": "sub-01_T1w.nii.gz",
"AtLocation": "sub-01_T1w.nii.gz",
"digest": {
@@ -208,34 +210,34 @@
}
},
{
- "@id": "urn:89d4725b-2aa6-443d-a502-65b941ec8bdc",
+ "@id": "bids::$output_dir",
"Label": "$output_dir",
"AtLocation": "$output_dir",
- "GeneratedBy": "urn:669e1fc0-0ce7-4613-8e8b-08db4a63db9b",
+ "GeneratedBy": "urn:autobloc-tFuAHJrf",
"digest": {
"sha256": "9fa4c635e6533ddf2fed54295920052818d948c3ffe97bc753bd7336b453f8cb"
}
},
{
- "@id": "urn:91719aa4-d2fc-40e6-acc3-636c5450f4d2",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:669e1fc0-0ce7-4613-8e8b-08db4a63db9b"
+ "GeneratedBy": "urn:autobloc-tFuAHJrf"
},
{
- "@id": "urn:cd99b9e2-3b36-46e3-95ec-8cb54f617d02",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:669e1fc0-0ce7-4613-8e8b-08db4a63db9b"
+ "GeneratedBy": "urn:autobloc-tFuAHJrf"
},
{
- "@id": "urn:e43a2d82-17b0-4519-90f0-4792c2240a1b",
+ "@id": "bids::$output_dir/sub-01_T1w",
"Label": "sub-01_T1w",
"AtLocation": "$output_dir/sub-01_T1w",
- "GeneratedBy": "urn:669e1fc0-0ce7-4613-8e8b-08db4a63db9b"
+ "GeneratedBy": "urn:autobloc-tFuAHJrf"
},
{
- "@id": "urn:3aa1e7d1-1fae-4173-89a7-0f4c340c28a2",
+ "@id": "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Label": "sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"digest": {
@@ -243,13 +245,13 @@
}
},
{
- "@id": "urn:07a480d2-ebdf-4aa8-884f-56d82de8cb3e",
+ "@id": "bids::$output_dir/pb00.$subj.r01.tcat",
"Label": "pb00.$subj.r01.tcat",
"AtLocation": "$output_dir/pb00.$subj.r01.tcat",
- "GeneratedBy": "urn:5a9fabb2-3b10-40fa-8806-332d6cd96b61"
+ "GeneratedBy": "urn:autobloc-MwLVnXkn"
},
{
- "@id": "urn:e27a29e8-02ac-43cb-8f10-e82b13654dc8",
+ "@id": "bids::pb00.$subj.r$run.tcat+orig",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -257,7 +259,7 @@
}
},
{
- "@id": "urn:0e2391fb-c48d-4922-b20e-de1d93161959",
+ "@id": "bids::outcount.r*.1D",
"Label": "outcount.r*.1D",
"AtLocation": "outcount.r*.1D",
"digest": {
@@ -265,25 +267,25 @@
}
},
{
- "@id": "urn:2654a643-80c9-43ff-a008-a658ed2b0fb6",
+ "@id": "bids::outcount.r$run.1D",
"Label": "outcount.r$run.1D",
"AtLocation": "outcount.r$run.1D",
- "GeneratedBy": "urn:68e5f037-ae24-4110-bf68-0f33967fcdb1",
+ "GeneratedBy": "urn:autobloc-2Iba5XAL",
"digest": {
"sha256": "63d9f539e5470badc625d557109f68bc4eecbb02ca2667483739d52f95e5d0dd"
}
},
{
- "@id": "urn:d322772d-356d-4029-b3c9-5e0801492b56",
+ "@id": "bids::outcount_rall.1D",
"Label": "outcount_rall.1D",
"AtLocation": "outcount_rall.1D",
- "GeneratedBy": "urn:68e5f037-ae24-4110-bf68-0f33967fcdb1",
+ "GeneratedBy": "urn:autobloc-2Iba5XAL",
"digest": {
"sha256": "cb887fd5e4d5e9acb3a24820d0f7a62ed38a5ffb0fdedd373440ac0219fb186a"
}
},
{
- "@id": "urn:e27a29e8-02ac-43cb-8f10-e82b13654dc8",
+ "@id": "bids::pb00.$subj.r$run.tcat+orig",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -291,16 +293,16 @@
}
},
{
- "@id": "urn:bc49a77f-927c-4ccd-8959-e00cae2dbe65",
+ "@id": "bids::pb01.$subj.r$run.tshift",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift",
- "GeneratedBy": "urn:23dc9eac-7e0a-4fb9-8c41-fd286cb8e6d4",
+ "GeneratedBy": "urn:tshift-J20yUWRy",
"digest": {
"sha256": "c6bf01cea8d2eac1d7a866f80b865c6e7d4b4e012dbb63d480ac9a8551162d72"
}
},
{
- "@id": "urn:fb3bb527-ace9-4fc0-aa87-c2013e3eec38",
+ "@id": "bids::sub-01_T1w+orig",
"Label": "sub-01_T1w",
"AtLocation": "sub-01_T1w+orig",
"digest": {
@@ -308,7 +310,7 @@
}
},
{
- "@id": "urn:d5e3f198-a9c4-4128-a3bc-7636be079ef3",
+ "@id": "bids::pb01.$subj.r01.tshift+orig",
"Label": "pb01.$subj.r01.tshift",
"AtLocation": "pb01.$subj.r01.tshift+orig",
"digest": {
@@ -316,16 +318,16 @@
}
},
{
- "@id": "urn:b75fdf24-cd6a-4012-801f-923ace034deb",
+ "@id": "bids::_al_junk",
"Label": "_al_junk",
"AtLocation": "_al_junk",
- "GeneratedBy": "urn:e284cc01-ac8b-4ecd-815d-0ca2f933f53d",
+ "GeneratedBy": "urn:align-Y6FaxgZA",
"digest": {
"sha256": "bd785a075a4c6446e1e54de9e628913f7f1c814e86b69a9fbfe933209e6d37b5"
}
},
{
- "@id": "urn:d6edc215-1f9b-4996-8ac6-215c125316b0",
+ "@id": "bids::TT_N27+tlrc",
"Label": "TT_N27",
"AtLocation": "TT_N27+tlrc",
"digest": {
@@ -333,7 +335,7 @@
}
},
{
- "@id": "urn:790edad4-6308-4c2b-9d08-5cf9b9a4a3e9",
+ "@id": "bids::sub-01_T1w_ns+orig",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+orig",
"digest": {
@@ -341,7 +343,7 @@
}
},
{
- "@id": "urn:ab38c57b-f9d1-418f-b7da-f63d7457eea2",
+ "@id": "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc::WARP_DATA",
"digest": {
@@ -349,16 +351,16 @@
}
},
{
- "@id": "urn:8eabd3c2-aef1-4561-a750-b18b5d99a114",
+ "@id": "bids::warp.anat.Xat.1D",
"Label": "warp.anat.Xat.1D",
"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:f4df6cb7-c701-436a-9430-d2721a0a52a6",
+ "GeneratedBy": "urn:tlrc-grbWf7H9",
"digest": {
"sha256": "800633fb5b4e9be64078bc181c4d5510ffb73fc5cccaf364c7fb6a294aa06728"
}
},
{
- "@id": "urn:ab38c57b-f9d1-418f-b7da-f63d7457eea2",
+ "@id": "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc::WARP_DATA",
"digest": {
@@ -366,16 +368,16 @@
}
},
{
- "@id": "urn:8eabd3c2-aef1-4561-a750-b18b5d99a114",
+ "@id": "bids::warp.anat.Xat.1D",
"Label": "warp.anat.Xat.1D",
"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:f4df6cb7-c701-436a-9430-d2721a0a52a6",
+ "GeneratedBy": "urn:tlrc-grbWf7H9",
"digest": {
"sha256": "800633fb5b4e9be64078bc181c4d5510ffb73fc5cccaf364c7fb6a294aa06728"
}
},
{
- "@id": "urn:049ce5bc-724a-4c47-9d72-b77a52f94361",
+ "@id": "bids::pb01.$subj.r$run.tshift+orig",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift+orig",
"digest": {
@@ -383,7 +385,7 @@
}
},
{
- "@id": "urn:cd986e5e-05c7-43b3-b72a-4808042f2c32",
+ "@id": "bids::sub-01_T1w_ns+tlrc",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc",
"digest": {
@@ -391,7 +393,7 @@
}
},
{
- "@id": "urn:2a874c72-652a-4395-a282-238a0e8df62d",
+ "@id": "bids::rm.epi.all1+orig",
"Label": "rm.epi.all1",
"AtLocation": "rm.epi.all1+orig",
"digest": {
@@ -399,7 +401,7 @@
}
},
{
- "@id": "urn:07e15c34-289b-4c89-93b3-2b34fda0c07b",
+ "@id": "bids::rm.epi.1.r$run+tlrc",
"Label": "rm.epi.1.r$run",
"AtLocation": "rm.epi.1.r$run+tlrc",
"digest": {
@@ -407,7 +409,7 @@
}
},
{
- "@id": "urn:30ce15aa-b1f3-470f-b216-c9bfba4b1af6",
+ "@id": "bids::dfile.r*.1D",
"Label": "dfile.r*.1D",
"AtLocation": "dfile.r*.1D",
"digest": {
@@ -415,7 +417,7 @@
}
},
{
- "@id": "urn:8a02b9ac-5f58-42b6-8490-6ca2a3ed4eb9",
+ "@id": "bids::rm.epi.min.r01+tlrc",
"Label": "rm.epi.min.r01",
"AtLocation": "rm.epi.min.r01+tlrc",
"digest": {
@@ -423,7 +425,7 @@
}
},
{
- "@id": "urn:b7b63411-c4b2-48d7-9f0a-01e2993bd15b",
+ "@id": "bids::rm.epi.nomask.r$run+tlrc",
"Label": "rm.epi.nomask.r$run",
"AtLocation": "rm.epi.nomask.r$run+tlrc",
"digest": {
@@ -431,7 +433,7 @@
}
},
{
- "@id": "urn:b2692284-5f1d-4184-8b98-7b75bfd8039b",
+ "@id": "bids::mask_epi_extents+tlrc",
"Label": "mask_epi_extents",
"AtLocation": "mask_epi_extents+tlrc",
"digest": {
@@ -439,97 +441,105 @@
}
},
{
- "@id": "urn:17b28bd3-87c8-4b49-a4bb-147ac5877515",
+ "@id": "bids::anat_final.$subj+tlrc",
+ "Label": "anat_final.$subj",
+ "AtLocation": "anat_final.$subj+tlrc",
+ "digest": {
+ "sha256": "94eb1853614cc085b22772c011f119f6a0ad7ec06cba2850587762e7f1a6eae6"
+ }
+ },
+ {
+ "@id": "bids::mat.r$run.vr.aff12.1D",
"Label": "mat.r$run.vr.aff12.1D",
"AtLocation": "mat.r$run.vr.aff12.1D",
- "GeneratedBy": "urn:55245bd5-e2b9-4e3d-89f6-898175db3b62",
+ "GeneratedBy": "urn:volreg-M7Va6mGv",
"digest": {
"sha256": "2e6e6c2ce8089cfa3c6e11dc72fca0cc8497f7a55faae2ced402de4867466c91"
}
},
{
- "@id": "urn:a8b4f6cd-a03e-41cf-96ef-9ab65aba7cbc",
+ "@id": "bids::rm.epi.all1",
"Label": "rm.epi.all1",
"AtLocation": "rm.epi.all1",
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- "GeneratedBy": "urn:55245bd5-e2b9-4e3d-89f6-898175db3b62",
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@@ -537,7 +547,7 @@
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@@ -545,7 +555,7 @@
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@@ -553,7 +563,7 @@
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{
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@@ -561,7 +571,7 @@
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@@ -569,7 +579,7 @@
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@@ -577,7 +587,7 @@
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{
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@@ -585,7 +595,7 @@
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{
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@@ -593,7 +603,7 @@
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{
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@@ -601,7 +611,7 @@
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{
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@@ -609,61 +619,61 @@
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- "GeneratedBy": "urn:095fe016-ca8c-4a9d-a138-9274f9d4f80a",
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- "GeneratedBy": "urn:095fe016-ca8c-4a9d-a138-9274f9d4f80a",
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- "GeneratedBy": "urn:095fe016-ca8c-4a9d-a138-9274f9d4f80a",
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@@ -671,7 +681,7 @@
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@@ -679,7 +689,7 @@
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@@ -687,34 +697,34 @@
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@@ -722,7 +732,7 @@
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@@ -730,7 +740,7 @@
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@@ -738,7 +748,7 @@
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@@ -746,7 +756,7 @@
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@@ -754,7 +764,7 @@
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@@ -762,7 +772,7 @@
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@@ -770,7 +780,7 @@
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{
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@@ -778,7 +788,7 @@
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{
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@@ -786,7 +796,7 @@
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{
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@@ -794,7 +804,7 @@
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{
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@@ -802,7 +812,7 @@
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@@ -810,7 +820,7 @@
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@@ -818,133 +828,133 @@
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{
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- "GeneratedBy": "urn:b5a3c5a4-ab0c-4be4-a61d-2bbfdd0b664b",
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{
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- "GeneratedBy": "urn:b5a3c5a4-ab0c-4be4-a61d-2bbfdd0b664b",
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{
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- "GeneratedBy": "urn:b5a3c5a4-ab0c-4be4-a61d-2bbfdd0b664b",
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{
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{
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- "GeneratedBy": "urn:b5a3c5a4-ab0c-4be4-a61d-2bbfdd0b664b",
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+ "GeneratedBy": "urn:regress-8sCPNBhu",
"digest": {
"sha256": "dac304c9f20899ca1ef5aa403e565345fd0ff4ed80c35f82007c9b03a68292b3"
}
},
{
- "@id": "urn:c078ea60-0808-461c-8512-6adabce32ada",
+ "@id": "bids::rm.DP",
"Label": "rm.DP",
"AtLocation": "rm.DP",
- "GeneratedBy": "urn:b5a3c5a4-ab0c-4be4-a61d-2bbfdd0b664b",
+ "GeneratedBy": "urn:regress-8sCPNBhu",
"digest": {
"sha256": "06a0bfbc609c1a06ecf93c479a3288d2911c7f5f3e93cf49c5d26f721c2035ed"
}
},
{
- "@id": "urn:24a2ba20-0de0-484c-b741-dfc9ea6fedff",
+ "@id": "bids::corr_brain",
"Label": "corr_brain",
"AtLocation": "corr_brain",
- "GeneratedBy": "urn:b5a3c5a4-ab0c-4be4-a61d-2bbfdd0b664b",
+ "GeneratedBy": "urn:regress-8sCPNBhu",
"digest": {
"sha256": "74e3aeae0da338b871ab5dc9e8859a4e81fcf1b3c0042cd22fe337eb7baf5eae"
}
},
{
- "@id": "urn:989aaab7-7b6e-420b-8760-23f945dbe032",
+ "@id": "bids::ideal_tone_counting.1D",
"Label": "ideal_tone_counting.1D",
"AtLocation": "ideal_tone_counting.1D",
- "GeneratedBy": "urn:b5a3c5a4-ab0c-4be4-a61d-2bbfdd0b664b",
+ "GeneratedBy": "urn:regress-8sCPNBhu",
"digest": {
"sha256": "9bb1cabac5ce7ca19dffa5cd6336a9bf82d362fea2ce9341978406e421b5333c"
}
},
{
- "@id": "urn:02423600-49a0-4f52-9935-0d9de622b7d1",
+ "@id": "bids::ideal_probe.1D",
"Label": "ideal_probe.1D",
"AtLocation": "ideal_probe.1D",
- "GeneratedBy": "urn:b5a3c5a4-ab0c-4be4-a61d-2bbfdd0b664b",
+ "GeneratedBy": "urn:regress-8sCPNBhu",
"digest": {
"sha256": "705d93afa8b6ded9f4f572db3f967b54e9906942669af51dd8287a9863bb4288"
}
},
{
- "@id": "urn:062e710f-3caf-4683-832a-3a81935a909c",
+ "@id": "bids::sum_ideal.1D",
"Label": "sum_ideal.1D",
"AtLocation": "sum_ideal.1D",
- "GeneratedBy": "urn:b5a3c5a4-ab0c-4be4-a61d-2bbfdd0b664b",
+ "GeneratedBy": "urn:regress-8sCPNBhu",
"digest": {
"sha256": "b2dccadcd84b2d26ec9685c4d1846baf2f11b867f31c36a08748d1c85467b01a"
}
},
{
- "@id": "urn:21d9dbb9-b8b6-47ac-8451-250b1a8f10ff",
+ "@id": "bids::X.stim.xmat.1D",
"Label": "X.stim.xmat.1D",
"AtLocation": "X.stim.xmat.1D",
- "GeneratedBy": "urn:b5a3c5a4-ab0c-4be4-a61d-2bbfdd0b664b",
+ "GeneratedBy": "urn:regress-8sCPNBhu",
"digest": {
"sha256": "7c61b2f4bbb9eb0cecb19f81faa3a79b94d547b7fb4087ed18e368619e0004e6"
}
},
{
- "@id": "urn:de18d140-2ad9-4fee-826c-495b339dfe68",
+ "@id": "bids::full_mask.$subj+tlrc",
"Label": "full_mask.$subj",
"AtLocation": "full_mask.$subj+tlrc",
"digest": {
@@ -952,34 +962,34 @@
}
},
{
- "@id": "urn:56608cbb-5e14-426b-8613-85eab3025d80",
+ "@id": "bids::blur.epits.1D",
"Label": "blur.epits.1D",
"AtLocation": "blur.epits.1D",
- "GeneratedBy": "urn:ad85f4d2-bc86-4eb0-b051-e88d0ec7f05c",
+ "GeneratedBy": "urn:bluresti-ZYY6Uhpa",
"digest": {
"sha256": "623e70a42214e56babc1f1dca156e0b11ba09865dbd6ca9549d54ca2fc601515"
}
},
{
- "@id": "urn:e453c56c-a245-49c6-a1df-805c8d4b55f8",
+ "@id": "bids::blur.errts.1D",
"Label": "blur.errts.1D",
"AtLocation": "blur.errts.1D",
- "GeneratedBy": "urn:ad85f4d2-bc86-4eb0-b051-e88d0ec7f05c",
+ "GeneratedBy": "urn:bluresti-ZYY6Uhpa",
"digest": {
"sha256": "73969700079b5d3275536ac7eaf0e17571d7e74ec49553b6940f90d5718fc800"
}
},
{
- "@id": "urn:e04b5ef2-2a17-4125-a6e2-6e59daa4fbfd",
+ "@id": "bids::ClustSim",
"Label": "ClustSim",
"AtLocation": "ClustSim",
- "GeneratedBy": "urn:ad85f4d2-bc86-4eb0-b051-e88d0ec7f05c",
+ "GeneratedBy": "urn:bluresti-ZYY6Uhpa",
"digest": {
"sha256": "2e0cdba2c91902ba12d742a39cb20df66cfd705ba8de767fbf68aae8eb65c6f0"
}
},
{
- "@id": "urn:2eb17bf4-6037-4b2b-8ee3-1b2c53770e8f",
+ "@id": "bids::pb00.$subj.r*.tcat+orig.HEAD",
"Label": "pb00.$subj.r*.tcat",
"AtLocation": "pb00.$subj.r*.tcat+orig.HEAD",
"digest": {
@@ -987,10 +997,10 @@
}
},
{
- "@id": "urn:41696253-13a1-4d14-a93f-f16cb8b3a7f9",
+ "@id": "bids::-exit0",
"Label": "-exit0",
"AtLocation": "-exit0",
- "GeneratedBy": "urn:e77c0498-1451-4586-9da6-e9057e9481a9",
+ "GeneratedBy": "urn:autobloc-2YsKSu6y",
"digest": {
"sha256": "871a4d3513ed2924cbb10c1c15a196eac4a46a05bdcc248e3bcdb23327b3ad90"
}
diff --git a/examples/from_parsers/afni/afni_bi_sided_t_test_proc_block.png b/examples/from_parsers/afni/afni_bi_sided_t_test_proc_block.png
index 9f65bc2ce..688dbf4e8 100644
Binary files a/examples/from_parsers/afni/afni_bi_sided_t_test_proc_block.png and b/examples/from_parsers/afni/afni_bi_sided_t_test_proc_block.png differ
diff --git a/examples/from_parsers/afni/afni_clustconn_18_proc.jsonld b/examples/from_parsers/afni/afni_clustconn_18_proc.jsonld
index a56ff961d..07238e1dc 100644
--- a/examples/from_parsers/afni/afni_clustconn_18_proc.jsonld
+++ b/examples/from_parsers/afni/afni_clustconn_18_proc.jsonld
@@ -4,578 +4,581 @@
"Records": {
"Software": [
{
- "@id": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:afni-CmWIlveU",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
- "Version": "afni24"
+ "Version": "afni24",
+ "AltIdentifier": "RRID:SCR_005927"
}
],
"Activities": [
{
- "@id": "urn:7c11963b-3914-4ac8-a5fc-a935011ad6e9",
+ "@id": "urn:makedire-kNRtyUuW",
"Label": "Make directory",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "mkdir $output_dir",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:b4169786-f8b4-4875-a20b-b4433c296029",
+ "@id": "urn:makedire-PUa4faAM",
"Label": "Make directory",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "mkdir $output_dir/stimuli",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:c09e350e-751b-4ef5-9a0f-48397e2fbe36",
+ "@id": "urn:cp-Dp5byids",
"Label": "cp",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "cp ./afni_cluster_nn2/tone_counting_onset_times.txt ./afni_cluster_nn2/tone_counting_probe_duration.txt $output_dir/stimuli",
"Parameters": {},
"Used": [
- "urn:696ebbff-1fbb-4a38-8b97-78f2901d8167",
- "urn:c318e459-6636-41c0-baad-6553d27b820c"
+ "bids::afni_cluster_nn2/tone_counting_onset_times.txt",
+ "bids::afni_cluster_nn2/tone_counting_probe_duration.txt"
]
},
{
- "@id": "urn:35fd6ff1-968d-40ab-aaad-7cf131cab8cf",
+ "@id": "urn:3dcopy-ZOmCezCl",
"Label": "3dcopy",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w",
"Parameters": {},
"Used": [
- "urn:38b5d57d-2ccc-4626-a8f7-de90eae750e4"
+ "bids::sub-01_T1w.nii.gz"
]
},
{
- "@id": "urn:8633c6ca-e187-4a73-8efa-926d8ca33d59",
+ "@id": "urn:3dtcat-SM2Sndnh",
"Label": "3dTcat",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Parameters": {},
"Used": [
- "urn:1c32b8dc-a3cb-4ef0-9c8f-eb21e635e505"
+ "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'"
]
},
{
- "@id": "urn:dc9e4fe0-6cef-4a23-9009-138e1ebb75a7",
+ "@id": "urn:3dtoutco-JB2Lmf2M",
"Label": "3dToutcount",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D",
"Parameters": {},
"Used": [
- "urn:40286f70-3d33-483c-bfc2-3432761e3c7f"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:46cf6b03-fe1d-4b26-9925-389bf65d67d2",
+ "@id": "urn:cat-w53akqHB",
"Label": "cat",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "cat outcount.r*.1D > outcount_rall.1D",
"Parameters": {},
"Used": [
- "urn:b66435cb-d795-4c33-b2e8-eeda2aab4832"
+ "bids::outcount.r*.1D"
]
},
{
- "@id": "urn:bf189218-ad14-4b5f-ba55-945ce218f2f7",
+ "@id": "urn:3dtshift-F2nPSes4",
"Label": "3dTshift",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig",
"Parameters": {},
"Used": [
- "urn:40286f70-3d33-483c-bfc2-3432761e3c7f"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:77c710e3-0894-4482-b181-3c7abd3a69ce",
+ "@id": "urn:alignepi-JN8RFfYg",
"Label": "align_epi_anat.py",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off",
"Parameters": {},
"Used": [
- "urn:4d1dd6f4-b4e4-40c8-b95f-5ec76e8bd89b",
- "urn:b51eb436-940b-4b1b-9e47-f995a797d1cf"
+ "bids::pb01.$subj.r01.tshift+orig",
+ "bids::sub-01_T1w+orig"
]
},
{
- "@id": "urn:eab0d8bc-2fe3-4c10-b167-28e88bc93fe3",
+ "@id": "urn:autotlrc-TOu6eKo1",
"Label": "@auto_tlrc",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss",
"Parameters": {},
"Used": [
- "urn:0636ee2d-a3a6-4f30-87fa-789e47259146",
- "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1"
+ "bids::TT_N27+tlrc",
+ "bids::sub-01_T1w_ns+orig"
]
},
{
- "@id": "urn:39308342-7914-48eb-91d5-9ea9173ec4b1",
+ "@id": "urn:catmatve-7fuoAhEa",
"Label": "cat_matvec",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D",
"Parameters": {},
"Used": [
- "urn:5bdbbc48-a5da-48e9-8fc4-7ad28e5afa5c"
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:0fbfcad6-aac6-4a11-b707-c6889495087a",
+ "@id": "urn:3dvolreg-aQqyS7dV",
"Label": "3dvolreg",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig",
"Parameters": {},
"Used": [
- "urn:e44cdba8-d786-497b-8d2c-c22c4c1c5389"
+ "bids::pb01.$subj.r$run.tshift+orig"
]
},
{
- "@id": "urn:af018c20-ff76-4d07-94f9-c469f5622002",
+ "@id": "urn:3dcalc-qreOQ2px",
"Label": "3dcalc",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1",
"Parameters": {},
"Used": [
- "urn:e44cdba8-d786-497b-8d2c-c22c4c1c5389"
+ "bids::pb01.$subj.r$run.tshift+orig"
]
},
{
- "@id": "urn:7b92747e-b90b-492d-8e7e-c99795accc90",
+ "@id": "urn:catmatve-wpNIh7gg",
"Label": "cat_matvec",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D",
"Parameters": {},
"Used": [
- "urn:5bdbbc48-a5da-48e9-8fc4-7ad28e5afa5c"
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:4b174d0f-45f3-4ea4-bcf1-99879d212ca4",
+ "@id": "urn:3dalline-vUSZLTiK",
"Label": "3dAllineate",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run",
"Parameters": {},
"Used": [
- "urn:2f3eeebb-8a4d-4310-a504-9a07f32015ac",
- "urn:877884bd-f37b-49d8-8854-b945da56459c",
- "urn:e44cdba8-d786-497b-8d2c-c22c4c1c5389"
+ "bids::mat.r$run.warp.aff12.1D",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:3b4003ca-4008-441b-a571-22ee1c9d81a5",
+ "@id": "urn:3dalline-VXjfo3UX",
"Label": "3dAllineate",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run",
"Parameters": {},
"Used": [
- "urn:2f3eeebb-8a4d-4310-a504-9a07f32015ac",
- "urn:7cbbbda6-46f6-488b-a056-0d6322750ac8",
- "urn:877884bd-f37b-49d8-8854-b945da56459c"
+ "bids::mat.r$run.warp.aff12.1D",
+ "bids::rm.epi.all1+orig",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:74748c41-4b12-4d11-8e2e-bad321a8500f",
+ "@id": "urn:3dtstat-6bAohDhA",
"Label": "3dTstat",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc",
"Parameters": {},
"Used": [
- "urn:415d2eff-a2e6-4ce0-b03b-4590dc0b938f"
+ "bids::rm.epi.1.r$run+tlrc"
]
},
{
- "@id": "urn:98899c4a-d46c-4fc4-8aa4-7e38f7fb0855",
+ "@id": "urn:cat-1rmVDUgs",
"Label": "cat",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "cat dfile.r*.1D > dfile_rall.1D",
"Parameters": {},
"Used": [
- "urn:7aad8cde-f615-412f-8471-4c996f88ed9d"
+ "bids::dfile.r*.1D"
]
},
{
- "@id": "urn:e4884732-273d-40a3-ba49-baf3b9d8c03f",
+ "@id": "urn:3dcopy-npAyTgUe",
"Label": "3dcopy",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents",
"Parameters": {},
"Used": [
- "urn:71b058b4-2de9-4859-84b4-b860b34fd6ba"
+ "bids::rm.epi.min.r01+tlrc"
]
},
{
- "@id": "urn:b6d01152-e3cd-4131-83f8-5146de72e061",
+ "@id": "urn:3dcalc-WXiyZGcZ",
"Label": "3dcalc",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg",
"Parameters": {},
"Used": [
- "urn:0df2b518-c426-40f8-afdf-be5a39b75735",
- "urn:4cf18a5d-9510-4dcf-85c4-97b4ab57855f"
+ "bids::mask_epi_extents+tlrc",
+ "bids::rm.epi.nomask.r$run+tlrc"
]
},
{
- "@id": "urn:083d8661-48cc-477b-8d5e-fa8106d0bfbc",
+ "@id": "urn:3dcopy-DESJSJWt",
"Label": "3dcopy",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj",
"Parameters": {},
"Used": [
- "urn:2f3eeebb-8a4d-4310-a504-9a07f32015ac"
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:d8954007-4612-40b0-8ded-1060a7c2d47c",
+ "@id": "urn:3dalline-ukfO7Wly",
"Label": "3dAllineate",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped",
"Parameters": {},
"Used": [
- "urn:550cc2b5-46c9-4929-b5ff-1fe49fb4ccba"
+ "bids::anat_final.$subj+tlrc",
+ "bids::warp.anat.Xat.1D"
]
},
{
- "@id": "urn:53fa78a6-d8f2-471e-a4fa-aa9fa8f08b36",
+ "@id": "urn:3dmerge-sMOoqBuW",
"Label": "3dmerge",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc",
"Parameters": {},
"Used": [
- "urn:198003ff-226a-4d5b-8a6c-df3577ccac7e",
- "urn:36fd6847-5445-4ba8-8af6-2cb7f77cdb72"
+ "bids::pb02.$subj.r$run.volreg+tlrc",
+ "bids::pb03.$subj.r$run.blur"
]
},
{
- "@id": "urn:af72a928-98bb-4d48-8b53-202d48c5dc9d",
+ "@id": "urn:3dautoma-EBQGL8Bo",
"Label": "3dAutomask",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:641312e6-512b-4bc0-9ef4-41f1779d8f3c"
+ "bids::pb03.$subj.r$run.blur+tlrc"
]
},
{
- "@id": "urn:f600d98c-6735-4fbf-a6b7-337f4f46426f",
+ "@id": "urn:3dmaskto-j2ye3Qb7",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:b9348b48-3226-4645-a415-3e1a9dd692a3",
+ "@id": "urn:3dresamp-iOYl3J2l",
"Label": "3dresample",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat",
"Parameters": {},
"Used": [
- "urn:0e625d98-8e7d-44c5-ab39-67df63fe0f85",
- "urn:2f3eeebb-8a4d-4310-a504-9a07f32015ac"
+ "bids::full_mask.$subj+tlrc",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:0b2d96d6-373d-48ee-8288-9b6630594059",
+ "@id": "urn:3dmaskto-BJdYm5m3",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj",
"Parameters": {},
"Used": [
- "urn:f5ec68d7-1e7c-4804-9ace-55bf80bd2e7d"
+ "bids::rm.resam.anat+tlrc"
]
},
{
- "@id": "urn:ea85f7a1-dba5-4224-9740-edd22cc70ed2",
+ "@id": "urn:3dabover-xm30TwwO",
"Label": "3dABoverlap",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt",
"Parameters": {},
"Used": [
- "urn:9a31dc1d-5048-4cfd-a60e-a2818eb4ae3a",
- "urn:e800456c-2420-4827-9eed-950861425106"
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee"
]
},
{
- "@id": "urn:539d468e-44bf-4431-95d2-12c1c8d23825",
+ "@id": "urn:3ddot-hr8gK19k",
"Label": "3ddot",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt",
"Parameters": {},
"Used": [
- "urn:9a31dc1d-5048-4cfd-a60e-a2818eb4ae3a",
- "urn:e800456c-2420-4827-9eed-950861425106"
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee"
]
},
{
- "@id": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "@id": "urn:3dresamp-9i4ByXB3",
"Label": "3dresample",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc",
"Parameters": {},
"Used": [
- "urn:0e625d98-8e7d-44c5-ab39-67df63fe0f85",
- "urn:2535402f-72cd-4bfd-89de-7e06823f466c"
+ "bids::/Users/u1591557/abin/TT_N27+tlrc",
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:aae6b639-27bb-41b0-8cff-5b0f280e5ede",
+ "@id": "urn:3dmaskto-eWyRvmXR",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group",
"Parameters": {},
"Used": [
- "urn:a65fd1d4-ef92-4252-b635-1d83cdf8bb6e"
+ "bids::rm.resam.group+tlrc"
]
},
{
- "@id": "urn:60e048f8-0a7c-4600-af2f-7c21f85881e9",
+ "@id": "urn:3dtstat-uIZaJ3D4",
"Label": "3dTstat",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:641312e6-512b-4bc0-9ef4-41f1779d8f3c"
+ "bids::pb03.$subj.r$run.blur+tlrc"
]
},
{
- "@id": "urn:a7caba33-8e03-4df1-99c4-144388c1051a",
+ "@id": "urn:3dcalc-NqtKgN7L",
"Label": "3dcalc",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale",
"Parameters": {},
"Used": [
- "urn:0df2b518-c426-40f8-afdf-be5a39b75735",
- "urn:641312e6-512b-4bc0-9ef4-41f1779d8f3c",
- "urn:cad34a35-b8a1-4d5a-ab7b-f8e6216ecc7b"
+ "bids::mask_epi_extents+tlrc",
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::rm.mean_r$run+tlrc"
]
},
{
- "@id": "urn:d08da7e7-5d5d-4ee6-9a14-4a037e35f9bc",
+ "@id": "urn:1dtoolpy-TH6fQ5VG",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D",
"Parameters": {},
"Used": [
- "urn:77e12367-533f-4f74-b209-4e4c7a234c4e"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:f5913280-0bd6-4a37-8ccd-bebabdaff219",
+ "@id": "urn:1dtoolpy-ymzHf0Gt",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D",
"Parameters": {},
"Used": [
- "urn:77e12367-533f-4f74-b209-4e4c7a234c4e"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:ca73e1d6-96e6-4773-b55c-2e72281f07cd",
+ "@id": "urn:1dtoolpy-JHoBwjXn",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}",
"Parameters": {},
"Used": [
- "urn:77e12367-533f-4f74-b209-4e4c7a234c4e"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:575e8845-cb64-412b-a3bd-03a8ca28dac8",
+ "@id": "urn:3ddeconv-XxUCoLoi",
"Label": "3dDeconvolve",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj",
"Parameters": {},
"Used": [
- "urn:23118e41-8c41-4e4c-9e3e-3c36de30538d"
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD"
]
},
{
- "@id": "urn:539cc786-d245-4e96-896f-106908ebe083",
+ "@id": "urn:1dtoolpy-RC3RWfGm",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt",
"Parameters": {},
"Used": [
- "urn:69086f35-26e1-4854-a167-a3329fe52c8b"
+ "bids::X.xmat.1D"
]
},
{
- "@id": "urn:28408038-4814-4994-93eb-6ec6c5e5217b",
+ "@id": "urn:3dtcat-RC7eDphV",
"Label": "3dTcat",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD",
"Parameters": {},
"Used": [
- "urn:23118e41-8c41-4e4c-9e3e-3c36de30538d"
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD"
]
},
{
- "@id": "urn:919b203e-22f8-4529-8a7c-0fd91cd96f88",
+ "@id": "urn:3dtstat-pa05OoSF",
"Label": "3dTstat",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:c5185326-5632-487d-9bad-382da355c44c"
+ "bids::all_runs.$subj+tlrc%22[$ktrs]%22"
]
},
{
- "@id": "urn:b92c80cd-35e5-4ed5-936a-1ec1f0154003",
+ "@id": "urn:3dtstat-mwrkqknK",
"Label": "3dTstat",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:ef3204e8-e1db-40ac-bf2b-fa7d12275329"
+ "bids::errts.$%7Bsubj%7D+tlrc%22[$ktrs]%22"
]
},
{
- "@id": "urn:bfecc9ae-1ef2-40a5-941a-89224c16e5b8",
+ "@id": "urn:3dcalc-rtR4c6Y4",
"Label": "3dcalc",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj",
"Parameters": {},
"Used": [
- "urn:0e625d98-8e7d-44c5-ab39-67df63fe0f85",
- "urn:67d4bff9-65dc-4160-b555-72d89dbb6005",
- "urn:f0f6e742-8baf-4107-a547-640947bbf8a0"
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.noise.all+tlrc",
+ "bids::rm.signal.all+tlrc"
]
},
{
- "@id": "urn:c88069ae-c297-4695-8d62-70419d3d1401",
+ "@id": "urn:3dtnorm-eRPmyiHR",
"Label": "3dTnorm",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc",
"Parameters": {},
"Used": [
- "urn:ce8afeee-0e8f-46ae-841d-b64bb7a018ab"
+ "bids::errts.$%7Bsubj%7D+tlrc"
]
},
{
- "@id": "urn:d9ee1420-a6df-4810-b8ff-7fee87594d0f",
+ "@id": "urn:3dmaskav-3wIxLLzt",
"Label": "3dmaskave",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D",
"Parameters": {},
- "Used": []
+ "Used": [
+ "bids::full_mask.$subj+tlrc"
+ ]
},
{
- "@id": "urn:da717efa-327f-4ffa-89d2-92f59a19a50e",
+ "@id": "urn:3dtstat-PJSc92bW",
"Label": "3dTstat",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D",
"Parameters": {},
"Used": [
- "urn:19f44ccc-9b2b-4751-bf58-45cb48c9c540"
+ "bids::out.gcor.1D"
]
},
{
- "@id": "urn:9ceeaf33-f1bf-42ea-953f-d6b7d6ae4452",
+ "@id": "urn:3dcalc-55Y24Rhd",
"Label": "3dcalc",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP",
"Parameters": {},
"Used": [
- "urn:0c78731e-ed75-4d97-bcdd-042cb3caa566",
- "urn:529ec39c-bfa2-4d42-9848-0d01fe2a5e55"
+ "bids::gmean.errts.unit.1D",
+ "bids::rm.errts.unit+tlrc"
]
},
{
- "@id": "urn:dc5ca47a-9548-4022-a31b-d6efb95b8ad9",
+ "@id": "urn:3dtstat-NRg8dT0t",
"Label": "3dTstat",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc",
"Parameters": {},
"Used": [
- "urn:cbfe29b0-9234-4b87-82c4-28b72f0df81c"
+ "bids::rm.DP+tlrc"
]
},
{
- "@id": "urn:f6b805b2-5c95-418c-9a87-0998cbca636e",
+ "@id": "urn:1dcat-qhgW9VR8",
"Label": "1dcat",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D",
"Parameters": {},
"Used": [
- "urn:0845cab6-e232-408e-b04b-bf8aefb3c349"
+ "bids::X.nocensor.xmat.1D'[3]'"
]
},
{
- "@id": "urn:616b3978-03f4-4a66-976d-8d3f371faaff",
+ "@id": "urn:1dcat-11fOLdjb",
"Label": "1dcat",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D",
"Parameters": {},
"Used": [
- "urn:8f06309e-a4e5-43e9-8254-ec43f9546520"
+ "bids::X.nocensor.xmat.1D'[4]'"
]
},
{
- "@id": "urn:7f04c2a9-c969-462a-bdb3-6c6fce9f667f",
+ "@id": "urn:3dtstat-S8EVxl05",
"Label": "3dTstat",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"",
"Parameters": {},
"Used": [
- "urn:de89a8da-ba9f-4738-92cf-632ab726d7cf"
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:ef0524f4-7b3a-4ea9-92dd-fb8c21054636",
+ "@id": "urn:1dcat-oVquvz2m",
"Label": "1dcat",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D",
"Parameters": {},
"Used": [
- "urn:de89a8da-ba9f-4738-92cf-632ab726d7cf"
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:b09cb11f-d7f5-44ae-8a83-f2b97277566e",
+ "@id": "urn:3dfwhmx-mYW0j1Yc",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D",
"Parameters": {},
"Used": [
- "urn:0e625d98-8e7d-44c5-ab39-67df63fe0f85"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:81d22aea-101a-4705-a80b-51377716f6ee",
+ "@id": "urn:3dfwhmx-Nasmfxwc",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D",
"Parameters": {},
"Used": [
- "urn:0e625d98-8e7d-44c5-ab39-67df63fe0f85"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:28923e81-c671-4c5b-aee9-5ef197eb5113",
+ "@id": "urn:3dclusts-TCHGcw3f",
"Label": "3dClustSim",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim",
"Parameters": {},
"Used": [
- "urn:0e625d98-8e7d-44c5-ab39-67df63fe0f85"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:7d18474e-1e58-4c36-b89a-e52932fe2015",
+ "@id": "urn:genepire-Q3xYfLZ1",
"Label": "gen_epi_review.py",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD",
"Parameters": {},
"Used": [
- "urn:030ac5c4-f590-4652-abfb-c2415e30f6d0"
+ "bids::pb00.$subj.r*.tcat+orig.HEAD"
]
},
{
- "@id": "urn:538a39c8-734b-4575-9dd3-02305261fdd6",
+ "@id": "urn:genssrev-6S179is9",
"Label": "gen_ss_review_scripts.py",
- "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
+ "AssociatedWith": "urn:afni-CmWIlveU",
"Command": "gen_ss_review_scripts.py -mot_limit 0.3 -exit0",
"Parameters": {
"-mot_limit": "0.3",
@@ -586,22 +589,22 @@
],
"Entities": [
{
- "@id": "urn:a04913d6-f6ed-402b-b110-cf49ce78016a",
+ "@id": "bids::$output_dir",
"Label": "$output_dir",
"AtLocation": "$output_dir",
- "GeneratedBy": "urn:7c11963b-3914-4ac8-a5fc-a935011ad6e9",
+ "GeneratedBy": "urn:makedire-kNRtyUuW",
"digest": {
"sha256": "9fa4c635e6533ddf2fed54295920052818d948c3ffe97bc753bd7336b453f8cb"
}
},
{
- "@id": "urn:f7950dc3-735b-4be3-a659-65d79c66cc27",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:b4169786-f8b4-4875-a20b-b4433c296029"
+ "GeneratedBy": "urn:makedire-PUa4faAM"
},
{
- "@id": "urn:696ebbff-1fbb-4a38-8b97-78f2901d8167",
+ "@id": "bids::afni_cluster_nn2/tone_counting_onset_times.txt",
"Label": "tone_counting_onset_times.txt",
"AtLocation": "./afni_cluster_nn2/tone_counting_onset_times.txt",
"digest": {
@@ -609,7 +612,7 @@
}
},
{
- "@id": "urn:c318e459-6636-41c0-baad-6553d27b820c",
+ "@id": "bids::afni_cluster_nn2/tone_counting_probe_duration.txt",
"Label": "tone_counting_probe_duration.txt",
"AtLocation": "./afni_cluster_nn2/tone_counting_probe_duration.txt",
"digest": {
@@ -617,13 +620,13 @@
}
},
{
- "@id": "urn:d614eace-303b-4e36-aade-7a255d1426f6",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:c09e350e-751b-4ef5-9a0f-48397e2fbe36"
+ "GeneratedBy": "urn:cp-Dp5byids"
},
{
- "@id": "urn:38b5d57d-2ccc-4626-a8f7-de90eae750e4",
+ "@id": "bids::sub-01_T1w.nii.gz",
"Label": "sub-01_T1w.nii.gz",
"AtLocation": "sub-01_T1w.nii.gz",
"digest": {
@@ -631,13 +634,13 @@
}
},
{
- "@id": "urn:36ff0b3c-ddbb-4e94-a6a3-56e2bfd7bb9d",
+ "@id": "bids::$output_dir/sub-01_T1w",
"Label": "sub-01_T1w",
"AtLocation": "$output_dir/sub-01_T1w",
- "GeneratedBy": "urn:35fd6ff1-968d-40ab-aaad-7cf131cab8cf"
+ "GeneratedBy": "urn:3dcopy-ZOmCezCl"
},
{
- "@id": "urn:1c32b8dc-a3cb-4ef0-9c8f-eb21e635e505",
+ "@id": "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Label": "sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"digest": {
@@ -645,13 +648,13 @@
}
},
{
- "@id": "urn:b3b5ba49-7388-4c3d-9bb8-bd7fc681ba7d",
+ "@id": "bids::$output_dir/pb00.$subj.r01.tcat",
"Label": "pb00.$subj.r01.tcat",
"AtLocation": "$output_dir/pb00.$subj.r01.tcat",
- "GeneratedBy": "urn:8633c6ca-e187-4a73-8efa-926d8ca33d59"
+ "GeneratedBy": "urn:3dtcat-SM2Sndnh"
},
{
- "@id": "urn:40286f70-3d33-483c-bfc2-3432761e3c7f",
+ "@id": "bids::pb00.$subj.r$run.tcat+orig",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -659,16 +662,16 @@
}
},
{
- "@id": "urn:bfffb695-6bce-460d-9745-484236201700",
+ "@id": "bids::outcount.r$run.1D",
"Label": "outcount.r$run.1D",
"AtLocation": "outcount.r$run.1D",
- "GeneratedBy": "urn:dc9e4fe0-6cef-4a23-9009-138e1ebb75a7",
+ "GeneratedBy": "urn:3dtoutco-JB2Lmf2M",
"digest": {
"sha256": "63d9f539e5470badc625d557109f68bc4eecbb02ca2667483739d52f95e5d0dd"
}
},
{
- "@id": "urn:b66435cb-d795-4c33-b2e8-eeda2aab4832",
+ "@id": "bids::outcount.r*.1D",
"Label": "outcount.r*.1D",
"AtLocation": "outcount.r*.1D",
"digest": {
@@ -676,25 +679,25 @@
}
},
{
- "@id": "urn:e2b31149-680d-4526-ab18-abcf4b480c88",
+ "@id": "bids::outcount_rall.1D",
"Label": "outcount_rall.1D",
"AtLocation": "outcount_rall.1D",
- "GeneratedBy": "urn:46cf6b03-fe1d-4b26-9925-389bf65d67d2",
+ "GeneratedBy": "urn:cat-w53akqHB",
"digest": {
"sha256": "cb887fd5e4d5e9acb3a24820d0f7a62ed38a5ffb0fdedd373440ac0219fb186a"
}
},
{
- "@id": "urn:47d90f56-3811-4499-b673-1ef07bb242a9",
+ "@id": "bids::pb01.$subj.r$run.tshift",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift",
- "GeneratedBy": "urn:bf189218-ad14-4b5f-ba55-945ce218f2f7",
+ "GeneratedBy": "urn:3dtshift-F2nPSes4",
"digest": {
"sha256": "c6bf01cea8d2eac1d7a866f80b865c6e7d4b4e012dbb63d480ac9a8551162d72"
}
},
{
- "@id": "urn:4d1dd6f4-b4e4-40c8-b95f-5ec76e8bd89b",
+ "@id": "bids::sub-01_T1w+orig",
"Label": "sub-01_T1w",
"AtLocation": "sub-01_T1w+orig",
"digest": {
@@ -702,7 +705,7 @@
}
},
{
- "@id": "urn:b51eb436-940b-4b1b-9e47-f995a797d1cf",
+ "@id": "bids::pb01.$subj.r01.tshift+orig",
"Label": "pb01.$subj.r01.tshift",
"AtLocation": "pb01.$subj.r01.tshift+orig",
"digest": {
@@ -710,16 +713,16 @@
}
},
{
- "@id": "urn:cac6aef4-2dc3-4335-861e-a393fffa2d09",
+ "@id": "bids::_al_junk",
"Label": "_al_junk",
"AtLocation": "_al_junk",
- "GeneratedBy": "urn:77c710e3-0894-4482-b181-3c7abd3a69ce",
+ "GeneratedBy": "urn:alignepi-JN8RFfYg",
"digest": {
"sha256": "bd785a075a4c6446e1e54de9e628913f7f1c814e86b69a9fbfe933209e6d37b5"
}
},
{
- "@id": "urn:0636ee2d-a3a6-4f30-87fa-789e47259146",
+ "@id": "bids::TT_N27+tlrc",
"Label": "TT_N27",
"AtLocation": "TT_N27+tlrc",
"digest": {
@@ -727,7 +730,7 @@
}
},
{
- "@id": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
+ "@id": "bids::sub-01_T1w_ns+orig",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+orig",
"digest": {
@@ -735,7 +738,7 @@
}
},
{
- "@id": "urn:5bdbbc48-a5da-48e9-8fc4-7ad28e5afa5c",
+ "@id": "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc::WARP_DATA",
"digest": {
@@ -743,16 +746,16 @@
}
},
{
- "@id": "urn:550cc2b5-46c9-4929-b5ff-1fe49fb4ccba",
+ "@id": "bids::warp.anat.Xat.1D",
"Label": "warp.anat.Xat.1D",
"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:39308342-7914-48eb-91d5-9ea9173ec4b1",
+ "GeneratedBy": "urn:catmatve-7fuoAhEa",
"digest": {
"sha256": "800633fb5b4e9be64078bc181c4d5510ffb73fc5cccaf364c7fb6a294aa06728"
}
},
{
- "@id": "urn:e44cdba8-d786-497b-8d2c-c22c4c1c5389",
+ "@id": "bids::pb01.$subj.r$run.tshift+orig",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift+orig",
"digest": {
@@ -760,34 +763,34 @@
}
},
{
- "@id": "urn:4b85fce0-fdf4-41f3-a881-081d26c45076",
+ "@id": "bids::mat.r$run.vr.aff12.1D",
"Label": "mat.r$run.vr.aff12.1D",
"AtLocation": "mat.r$run.vr.aff12.1D",
- "GeneratedBy": "urn:0fbfcad6-aac6-4a11-b707-c6889495087a",
+ "GeneratedBy": "urn:3dvolreg-aQqyS7dV",
"digest": {
"sha256": "2e6e6c2ce8089cfa3c6e11dc72fca0cc8497f7a55faae2ced402de4867466c91"
}
},
{
- "@id": "urn:8c989260-b8e4-4730-84f6-c9f317b5e801",
+ "@id": "bids::rm.epi.all1",
"Label": "rm.epi.all1",
"AtLocation": "rm.epi.all1",
- "GeneratedBy": "urn:af018c20-ff76-4d07-94f9-c469f5622002",
+ "GeneratedBy": "urn:3dcalc-qreOQ2px",
"digest": {
"sha256": "1023e3c16cecdbdc73ea456bcf33c2e5bb4f1e07094b73d29022d651e5fa3f85"
}
},
{
- "@id": "urn:877884bd-f37b-49d8-8854-b945da56459c",
+ "@id": "bids::mat.r$run.warp.aff12.1D",
"Label": "mat.r$run.warp.aff12.1D",
"AtLocation": "mat.r$run.warp.aff12.1D",
- "GeneratedBy": "urn:7b92747e-b90b-492d-8e7e-c99795accc90",
+ "GeneratedBy": "urn:catmatve-wpNIh7gg",
"digest": {
"sha256": "7c536b6f582a067c718f9e5ea2566cb535c73b43b4e15116c4c46045734d6eee"
}
},
{
- "@id": "urn:2f3eeebb-8a4d-4310-a504-9a07f32015ac",
+ "@id": "bids::sub-01_T1w_ns+tlrc",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc",
"digest": {
@@ -795,16 +798,16 @@
}
},
{
- "@id": "urn:7e6793d1-0414-4d9b-af8c-a9dd3f28798d",
+ "@id": "bids::rm.epi.nomask.r$run",
"Label": "rm.epi.nomask.r$run",
"AtLocation": "rm.epi.nomask.r$run",
- "GeneratedBy": "urn:4b174d0f-45f3-4ea4-bcf1-99879d212ca4",
+ "GeneratedBy": "urn:3dalline-vUSZLTiK",
"digest": {
"sha256": "03d6cba0426c5545e350e6b63a19b0e46f8dfa2223fd08691753e8914a479e36"
}
},
{
- "@id": "urn:7cbbbda6-46f6-488b-a056-0d6322750ac8",
+ "@id": "bids::rm.epi.all1+orig",
"Label": "rm.epi.all1",
"AtLocation": "rm.epi.all1+orig",
"digest": {
@@ -812,16 +815,16 @@
}
},
{
- "@id": "urn:36ad2408-0778-45a6-875d-12bf7277cac0",
+ "@id": "bids::rm.epi.1.r$run",
"Label": "rm.epi.1.r$run",
"AtLocation": "rm.epi.1.r$run",
- "GeneratedBy": "urn:3b4003ca-4008-441b-a571-22ee1c9d81a5",
+ "GeneratedBy": "urn:3dalline-VXjfo3UX",
"digest": {
"sha256": "b1b9128c103ea246625db1a35e6f474a221ca6c1105a30df38aefdc4d5421e84"
}
},
{
- "@id": "urn:415d2eff-a2e6-4ce0-b03b-4590dc0b938f",
+ "@id": "bids::rm.epi.1.r$run+tlrc",
"Label": "rm.epi.1.r$run",
"AtLocation": "rm.epi.1.r$run+tlrc",
"digest": {
@@ -829,16 +832,16 @@
}
},
{
- "@id": "urn:dbed9a86-280e-4ab0-a362-f8eac8382da6",
+ "@id": "bids::rm.epi.min.r$run",
"Label": "rm.epi.min.r$run",
"AtLocation": "rm.epi.min.r$run",
- "GeneratedBy": "urn:74748c41-4b12-4d11-8e2e-bad321a8500f",
+ "GeneratedBy": "urn:3dtstat-6bAohDhA",
"digest": {
"sha256": "b4418a96ddbbf25afdfd01ed0506ddebe009011ba18aed10137f994260fd1a66"
}
},
{
- "@id": "urn:7aad8cde-f615-412f-8471-4c996f88ed9d",
+ "@id": "bids::dfile.r*.1D",
"Label": "dfile.r*.1D",
"AtLocation": "dfile.r*.1D",
"digest": {
@@ -846,16 +849,16 @@
}
},
{
- "@id": "urn:77e12367-533f-4f74-b209-4e4c7a234c4e",
+ "@id": "bids::dfile_rall.1D",
"Label": "dfile_rall.1D",
"AtLocation": "dfile_rall.1D",
- "GeneratedBy": "urn:98899c4a-d46c-4fc4-8aa4-7e38f7fb0855",
+ "GeneratedBy": "urn:cat-1rmVDUgs",
"digest": {
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}
},
{
- "@id": "urn:71b058b4-2de9-4859-84b4-b860b34fd6ba",
+ "@id": "bids::rm.epi.min.r01+tlrc",
"Label": "rm.epi.min.r01",
"AtLocation": "rm.epi.min.r01+tlrc",
"digest": {
@@ -863,16 +866,16 @@
}
},
{
- "@id": "urn:9e9513d0-a33e-46aa-946c-56d1ed1d2b3c",
+ "@id": "bids::mask_epi_extents",
"Label": "mask_epi_extents",
"AtLocation": "mask_epi_extents",
- "GeneratedBy": "urn:e4884732-273d-40a3-ba49-baf3b9d8c03f",
+ "GeneratedBy": "urn:3dcopy-npAyTgUe",
"digest": {
"sha256": "a69dd71209516ec24e2b3364072ed54adff16619459b1c369866210ec642e987"
}
},
{
- "@id": "urn:4cf18a5d-9510-4dcf-85c4-97b4ab57855f",
+ "@id": "bids::rm.epi.nomask.r$run+tlrc",
"Label": "rm.epi.nomask.r$run",
"AtLocation": "rm.epi.nomask.r$run+tlrc",
"digest": {
@@ -880,7 +883,7 @@
}
},
{
- "@id": "urn:0df2b518-c426-40f8-afdf-be5a39b75735",
+ "@id": "bids::mask_epi_extents+tlrc",
"Label": "mask_epi_extents",
"AtLocation": "mask_epi_extents+tlrc",
"digest": {
@@ -888,34 +891,42 @@
}
},
{
- "@id": "urn:a76eb703-72e3-4454-ad06-13b0cfa15116",
+ "@id": "bids::pb02.$subj.r$run.volreg",
"Label": "pb02.$subj.r$run.volreg",
"AtLocation": "pb02.$subj.r$run.volreg",
- "GeneratedBy": "urn:b6d01152-e3cd-4131-83f8-5146de72e061",
+ "GeneratedBy": "urn:3dcalc-WXiyZGcZ",
"digest": {
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}
},
{
- "@id": "urn:bee9590c-02d3-4103-9e35-7a63dae85dc7",
+ "@id": "bids::anat_final.$subj",
"Label": "anat_final.$subj",
"AtLocation": "anat_final.$subj",
- "GeneratedBy": "urn:083d8661-48cc-477b-8d5e-fa8106d0bfbc",
+ "GeneratedBy": "urn:3dcopy-DESJSJWt",
"digest": {
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}
},
{
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+ "@id": "bids::anat_final.$subj+tlrc",
+ "Label": "anat_final.$subj",
+ "AtLocation": "anat_final.$subj+tlrc",
+ "digest": {
+ "sha256": "94eb1853614cc085b22772c011f119f6a0ad7ec06cba2850587762e7f1a6eae6"
+ }
+ },
+ {
+ "@id": "bids::anat_w_skull_warped",
"Label": "anat_w_skull_warped",
"AtLocation": "anat_w_skull_warped",
- "GeneratedBy": "urn:d8954007-4612-40b0-8ded-1060a7c2d47c",
+ "GeneratedBy": "urn:3dalline-ukfO7Wly",
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},
{
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+ "@id": "bids::pb03.$subj.r$run.blur",
"Label": "pb03.$subj.r$run.blur",
"AtLocation": "pb03.$subj.r$run.blur",
"digest": {
@@ -923,7 +934,7 @@
}
},
{
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+ "@id": "bids::pb02.$subj.r$run.volreg+tlrc",
"Label": "pb02.$subj.r$run.volreg",
"AtLocation": "pb02.$subj.r$run.volreg+tlrc",
"digest": {
@@ -931,7 +942,7 @@
}
},
{
- "@id": "urn:641312e6-512b-4bc0-9ef4-41f1779d8f3c",
+ "@id": "bids::pb03.$subj.r$run.blur+tlrc",
"Label": "pb03.$subj.r$run.blur",
"AtLocation": "pb03.$subj.r$run.blur+tlrc",
"digest": {
@@ -939,25 +950,25 @@
}
},
{
- "@id": "urn:a7caa9f1-d947-4eba-957b-ab55a6acba0c",
+ "@id": "bids::rm.mask_r$run",
"Label": "rm.mask_r$run",
"AtLocation": "rm.mask_r$run",
- "GeneratedBy": "urn:af72a928-98bb-4d48-8b53-202d48c5dc9d",
+ "GeneratedBy": "urn:3dautoma-EBQGL8Bo",
"digest": {
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}
},
{
- "@id": "urn:9b7f5f79-f24a-4919-9491-b51f9162268c",
+ "@id": "bids::full_mask.$subj",
"Label": "full_mask.$subj",
"AtLocation": "full_mask.$subj",
- "GeneratedBy": "urn:f600d98c-6735-4fbf-a6b7-337f4f46426f",
+ "GeneratedBy": "urn:3dmaskto-j2ye3Qb7",
"digest": {
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@@ -999,7 +1010,7 @@
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@@ -1015,16 +1026,16 @@
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@@ -1093,25 +1104,25 @@
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@@ -1119,16 +1130,16 @@
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@@ -1136,16 +1147,16 @@
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@@ -1153,7 +1164,7 @@
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@@ -1161,16 +1172,16 @@
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{
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@@ -1178,25 +1189,25 @@
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@@ -1221,16 +1232,16 @@
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@@ -1255,16 +1266,16 @@
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@@ -1272,16 +1283,16 @@
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- "GeneratedBy": "urn:616b3978-03f4-4a66-976d-8d3f371faaff",
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{
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@@ -1289,52 +1300,52 @@
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{
- "@id": "urn:001e2ebb-0f2e-4dbe-a80b-ad351aa0bcbe",
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- "GeneratedBy": "urn:ef0524f4-7b3a-4ea9-92dd-fb8c21054636",
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{
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- "GeneratedBy": "urn:b09cb11f-d7f5-44ae-8a83-f2b97277566e",
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- "GeneratedBy": "urn:81d22aea-101a-4705-a80b-51377716f6ee",
+ "GeneratedBy": "urn:3dfwhmx-Nasmfxwc",
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{
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+ "@id": "bids::ClustSim",
"Label": "ClustSim",
"AtLocation": "ClustSim",
- "GeneratedBy": "urn:28923e81-c671-4c5b-aee9-5ef197eb5113",
+ "GeneratedBy": "urn:3dclusts-TCHGcw3f",
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{
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@@ -1342,10 +1353,10 @@
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{
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diff --git a/examples/from_parsers/afni/afni_clustconn_18_proc.png b/examples/from_parsers/afni/afni_clustconn_18_proc.png
index 2b15eadd6..e41fdd48f 100644
Binary files a/examples/from_parsers/afni/afni_clustconn_18_proc.png and b/examples/from_parsers/afni/afni_clustconn_18_proc.png differ
diff --git a/examples/from_parsers/afni/afni_clustconn_18_proc_block.jsonld b/examples/from_parsers/afni/afni_clustconn_18_proc_block.jsonld
index 91e41d5d6..de82cb464 100644
--- a/examples/from_parsers/afni/afni_clustconn_18_proc_block.jsonld
+++ b/examples/from_parsers/afni/afni_clustconn_18_proc_block.jsonld
@@ -4,187 +4,189 @@
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{
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- "RRID": "RRID:SCR_007037",
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"Command": "mkdir $output_dir; mkdir $output_dir/stimuli; cp ./afni_cluster_nn2/tone_counting_onset_times.txt ./afni_cluster_nn2/tone_counting_probe_duration.txt $output_dir/stimuli; 3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w; ",
"Used": [
- "urn:13f3c9b9-1449-4f53-8294-6f8a6b77b3d3",
- "urn:c12def47-7729-4f52-94a9-db975e35d749",
- "urn:853061ad-42a3-405c-8ea4-4cdf534495d6"
+ "bids::afni_cluster_nn2/tone_counting_onset_times.txt",
+ "bids::afni_cluster_nn2/tone_counting_probe_duration.txt",
+ "bids::sub-01_T1w.nii.gz"
]
},
{
- "@id": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "@id": "urn:autobloc-Zf7w9JEy",
"Label": "auto block: tcat",
- "AssociatedWith": "urn:7301e5d4-ee74-4643-b174-04dac2bc17bd",
+ "AssociatedWith": "urn:afni-z9kTdI7Z",
"Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ",
"Used": [
- "urn:3e06e6a4-7e79-4404-a663-29c90662e70d"
+ "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'"
]
},
{
- "@id": "urn:82fea590-f798-46fe-a78f-7601887e0245",
+ "@id": "urn:autobloc-j56ceVlC",
"Label": "auto block: outcount",
- "AssociatedWith": "urn:7301e5d4-ee74-4643-b174-04dac2bc17bd",
+ "AssociatedWith": "urn:afni-z9kTdI7Z",
"Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ",
"Used": [
- "urn:b0246264-c0ee-4a84-afb9-bff6a8ca208c",
- "urn:2b88e9cd-f0ae-44d5-b8f5-aac0f7d43b5b"
+ "bids::pb00.$subj.r$run.tcat+orig",
+ "bids::outcount.r*.1D"
]
},
{
- "@id": "urn:bef9ed4d-8750-42d6-bf36-1a2484eca02d",
+ "@id": "urn:tshift-5OatDA2b",
"Label": "tshift",
- "AssociatedWith": "urn:7301e5d4-ee74-4643-b174-04dac2bc17bd",
+ "AssociatedWith": "urn:afni-z9kTdI7Z",
"Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ",
"Used": [
- "urn:b0246264-c0ee-4a84-afb9-bff6a8ca208c"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:116e0cb2-5547-433d-9b0a-cd59c277c6b8",
+ "@id": "urn:align-BGiZ7wtY",
"Label": "align",
- "AssociatedWith": "urn:7301e5d4-ee74-4643-b174-04dac2bc17bd",
+ "AssociatedWith": "urn:afni-z9kTdI7Z",
"Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ",
"Used": [
- "urn:22db26bd-486f-4dc5-980d-f943143a3734",
- "urn:c48eb7b9-b8c4-4983-b55e-e69acedcf06c"
+ "bids::pb01.$subj.r01.tshift+orig",
+ "bids::sub-01_T1w+orig"
]
},
{
- "@id": "urn:6d1d8579-6a61-4011-b989-95c24e68e879",
+ "@id": "urn:tlrc-1wOwYQxO",
"Label": "tlrc",
- "AssociatedWith": "urn:7301e5d4-ee74-4643-b174-04dac2bc17bd",
+ "AssociatedWith": "urn:afni-z9kTdI7Z",
"Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ",
"Used": [
- "urn:3c565e3e-f7b2-4c8c-82c7-06c46a42c8a9",
- "urn:4324d607-6f82-4b26-9b3f-be7b6646d02c",
- "urn:da251042-e0c9-4a5d-aa0f-65586a9afef2"
+ "bids::TT_N27+tlrc",
+ "bids::sub-01_T1w_ns+orig",
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:0ce32f62-4fc0-42c0-893b-b03f2e4ae488",
+ "@id": "urn:volreg-i4b2s3ls",
"Label": "volreg",
- "AssociatedWith": "urn:7301e5d4-ee74-4643-b174-04dac2bc17bd",
+ "AssociatedWith": "urn:afni-z9kTdI7Z",
"Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig; 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1; cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D; 3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run; 3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run; 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc; cat dfile.r*.1D > dfile_rall.1D; 3dcopy rm.epi.min.r01+tlrc mask_epi_extents; 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg; 3dcopy sub-01_T1w_ns+tlrc anat_final.$subj; 3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped; ",
"Used": [
- "urn:2f72377d-7460-4e27-902b-a8fd279f404c",
- "urn:2f72377d-7460-4e27-902b-a8fd279f404c",
- "urn:da251042-e0c9-4a5d-aa0f-65586a9afef2",
- "urn:2f72377d-7460-4e27-902b-a8fd279f404c",
- "urn:7923f169-1149-48d3-ab90-aa7b13f7438f",
- "urn:20bde1e7-dd88-4056-81dd-b02a9243bc96",
- "urn:7923f169-1149-48d3-ab90-aa7b13f7438f",
- "urn:fb111b45-6a50-416e-9ebc-47853b4ae1e8",
- "urn:4b53fd78-baf2-4ad9-b03b-f6950080ffc8",
- "urn:1d532a3f-d2f2-4331-8a39-1f17fa9cb5c0",
- "urn:42b186e8-d358-4693-9d8c-cf46840ea4e4",
- "urn:a5ad4a2f-8b9e-420f-a5de-b26f57462d20",
- "urn:7923f169-1149-48d3-ab90-aa7b13f7438f",
- "urn:7e86c053-51ee-4584-8815-4172d57aba3b"
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.epi.all1+orig",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.epi.1.r$run+tlrc",
+ "bids::dfile.r*.1D",
+ "bids::rm.epi.min.r01+tlrc",
+ "bids::mask_epi_extents+tlrc",
+ "bids::rm.epi.nomask.r$run+tlrc",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::anat_final.$subj+tlrc",
+ "bids::warp.anat.Xat.1D"
]
},
{
- "@id": "urn:fee3ecea-2b2c-433e-bb26-e3e78eea72fd",
+ "@id": "urn:blur-4wgzuIvB",
"Label": "blur",
- "AssociatedWith": "urn:7301e5d4-ee74-4643-b174-04dac2bc17bd",
+ "AssociatedWith": "urn:afni-z9kTdI7Z",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc; ",
"Used": [
- "urn:62e3812e-a3e8-4836-8119-a98496a70101",
- "urn:7921758c-6274-495a-9ddb-602ba1b1b33d"
+ "bids::pb02.$subj.r$run.volreg+tlrc",
+ "bids::pb03.$subj.r$run.blur"
]
},
{
- "@id": "urn:732a3588-6036-4290-9585-5aac582dd89e",
+ "@id": "urn:mask-0nTKbiWT",
"Label": "mask",
- "AssociatedWith": "urn:7301e5d4-ee74-4643-b174-04dac2bc17bd",
+ "AssociatedWith": "urn:afni-z9kTdI7Z",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc; 3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj; 3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj; 3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt; 3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt; 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group; ",
"Used": [
- "urn:26741b71-6f61-4097-8aac-3b7a6f95efa2",
- "urn:7923f169-1149-48d3-ab90-aa7b13f7438f",
- "urn:ae14ed40-d28f-491f-ad7f-f9364a2daeca",
- "urn:c5da5c16-852c-4a75-a6e6-f70fcc9bc766",
- "urn:cb038b70-f5e5-4619-a661-3b6f816e4043",
- "urn:f63bd3cb-5e25-43e7-9b62-0a6b714b9fd0",
- "urn:cb038b70-f5e5-4619-a661-3b6f816e4043",
- "urn:f63bd3cb-5e25-43e7-9b62-0a6b714b9fd0",
- "urn:ae14ed40-d28f-491f-ad7f-f9364a2daeca",
- "urn:c3457a35-c5f9-45de-931c-89a71bb169f0",
- "urn:32e9944d-72b1-4e01-8c59-14a8ffb09a0f"
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.resam.anat+tlrc",
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee",
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee",
+ "bids::/Users/u1591557/abin/TT_N27+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.resam.group+tlrc"
]
},
{
- "@id": "urn:5c92426e-803d-4eb0-81de-03f890ca7386",
+ "@id": "urn:scale-ZalM8U1e",
"Label": "scale",
- "AssociatedWith": "urn:7301e5d4-ee74-4643-b174-04dac2bc17bd",
+ "AssociatedWith": "urn:afni-z9kTdI7Z",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc; 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale; ",
"Used": [
- "urn:26741b71-6f61-4097-8aac-3b7a6f95efa2",
- "urn:26741b71-6f61-4097-8aac-3b7a6f95efa2",
- "urn:45516259-81b3-4845-9a96-dcc09711ebd1",
- "urn:a5ad4a2f-8b9e-420f-a5de-b26f57462d20"
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::mask_epi_extents+tlrc",
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::rm.mean_r$run+tlrc"
]
},
{
- "@id": "urn:42f5e934-e5d2-4707-ad09-4dd6a6b280fc",
+ "@id": "urn:regress-I0fV2FI8",
"Label": "regress",
- "AssociatedWith": "urn:7301e5d4-ee74-4643-b174-04dac2bc17bd",
+ "AssociatedWith": "urn:afni-z9kTdI7Z",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}; 3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj; 1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt; 3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD; 3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"; 3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"; 3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj; 3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc; 3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D; 3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D; 3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP; 3dTstat -sum -prefix corr_brain rm.DP+tlrc; 1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D; 1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D; 3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"; 1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D; ",
"Used": [
- "urn:e9d84da7-d15b-4a7a-8c90-240b2a88a4fb",
- "urn:e9d84da7-d15b-4a7a-8c90-240b2a88a4fb",
- "urn:e9d84da7-d15b-4a7a-8c90-240b2a88a4fb",
- "urn:bb9634f9-be32-4008-9ba3-ffea4e168cba",
- "urn:bb9634f9-be32-4008-9ba3-ffea4e168cba",
- "urn:1a04bdf8-5441-4f18-a241-1b3ecf3a0a09",
- "urn:1f3989e8-ea60-4cbc-9444-3a3b6e170b93",
- "urn:ae14ed40-d28f-491f-ad7f-f9364a2daeca",
- "urn:d8acd265-715c-4787-ac99-ecc8ed9c1a30",
- "urn:dff39876-ad27-4e98-8d9a-30be0fc479ef",
- "urn:a49716a7-0b9c-4f99-8d39-e86d9e708e16",
- "urn:ab1d786e-77c3-4a9b-8038-0202a1531374",
- "urn:c0623cbc-3022-46fa-a837-1ac4e08f23d6",
- "urn:7b9573eb-6f4b-428c-a624-a39ae72d7ba3",
- "urn:00bc09c4-e285-462f-b5df-8454180948a3",
- "urn:7c7bf2d5-e7ab-4f62-aa37-76d4b7cad69d",
- "urn:27b58ae0-82eb-423d-83c1-b8b2181da88d",
- "urn:27b58ae0-82eb-423d-83c1-b8b2181da88d"
+ "bids::dfile_rall.1D",
+ "bids::dfile_rall.1D",
+ "bids::dfile_rall.1D",
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD",
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD",
+ "bids::all_runs.$subj+tlrc%22[$ktrs]%22",
+ "bids::errts.$%7Bsubj%7D+tlrc%22[$ktrs]%22",
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.noise.all+tlrc",
+ "bids::rm.signal.all+tlrc",
+ "bids::errts.$%7Bsubj%7D+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::out.gcor.1D",
+ "bids::rm.errts.unit+tlrc",
+ "bids::rm.DP+tlrc",
+ "bids::X.nocensor.xmat.1D'[3]'",
+ "bids::X.nocensor.xmat.1D'[4]'",
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22",
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:0f0d8d27-624e-4177-a4ce-0e4655ee2e68",
+ "@id": "urn:bluresti-9I25pzvg",
"Label": "blur estimation",
- "AssociatedWith": "urn:7301e5d4-ee74-4643-b174-04dac2bc17bd",
+ "AssociatedWith": "urn:afni-z9kTdI7Z",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D; 3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D; 3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim; ",
"Used": [
- "urn:ae14ed40-d28f-491f-ad7f-f9364a2daeca",
- "urn:ae14ed40-d28f-491f-ad7f-f9364a2daeca",
- "urn:ae14ed40-d28f-491f-ad7f-f9364a2daeca"
+ "bids::full_mask.$subj+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:2a3417b9-7227-46c9-a91d-42c5f271dc5f",
+ "@id": "urn:autobloc-oFzbi7jF",
"Label": "auto block: generate review scripts",
- "AssociatedWith": "urn:7301e5d4-ee74-4643-b174-04dac2bc17bd",
+ "AssociatedWith": "urn:afni-z9kTdI7Z",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD; gen_ss_review_scripts.py -mot_limit 0.3 -exit0; ",
"Used": [
- "urn:753c9b01-3b08-43d7-9a2a-55787d643953"
+ "bids::pb00.$subj.r*.tcat+orig.HEAD"
]
}
],
"Entities": [
{
- "@id": "urn:13f3c9b9-1449-4f53-8294-6f8a6b77b3d3",
+ "@id": "bids::afni_cluster_nn2/tone_counting_onset_times.txt",
"Label": "tone_counting_onset_times.txt",
"AtLocation": "./afni_cluster_nn2/tone_counting_onset_times.txt",
"digest": {
@@ -192,7 +194,7 @@
}
},
{
- "@id": "urn:c12def47-7729-4f52-94a9-db975e35d749",
+ "@id": "bids::afni_cluster_nn2/tone_counting_probe_duration.txt",
"Label": "tone_counting_probe_duration.txt",
"AtLocation": "./afni_cluster_nn2/tone_counting_probe_duration.txt",
"digest": {
@@ -200,7 +202,7 @@
}
},
{
- "@id": "urn:853061ad-42a3-405c-8ea4-4cdf534495d6",
+ "@id": "bids::sub-01_T1w.nii.gz",
"Label": "sub-01_T1w.nii.gz",
"AtLocation": "sub-01_T1w.nii.gz",
"digest": {
@@ -208,34 +210,34 @@
}
},
{
- "@id": "urn:00e10563-13fe-4043-bb63-2475389e3ca9",
+ "@id": "bids::$output_dir",
"Label": "$output_dir",
"AtLocation": "$output_dir",
- "GeneratedBy": "urn:c55b4e40-acb8-4cb9-a44f-a885c97f4ea7",
+ "GeneratedBy": "urn:autobloc-lncqLtf4",
"digest": {
"sha256": "9fa4c635e6533ddf2fed54295920052818d948c3ffe97bc753bd7336b453f8cb"
}
},
{
- "@id": "urn:5150ea63-253e-4632-8e1c-e6d6f66d3f9b",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:c55b4e40-acb8-4cb9-a44f-a885c97f4ea7"
+ "GeneratedBy": "urn:autobloc-lncqLtf4"
},
{
- "@id": "urn:38704d9b-61c8-49cc-9b71-84de095523bf",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:c55b4e40-acb8-4cb9-a44f-a885c97f4ea7"
+ "GeneratedBy": "urn:autobloc-lncqLtf4"
},
{
- "@id": "urn:b97ce5dd-8d4e-45b6-8bfb-c148e2c4eee5",
+ "@id": "bids::$output_dir/sub-01_T1w",
"Label": "sub-01_T1w",
"AtLocation": "$output_dir/sub-01_T1w",
- "GeneratedBy": "urn:c55b4e40-acb8-4cb9-a44f-a885c97f4ea7"
+ "GeneratedBy": "urn:autobloc-lncqLtf4"
},
{
- "@id": "urn:3e06e6a4-7e79-4404-a663-29c90662e70d",
+ "@id": "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Label": "sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"digest": {
@@ -243,13 +245,13 @@
}
},
{
- "@id": "urn:811288a2-49a2-4a25-a88d-b9428fcb266e",
+ "@id": "bids::$output_dir/pb00.$subj.r01.tcat",
"Label": "pb00.$subj.r01.tcat",
"AtLocation": "$output_dir/pb00.$subj.r01.tcat",
- "GeneratedBy": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c"
+ "GeneratedBy": "urn:autobloc-Zf7w9JEy"
},
{
- "@id": "urn:b0246264-c0ee-4a84-afb9-bff6a8ca208c",
+ "@id": "bids::pb00.$subj.r$run.tcat+orig",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -257,7 +259,7 @@
}
},
{
- "@id": "urn:2b88e9cd-f0ae-44d5-b8f5-aac0f7d43b5b",
+ "@id": "bids::outcount.r*.1D",
"Label": "outcount.r*.1D",
"AtLocation": "outcount.r*.1D",
"digest": {
@@ -265,25 +267,25 @@
}
},
{
- "@id": "urn:f5d7521b-b160-4096-8ba1-a7560ca00126",
+ "@id": "bids::outcount.r$run.1D",
"Label": "outcount.r$run.1D",
"AtLocation": "outcount.r$run.1D",
- "GeneratedBy": "urn:82fea590-f798-46fe-a78f-7601887e0245",
+ "GeneratedBy": "urn:autobloc-j56ceVlC",
"digest": {
"sha256": "63d9f539e5470badc625d557109f68bc4eecbb02ca2667483739d52f95e5d0dd"
}
},
{
- "@id": "urn:2d3597e6-3bc3-4588-ad30-2b66d5d8c409",
+ "@id": "bids::outcount_rall.1D",
"Label": "outcount_rall.1D",
"AtLocation": "outcount_rall.1D",
- "GeneratedBy": "urn:82fea590-f798-46fe-a78f-7601887e0245",
+ "GeneratedBy": "urn:autobloc-j56ceVlC",
"digest": {
"sha256": "cb887fd5e4d5e9acb3a24820d0f7a62ed38a5ffb0fdedd373440ac0219fb186a"
}
},
{
- "@id": "urn:b0246264-c0ee-4a84-afb9-bff6a8ca208c",
+ "@id": "bids::pb00.$subj.r$run.tcat+orig",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -291,16 +293,16 @@
}
},
{
- "@id": "urn:6a10282f-6a38-4a4e-b8d8-91e7875c4262",
+ "@id": "bids::pb01.$subj.r$run.tshift",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift",
- "GeneratedBy": "urn:bef9ed4d-8750-42d6-bf36-1a2484eca02d",
+ "GeneratedBy": "urn:tshift-5OatDA2b",
"digest": {
"sha256": "c6bf01cea8d2eac1d7a866f80b865c6e7d4b4e012dbb63d480ac9a8551162d72"
}
},
{
- "@id": "urn:c48eb7b9-b8c4-4983-b55e-e69acedcf06c",
+ "@id": "bids::sub-01_T1w+orig",
"Label": "sub-01_T1w",
"AtLocation": "sub-01_T1w+orig",
"digest": {
@@ -308,7 +310,7 @@
}
},
{
- "@id": "urn:22db26bd-486f-4dc5-980d-f943143a3734",
+ "@id": "bids::pb01.$subj.r01.tshift+orig",
"Label": "pb01.$subj.r01.tshift",
"AtLocation": "pb01.$subj.r01.tshift+orig",
"digest": {
@@ -316,16 +318,16 @@
}
},
{
- "@id": "urn:abb994eb-f289-446f-b568-e9ebdb638e9d",
+ "@id": "bids::_al_junk",
"Label": "_al_junk",
"AtLocation": "_al_junk",
- "GeneratedBy": "urn:116e0cb2-5547-433d-9b0a-cd59c277c6b8",
+ "GeneratedBy": "urn:align-BGiZ7wtY",
"digest": {
"sha256": "bd785a075a4c6446e1e54de9e628913f7f1c814e86b69a9fbfe933209e6d37b5"
}
},
{
- "@id": "urn:3c565e3e-f7b2-4c8c-82c7-06c46a42c8a9",
+ "@id": "bids::TT_N27+tlrc",
"Label": "TT_N27",
"AtLocation": "TT_N27+tlrc",
"digest": {
@@ -333,7 +335,7 @@
}
},
{
- "@id": "urn:4324d607-6f82-4b26-9b3f-be7b6646d02c",
+ "@id": "bids::sub-01_T1w_ns+orig",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+orig",
"digest": {
@@ -341,7 +343,7 @@
}
},
{
- "@id": "urn:da251042-e0c9-4a5d-aa0f-65586a9afef2",
+ "@id": "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc::WARP_DATA",
"digest": {
@@ -349,16 +351,16 @@
}
},
{
- "@id": "urn:7e86c053-51ee-4584-8815-4172d57aba3b",
+ "@id": "bids::warp.anat.Xat.1D",
"Label": "warp.anat.Xat.1D",
"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:6d1d8579-6a61-4011-b989-95c24e68e879",
+ "GeneratedBy": "urn:tlrc-1wOwYQxO",
"digest": {
"sha256": "800633fb5b4e9be64078bc181c4d5510ffb73fc5cccaf364c7fb6a294aa06728"
}
},
{
- "@id": "urn:da251042-e0c9-4a5d-aa0f-65586a9afef2",
+ "@id": "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc::WARP_DATA",
"digest": {
@@ -366,16 +368,16 @@
}
},
{
- "@id": "urn:7e86c053-51ee-4584-8815-4172d57aba3b",
+ "@id": "bids::warp.anat.Xat.1D",
"Label": "warp.anat.Xat.1D",
"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:6d1d8579-6a61-4011-b989-95c24e68e879",
+ "GeneratedBy": "urn:tlrc-1wOwYQxO",
"digest": {
"sha256": "800633fb5b4e9be64078bc181c4d5510ffb73fc5cccaf364c7fb6a294aa06728"
}
},
{
- "@id": "urn:2f72377d-7460-4e27-902b-a8fd279f404c",
+ "@id": "bids::pb01.$subj.r$run.tshift+orig",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift+orig",
"digest": {
@@ -383,7 +385,7 @@
}
},
{
- "@id": "urn:7923f169-1149-48d3-ab90-aa7b13f7438f",
+ "@id": "bids::sub-01_T1w_ns+tlrc",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc",
"digest": {
@@ -391,7 +393,7 @@
}
},
{
- "@id": "urn:20bde1e7-dd88-4056-81dd-b02a9243bc96",
+ "@id": "bids::rm.epi.all1+orig",
"Label": "rm.epi.all1",
"AtLocation": "rm.epi.all1+orig",
"digest": {
@@ -399,7 +401,7 @@
}
},
{
- "@id": "urn:fb111b45-6a50-416e-9ebc-47853b4ae1e8",
+ "@id": "bids::rm.epi.1.r$run+tlrc",
"Label": "rm.epi.1.r$run",
"AtLocation": "rm.epi.1.r$run+tlrc",
"digest": {
@@ -407,7 +409,7 @@
}
},
{
- "@id": "urn:4b53fd78-baf2-4ad9-b03b-f6950080ffc8",
+ "@id": "bids::dfile.r*.1D",
"Label": "dfile.r*.1D",
"AtLocation": "dfile.r*.1D",
"digest": {
@@ -415,7 +417,7 @@
}
},
{
- "@id": "urn:1d532a3f-d2f2-4331-8a39-1f17fa9cb5c0",
+ "@id": "bids::rm.epi.min.r01+tlrc",
"Label": "rm.epi.min.r01",
"AtLocation": "rm.epi.min.r01+tlrc",
"digest": {
@@ -423,7 +425,7 @@
}
},
{
- "@id": "urn:42b186e8-d358-4693-9d8c-cf46840ea4e4",
+ "@id": "bids::rm.epi.nomask.r$run+tlrc",
"Label": "rm.epi.nomask.r$run",
"AtLocation": "rm.epi.nomask.r$run+tlrc",
"digest": {
@@ -431,7 +433,7 @@
}
},
{
- "@id": "urn:a5ad4a2f-8b9e-420f-a5de-b26f57462d20",
+ "@id": "bids::mask_epi_extents+tlrc",
"Label": "mask_epi_extents",
"AtLocation": "mask_epi_extents+tlrc",
"digest": {
@@ -439,97 +441,105 @@
}
},
{
- "@id": "urn:7b48b2ff-cf50-4ebc-bf3e-89864d8e6665",
+ "@id": "bids::anat_final.$subj+tlrc",
+ "Label": "anat_final.$subj",
+ "AtLocation": "anat_final.$subj+tlrc",
+ "digest": {
+ "sha256": "94eb1853614cc085b22772c011f119f6a0ad7ec06cba2850587762e7f1a6eae6"
+ }
+ },
+ {
+ "@id": "bids::mat.r$run.vr.aff12.1D",
"Label": "mat.r$run.vr.aff12.1D",
"AtLocation": "mat.r$run.vr.aff12.1D",
- "GeneratedBy": "urn:0ce32f62-4fc0-42c0-893b-b03f2e4ae488",
+ "GeneratedBy": "urn:volreg-i4b2s3ls",
"digest": {
"sha256": "2e6e6c2ce8089cfa3c6e11dc72fca0cc8497f7a55faae2ced402de4867466c91"
}
},
{
- "@id": "urn:7ef93785-2d16-4eb2-9651-a05fd8350c3a",
+ "@id": "bids::rm.epi.all1",
"Label": "rm.epi.all1",
"AtLocation": "rm.epi.all1",
- "GeneratedBy": "urn:0ce32f62-4fc0-42c0-893b-b03f2e4ae488",
+ "GeneratedBy": "urn:volreg-i4b2s3ls",
"digest": {
"sha256": "1023e3c16cecdbdc73ea456bcf33c2e5bb4f1e07094b73d29022d651e5fa3f85"
}
},
{
- "@id": "urn:14839d0c-c9ad-4342-b8e3-8ad6ccfcbc28",
+ "@id": "bids::rm.epi.nomask.r$run",
"Label": "rm.epi.nomask.r$run",
"AtLocation": "rm.epi.nomask.r$run",
- "GeneratedBy": "urn:0ce32f62-4fc0-42c0-893b-b03f2e4ae488",
+ "GeneratedBy": "urn:volreg-i4b2s3ls",
"digest": {
"sha256": "03d6cba0426c5545e350e6b63a19b0e46f8dfa2223fd08691753e8914a479e36"
}
},
{
- "@id": "urn:e571d0ba-5590-4c78-8061-3aaebe4095b6",
+ "@id": "bids::rm.epi.1.r$run",
"Label": "rm.epi.1.r$run",
"AtLocation": "rm.epi.1.r$run",
- "GeneratedBy": "urn:0ce32f62-4fc0-42c0-893b-b03f2e4ae488",
+ "GeneratedBy": "urn:volreg-i4b2s3ls",
"digest": {
"sha256": "b1b9128c103ea246625db1a35e6f474a221ca6c1105a30df38aefdc4d5421e84"
}
},
{
- "@id": "urn:a1248b06-2827-402c-a459-bf581539c214",
+ "@id": "bids::rm.epi.min.r$run",
"Label": "rm.epi.min.r$run",
"AtLocation": "rm.epi.min.r$run",
- "GeneratedBy": "urn:0ce32f62-4fc0-42c0-893b-b03f2e4ae488",
+ "GeneratedBy": "urn:volreg-i4b2s3ls",
"digest": {
"sha256": "b4418a96ddbbf25afdfd01ed0506ddebe009011ba18aed10137f994260fd1a66"
}
},
{
- "@id": "urn:e9d84da7-d15b-4a7a-8c90-240b2a88a4fb",
+ "@id": "bids::dfile_rall.1D",
"Label": "dfile_rall.1D",
"AtLocation": "dfile_rall.1D",
- "GeneratedBy": "urn:0ce32f62-4fc0-42c0-893b-b03f2e4ae488",
+ "GeneratedBy": "urn:volreg-i4b2s3ls",
"digest": {
"sha256": "011e7296870a1ac7e15377fb0d529ed68710bb16b138bef6aeb6c645f437dcf2"
}
},
{
- "@id": "urn:35156813-da64-4e25-a9be-f174a0d4fe62",
+ "@id": "bids::mask_epi_extents",
"Label": "mask_epi_extents",
"AtLocation": "mask_epi_extents",
- "GeneratedBy": "urn:0ce32f62-4fc0-42c0-893b-b03f2e4ae488",
+ "GeneratedBy": "urn:volreg-i4b2s3ls",
"digest": {
"sha256": "a69dd71209516ec24e2b3364072ed54adff16619459b1c369866210ec642e987"
}
},
{
- "@id": "urn:4e6d3431-054c-48d3-b7c9-8bd56f26a529",
+ "@id": "bids::pb02.$subj.r$run.volreg",
"Label": "pb02.$subj.r$run.volreg",
"AtLocation": "pb02.$subj.r$run.volreg",
- "GeneratedBy": "urn:0ce32f62-4fc0-42c0-893b-b03f2e4ae488",
+ "GeneratedBy": "urn:volreg-i4b2s3ls",
"digest": {
"sha256": "8821927190ac1b3f8f9d9a5ec74f6468ae6c1cb736e58e5de2cdbe3543d5cc0c"
}
},
{
- "@id": "urn:a4f27e7d-029b-48ed-b095-09e6c129877d",
+ "@id": "bids::anat_final.$subj",
"Label": "anat_final.$subj",
"AtLocation": "anat_final.$subj",
- "GeneratedBy": "urn:0ce32f62-4fc0-42c0-893b-b03f2e4ae488",
+ "GeneratedBy": "urn:volreg-i4b2s3ls",
"digest": {
"sha256": "69b750d004bdba337de0b4ffa683bd92bc8f34b854d320327839ad264b28c4c5"
}
},
{
- "@id": "urn:7e77794f-c84b-4ec9-8330-ff8e325e3c25",
+ "@id": "bids::anat_w_skull_warped",
"Label": "anat_w_skull_warped",
"AtLocation": "anat_w_skull_warped",
- "GeneratedBy": "urn:0ce32f62-4fc0-42c0-893b-b03f2e4ae488",
+ "GeneratedBy": "urn:volreg-i4b2s3ls",
"digest": {
"sha256": "462fdb8cd2b882e250fee3c6adb7acf0b0b9a9edb3e1cadf9d45d16180871105"
}
},
{
- "@id": "urn:7921758c-6274-495a-9ddb-602ba1b1b33d",
+ "@id": "bids::pb03.$subj.r$run.blur",
"Label": "pb03.$subj.r$run.blur",
"AtLocation": "pb03.$subj.r$run.blur",
"digest": {
@@ -537,7 +547,7 @@
}
},
{
- "@id": "urn:62e3812e-a3e8-4836-8119-a98496a70101",
+ "@id": "bids::pb02.$subj.r$run.volreg+tlrc",
"Label": "pb02.$subj.r$run.volreg",
"AtLocation": "pb02.$subj.r$run.volreg+tlrc",
"digest": {
@@ -545,7 +555,7 @@
}
},
{
- "@id": "urn:7923f169-1149-48d3-ab90-aa7b13f7438f",
+ "@id": "bids::sub-01_T1w_ns+tlrc",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc",
"digest": {
@@ -553,7 +563,7 @@
}
},
{
- "@id": "urn:26741b71-6f61-4097-8aac-3b7a6f95efa2",
+ "@id": "bids::pb03.$subj.r$run.blur+tlrc",
"Label": "pb03.$subj.r$run.blur",
"AtLocation": "pb03.$subj.r$run.blur+tlrc",
"digest": {
@@ -561,7 +571,7 @@
}
},
{
- "@id": "urn:ae14ed40-d28f-491f-ad7f-f9364a2daeca",
+ "@id": "bids::full_mask.$subj+tlrc",
"Label": "full_mask.$subj",
"AtLocation": "full_mask.$subj+tlrc",
"digest": {
@@ -569,7 +579,7 @@
}
},
{
- "@id": "urn:c5da5c16-852c-4a75-a6e6-f70fcc9bc766",
+ "@id": "bids::rm.resam.anat+tlrc",
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"AtLocation": "rm.resam.anat+tlrc",
"digest": {
@@ -577,7 +587,7 @@
}
},
{
- "@id": "urn:f63bd3cb-5e25-43e7-9b62-0a6b714b9fd0",
+ "@id": "bids::mask_anat.$subj+tlrc",
"Label": "mask_anat.$subj",
"AtLocation": "mask_anat.$subj+tlrc",
"digest": {
@@ -585,7 +595,7 @@
}
},
{
- "@id": "urn:cb038b70-f5e5-4619-a661-3b6f816e4043",
+ "@id": "bids::tee",
"Label": "tee",
"AtLocation": "tee",
"digest": {
@@ -593,7 +603,7 @@
}
},
{
- "@id": "urn:c3457a35-c5f9-45de-931c-89a71bb169f0",
+ "@id": "bids::/Users/u1591557/abin/TT_N27+tlrc",
"Label": "TT_N27",
"AtLocation": "/Users/u1591557/abin/TT_N27+tlrc",
"digest": {
@@ -601,7 +611,7 @@
}
},
{
- "@id": "urn:32e9944d-72b1-4e01-8c59-14a8ffb09a0f",
+ "@id": "bids::rm.resam.group+tlrc",
"Label": "rm.resam.group",
"AtLocation": "rm.resam.group+tlrc",
"digest": {
@@ -609,61 +619,61 @@
}
},
{
- "@id": "urn:8e7762a4-60d2-4b68-a52a-b1cdecaa5a5b",
+ "@id": "bids::rm.mask_r$run",
"Label": "rm.mask_r$run",
"AtLocation": "rm.mask_r$run",
- "GeneratedBy": "urn:732a3588-6036-4290-9585-5aac582dd89e",
+ "GeneratedBy": "urn:mask-0nTKbiWT",
"digest": {
"sha256": "d251275ec819884fd84596da3fa356f3d83709d66170c45ad73c2f14ee830b35"
}
},
{
- "@id": "urn:3daddd79-e238-4f90-a46e-a7ee2638e983",
+ "@id": "bids::full_mask.$subj",
"Label": "full_mask.$subj",
"AtLocation": "full_mask.$subj",
- "GeneratedBy": "urn:732a3588-6036-4290-9585-5aac582dd89e",
+ "GeneratedBy": "urn:mask-0nTKbiWT",
"digest": {
"sha256": "02da8c6ed741c00cb6ccb8da25bf6ca853afb9100b992c854209afde9e30918f"
}
},
{
- "@id": "urn:dad480ac-f312-4758-89c9-2c6765d6393a",
+ "@id": "bids::rm.resam.anat",
"Label": "rm.resam.anat",
"AtLocation": "rm.resam.anat",
- "GeneratedBy": "urn:732a3588-6036-4290-9585-5aac582dd89e",
+ "GeneratedBy": "urn:mask-0nTKbiWT",
"digest": {
"sha256": "fe716d2bdbce773476ef264f2cd990f7114d7f2d7245c0cbeb10e8abc7feff9b"
}
},
{
- "@id": "urn:0657b059-0285-4d8a-8fae-2fb268511c34",
+ "@id": "bids::mask_anat.$subj",
"Label": "mask_anat.$subj",
"AtLocation": "mask_anat.$subj",
- "GeneratedBy": "urn:732a3588-6036-4290-9585-5aac582dd89e",
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@@ -679,7 +689,7 @@
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@@ -722,7 +732,7 @@
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@@ -730,7 +740,7 @@
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@@ -762,7 +772,7 @@
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@@ -770,7 +780,7 @@
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@@ -778,7 +788,7 @@
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@@ -786,7 +796,7 @@
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@@ -794,7 +804,7 @@
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@@ -802,7 +812,7 @@
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@@ -810,7 +820,7 @@
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@@ -818,133 +828,133 @@
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{
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"AtLocation": "sum_ideal.1D",
- "GeneratedBy": "urn:42f5e934-e5d2-4707-ad09-4dd6a6b280fc",
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{
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"AtLocation": "X.stim.xmat.1D",
- "GeneratedBy": "urn:42f5e934-e5d2-4707-ad09-4dd6a6b280fc",
+ "GeneratedBy": "urn:regress-I0fV2FI8",
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{
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+ "@id": "bids::full_mask.$subj+tlrc",
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"digest": {
@@ -952,34 +962,34 @@
}
},
{
- "@id": "urn:4d55ae09-a747-4397-a177-d909c1abdec2",
+ "@id": "bids::blur.epits.1D",
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"AtLocation": "blur.epits.1D",
- "GeneratedBy": "urn:0f0d8d27-624e-4177-a4ce-0e4655ee2e68",
+ "GeneratedBy": "urn:bluresti-9I25pzvg",
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{
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"AtLocation": "blur.errts.1D",
- "GeneratedBy": "urn:0f0d8d27-624e-4177-a4ce-0e4655ee2e68",
+ "GeneratedBy": "urn:bluresti-9I25pzvg",
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}
},
{
- "@id": "urn:893c5726-58fc-44e9-a077-2af27aa758a2",
+ "@id": "bids::ClustSim",
"Label": "ClustSim",
"AtLocation": "ClustSim",
- "GeneratedBy": "urn:0f0d8d27-624e-4177-a4ce-0e4655ee2e68",
+ "GeneratedBy": "urn:bluresti-9I25pzvg",
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},
{
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+ "@id": "bids::pb00.$subj.r*.tcat+orig.HEAD",
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"AtLocation": "pb00.$subj.r*.tcat+orig.HEAD",
"digest": {
@@ -987,10 +997,10 @@
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{
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+ "GeneratedBy": "urn:autobloc-oFzbi7jF",
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diff --git a/examples/from_parsers/afni/afni_clustconn_18_proc_block.png b/examples/from_parsers/afni/afni_clustconn_18_proc_block.png
index 7440146fb..e5c60a25b 100644
Binary files a/examples/from_parsers/afni/afni_clustconn_18_proc_block.png and b/examples/from_parsers/afni/afni_clustconn_18_proc_block.png differ
diff --git a/examples/from_parsers/afni/afni_clustconn_26_proc.jsonld b/examples/from_parsers/afni/afni_clustconn_26_proc.jsonld
index f312dfaa0..32d6783a9 100644
--- a/examples/from_parsers/afni/afni_clustconn_26_proc.jsonld
+++ b/examples/from_parsers/afni/afni_clustconn_26_proc.jsonld
@@ -4,578 +4,581 @@
"Records": {
"Software": [
{
- "@id": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:afni-vU2XdaEn",
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"Label": "AFNI",
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+ "Version": "afni24",
+ "AltIdentifier": "RRID:SCR_005927"
}
],
"Activities": [
{
- "@id": "urn:1926242a-0d21-447f-99e9-e5dc8941f48c",
+ "@id": "urn:makedire-kHWIFSta",
"Label": "Make directory",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
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"Used": []
},
{
- "@id": "urn:fcf8088f-b2b9-4a81-a7e0-09c6db3b4aed",
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- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
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"Parameters": {},
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},
{
- "@id": "urn:28047038-52b6-4198-9ecc-50df0c6ad0da",
+ "@id": "urn:cp-pJJ01Duo",
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- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
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- "urn:d5506b4c-ab38-46d9-b17a-0e03a202eac8",
- "urn:ebb97d70-b892-4949-9449-97c5864b16ae"
+ "bids::afni_cluster_nn3/tone_counting_onset_times.txt",
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]
},
{
- "@id": "urn:3f94e5a2-855a-48ed-bcc8-11f9506e1f6f",
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- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
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"Used": [
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+ "bids::sub-01_T1w.nii.gz"
]
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{
- "@id": "urn:bf16fd27-cf3d-4155-9416-ad1c8cbe4fe2",
+ "@id": "urn:3dtcat-o4ryHUvB",
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+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Parameters": {},
"Used": [
- "urn:a899046d-1abd-4476-b24f-bb78675772cd"
+ "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'"
]
},
{
- "@id": "urn:1a0347c5-1103-4187-9fe3-2e53100f089c",
+ "@id": "urn:3dtoutco-V195mr84",
"Label": "3dToutcount",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D",
"Parameters": {},
"Used": [
- "urn:11ebe6d2-2926-485f-90ea-56154c85bab1"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:b76ddcb4-bac5-49f8-bccb-e7c55c21b716",
+ "@id": "urn:cat-oplZknOp",
"Label": "cat",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "cat outcount.r*.1D > outcount_rall.1D",
"Parameters": {},
"Used": [
- "urn:1e4a1da0-955c-4597-81e4-87a8bf71b55f"
+ "bids::outcount.r*.1D"
]
},
{
- "@id": "urn:fcd0434b-5af5-4ca3-a091-42d2f7a8f886",
+ "@id": "urn:3dtshift-A8ONAV4i",
"Label": "3dTshift",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig",
"Parameters": {},
"Used": [
- "urn:11ebe6d2-2926-485f-90ea-56154c85bab1"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:592fd391-a562-4f9b-b0be-432c3de0f0a1",
+ "@id": "urn:alignepi-FPNGWQ3q",
"Label": "align_epi_anat.py",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off",
"Parameters": {},
"Used": [
- "urn:4d67debf-04bf-4d39-80b4-3bfaafb9bf08",
- "urn:9ad800da-5bfa-4f12-b2e5-3028be4f20cf"
+ "bids::pb01.$subj.r01.tshift+orig",
+ "bids::sub-01_T1w+orig"
]
},
{
- "@id": "urn:e4fd13bd-1c92-4e3b-9674-25ec45487409",
+ "@id": "urn:autotlrc-tzW1b3Mo",
"Label": "@auto_tlrc",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss",
"Parameters": {},
"Used": [
- "urn:57519ad5-a5ee-4b54-95a1-995405cbc897",
- "urn:64796cac-f8f3-46ff-a608-ec8f2f452bff"
+ "bids::TT_N27+tlrc",
+ "bids::sub-01_T1w_ns+orig"
]
},
{
- "@id": "urn:9e9057eb-e197-4c3e-b411-5cc092df19e5",
+ "@id": "urn:catmatve-uVdPf8fA",
"Label": "cat_matvec",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D",
"Parameters": {},
"Used": [
- "urn:22a28170-7c0e-4430-b02f-0800d1ecf2a4"
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:fedcd683-f414-4126-b5e2-45ac6fbeb7a6",
+ "@id": "urn:3dvolreg-zM9H4lk7",
"Label": "3dvolreg",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig",
"Parameters": {},
"Used": [
- "urn:db8f33dc-3bfa-470f-93dd-7d1d8d61e2a8"
+ "bids::pb01.$subj.r$run.tshift+orig"
]
},
{
- "@id": "urn:91516a9b-26bb-4933-a4e1-563ee506a9b1",
+ "@id": "urn:3dcalc-l0e6HDgL",
"Label": "3dcalc",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1",
"Parameters": {},
"Used": [
- "urn:db8f33dc-3bfa-470f-93dd-7d1d8d61e2a8"
+ "bids::pb01.$subj.r$run.tshift+orig"
]
},
{
- "@id": "urn:40828fc2-6694-4c66-98a2-66f47b52da95",
+ "@id": "urn:catmatve-cz4w4ciN",
"Label": "cat_matvec",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D",
"Parameters": {},
"Used": [
- "urn:22a28170-7c0e-4430-b02f-0800d1ecf2a4"
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:d7435782-a021-4eae-a533-fbeccbabbf59",
+ "@id": "urn:3dalline-fX5euqYh",
"Label": "3dAllineate",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run",
"Parameters": {},
"Used": [
- "urn:47c2ec0e-da50-49f4-81fc-36c6e5a8251d",
- "urn:8774df07-e4e7-4f9e-b856-8d0b9dadadba",
- "urn:db8f33dc-3bfa-470f-93dd-7d1d8d61e2a8"
+ "bids::mat.r$run.warp.aff12.1D",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:01695c88-880b-4165-a6c4-0832f9174f62",
+ "@id": "urn:3dalline-TPR4Lm3D",
"Label": "3dAllineate",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run",
"Parameters": {},
"Used": [
- "urn:47c2ec0e-da50-49f4-81fc-36c6e5a8251d",
- "urn:8774df07-e4e7-4f9e-b856-8d0b9dadadba",
- "urn:ecd84b96-96f0-4bc4-8120-3aa6ff2454cc"
+ "bids::mat.r$run.warp.aff12.1D",
+ "bids::rm.epi.all1+orig",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:fe05c888-5fed-4c01-975b-b63fd0f5a820",
+ "@id": "urn:3dtstat-aCZ46C6B",
"Label": "3dTstat",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc",
"Parameters": {},
"Used": [
- "urn:fcc1f2b7-e347-48be-9bfa-66d805405da8"
+ "bids::rm.epi.1.r$run+tlrc"
]
},
{
- "@id": "urn:3540e9a9-468a-4af4-856c-88accf4a79c9",
+ "@id": "urn:cat-Euapflnv",
"Label": "cat",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "cat dfile.r*.1D > dfile_rall.1D",
"Parameters": {},
"Used": [
- "urn:16dfbd17-9e1a-4db2-b261-ed07c3f0dc28"
+ "bids::dfile.r*.1D"
]
},
{
- "@id": "urn:d5dd2de4-21d3-4f70-94c0-ebdac0c475c7",
+ "@id": "urn:3dcopy-PJwYcYCL",
"Label": "3dcopy",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents",
"Parameters": {},
"Used": [
- "urn:2f9bb8f0-6d78-4390-a502-3fcf6741b82c"
+ "bids::rm.epi.min.r01+tlrc"
]
},
{
- "@id": "urn:ba668017-e912-4946-b252-0bf10dffbfea",
+ "@id": "urn:3dcalc-vQmwqsuZ",
"Label": "3dcalc",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg",
"Parameters": {},
"Used": [
- "urn:11a19e58-b18a-4068-9317-2e48372cc90a",
- "urn:5d17d672-2c7c-4a90-aa51-7047bdba2a44"
+ "bids::mask_epi_extents+tlrc",
+ "bids::rm.epi.nomask.r$run+tlrc"
]
},
{
- "@id": "urn:afd5f1ae-2faf-4017-bf1b-0e6bf599fdf2",
+ "@id": "urn:3dcopy-F8z4WYm7",
"Label": "3dcopy",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj",
"Parameters": {},
"Used": [
- "urn:47c2ec0e-da50-49f4-81fc-36c6e5a8251d"
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:1ff0b7f3-ec3f-4e1e-a0e4-fb0a451c3b7b",
+ "@id": "urn:3dalline-CKdjxtz1",
"Label": "3dAllineate",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped",
"Parameters": {},
"Used": [
- "urn:0f9b9bf5-4213-468d-a35c-0b18e6ea023d"
+ "bids::anat_final.$subj+tlrc",
+ "bids::warp.anat.Xat.1D"
]
},
{
- "@id": "urn:90224fd2-1deb-4b86-8b71-b94bd3664cc2",
+ "@id": "urn:3dmerge-5sbgCFxR",
"Label": "3dmerge",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc",
"Parameters": {},
"Used": [
- "urn:422bb061-d84a-4c7c-b975-081f8102361d",
- "urn:69a2cfcd-bd40-4b1d-964e-f54c1ac6c91e"
+ "bids::pb02.$subj.r$run.volreg+tlrc",
+ "bids::pb03.$subj.r$run.blur"
]
},
{
- "@id": "urn:abce3868-1f35-4d6d-ac4e-069f2712654a",
+ "@id": "urn:3dautoma-D1LJF0af",
"Label": "3dAutomask",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:930ba2ac-0533-40e1-bcdd-f539a8bb6381"
+ "bids::pb03.$subj.r$run.blur+tlrc"
]
},
{
- "@id": "urn:36c7c714-a31d-412a-84ab-3af060136b00",
+ "@id": "urn:3dmaskto-hJsNwKG6",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:b81b2dfe-0bcd-4b15-aea4-d405547ecd56",
+ "@id": "urn:3dresamp-pmoCtLWS",
"Label": "3dresample",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat",
"Parameters": {},
"Used": [
- "urn:47c2ec0e-da50-49f4-81fc-36c6e5a8251d",
- "urn:59c7d43f-8ff4-4168-b238-59b4a76e8be2"
+ "bids::full_mask.$subj+tlrc",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:41bc576b-47d1-402a-9125-ecdce4d27320",
+ "@id": "urn:3dmaskto-3KxzVryU",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj",
"Parameters": {},
"Used": [
- "urn:ff8f77a8-822e-474e-a600-d65d5ec87e8b"
+ "bids::rm.resam.anat+tlrc"
]
},
{
- "@id": "urn:c27757d4-0aae-4dce-b0fd-bc9b48765185",
+ "@id": "urn:3dabover-nW4bIw9t",
"Label": "3dABoverlap",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt",
"Parameters": {},
"Used": [
- "urn:b48eeb34-ab78-494e-813e-c9c70ddb53f0",
- "urn:ebfb1e00-7e6d-44ea-ac4d-9960f3dd8f56"
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee"
]
},
{
- "@id": "urn:b546e78d-5990-41cb-b83d-f3df88524314",
+ "@id": "urn:3ddot-z0QzuRgL",
"Label": "3ddot",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt",
"Parameters": {},
"Used": [
- "urn:b48eeb34-ab78-494e-813e-c9c70ddb53f0",
- "urn:ebfb1e00-7e6d-44ea-ac4d-9960f3dd8f56"
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee"
]
},
{
- "@id": "urn:63005485-a633-492b-aab2-46783a515b0a",
+ "@id": "urn:3dresamp-rKiLK5l3",
"Label": "3dresample",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc",
"Parameters": {},
"Used": [
- "urn:213994e9-16cb-499b-9268-3e1f4bdee35a",
- "urn:59c7d43f-8ff4-4168-b238-59b4a76e8be2"
+ "bids::/Users/u1591557/abin/TT_N27+tlrc",
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:f53bfc0f-986a-4314-ad77-26b1afe0eb09",
+ "@id": "urn:3dmaskto-AtbA6aKd",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group",
"Parameters": {},
"Used": [
- "urn:d310869a-29d5-4b08-9fad-1cada2493e08"
+ "bids::rm.resam.group+tlrc"
]
},
{
- "@id": "urn:86b1e3b7-e96c-4bae-8426-db0e46a18436",
+ "@id": "urn:3dtstat-tRADjMrz",
"Label": "3dTstat",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:930ba2ac-0533-40e1-bcdd-f539a8bb6381"
+ "bids::pb03.$subj.r$run.blur+tlrc"
]
},
{
- "@id": "urn:d47393c3-4814-410b-b575-15617e79b6d6",
+ "@id": "urn:3dcalc-XM5Og8FN",
"Label": "3dcalc",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale",
"Parameters": {},
"Used": [
- "urn:0d04acc3-8cda-49f9-abe0-aeafcfd63461",
- "urn:5d17d672-2c7c-4a90-aa51-7047bdba2a44",
- "urn:930ba2ac-0533-40e1-bcdd-f539a8bb6381"
+ "bids::mask_epi_extents+tlrc",
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::rm.mean_r$run+tlrc"
]
},
{
- "@id": "urn:47a56e67-cb71-472f-8efa-c048220d3fab",
+ "@id": "urn:1dtoolpy-YhGXZbB6",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D",
"Parameters": {},
"Used": [
- "urn:c107ddf9-4793-48b4-b1db-74f660d9b4a5"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:c874b5fd-25bf-4784-8200-a2ea41b25922",
+ "@id": "urn:1dtoolpy-Som6XeES",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D",
"Parameters": {},
"Used": [
- "urn:c107ddf9-4793-48b4-b1db-74f660d9b4a5"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:5ae22539-5ee8-41d6-ac9b-8fc06f93b886",
+ "@id": "urn:1dtoolpy-3HdHPQUT",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}",
"Parameters": {},
"Used": [
- "urn:c107ddf9-4793-48b4-b1db-74f660d9b4a5"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:2a408795-ebd3-4029-a8b9-3405eba4bdca",
+ "@id": "urn:3ddeconv-BMg9ILIN",
"Label": "3dDeconvolve",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj",
"Parameters": {},
"Used": [
- "urn:574d3e7d-e246-4b11-965f-aa666574b423"
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD"
]
},
{
- "@id": "urn:3cc19a04-79cd-4981-913b-a18b88d06449",
+ "@id": "urn:1dtoolpy-7vFHTBen",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt",
"Parameters": {},
"Used": [
- "urn:3a5ec85b-4649-4e66-ae61-3226ead3490b"
+ "bids::X.xmat.1D"
]
},
{
- "@id": "urn:85de6a2e-faae-4cb2-b1be-233684dc4309",
+ "@id": "urn:3dtcat-hZaDOJov",
"Label": "3dTcat",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD",
"Parameters": {},
"Used": [
- "urn:574d3e7d-e246-4b11-965f-aa666574b423"
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD"
]
},
{
- "@id": "urn:26040560-8893-4c08-835e-2ae7ae40e431",
+ "@id": "urn:3dtstat-gMVMVnnv",
"Label": "3dTstat",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:60e316e3-5de9-4cf0-a078-e0e086a169c5"
+ "bids::all_runs.$subj+tlrc%22[$ktrs]%22"
]
},
{
- "@id": "urn:8a911323-f909-40de-950d-d0cd49e1e599",
+ "@id": "urn:3dtstat-Zngd2T3h",
"Label": "3dTstat",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:33552b33-dc97-4793-8385-2a87de22c0a4"
+ "bids::errts.$%7Bsubj%7D+tlrc%22[$ktrs]%22"
]
},
{
- "@id": "urn:88d6bd28-7a69-4044-b46a-836e2f61ccd3",
+ "@id": "urn:3dcalc-c55gFJ4p",
"Label": "3dcalc",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj",
"Parameters": {},
"Used": [
- "urn:4f45a00b-727c-40b2-a2c5-5cae947a56a8",
- "urn:59c7d43f-8ff4-4168-b238-59b4a76e8be2",
- "urn:5a177f0b-f843-4725-9475-1b1e4ddf5e18"
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.noise.all+tlrc",
+ "bids::rm.signal.all+tlrc"
]
},
{
- "@id": "urn:b4680683-ecd5-4088-8bc2-63c2d6c6a59b",
+ "@id": "urn:3dtnorm-CGD6UuHs",
"Label": "3dTnorm",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc",
"Parameters": {},
"Used": [
- "urn:035c3970-5a13-491b-a04b-584ca86e8397"
+ "bids::errts.$%7Bsubj%7D+tlrc"
]
},
{
- "@id": "urn:0935d3f6-d3b7-44a9-877c-9e3cc384b111",
+ "@id": "urn:3dmaskav-qgH8zcGm",
"Label": "3dmaskave",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D",
"Parameters": {},
- "Used": []
+ "Used": [
+ "bids::full_mask.$subj+tlrc"
+ ]
},
{
- "@id": "urn:153b277a-635d-42c0-a884-4bbfa0c6dd1b",
+ "@id": "urn:3dtstat-1aRdzV5C",
"Label": "3dTstat",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D",
"Parameters": {},
"Used": [
- "urn:a9fca6d2-d86c-450d-97a9-50415da048a5"
+ "bids::out.gcor.1D"
]
},
{
- "@id": "urn:b86ebb2d-75c1-4ea3-a50c-aab763d3bc41",
+ "@id": "urn:3dcalc-VorpNvMG",
"Label": "3dcalc",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP",
"Parameters": {},
"Used": [
- "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
- "urn:ddb15529-6e64-418a-a74b-7a3d384dc0ab"
+ "bids::gmean.errts.unit.1D",
+ "bids::rm.errts.unit+tlrc"
]
},
{
- "@id": "urn:3de44cfa-745b-4bfe-8115-0095c9f923ea",
+ "@id": "urn:3dtstat-FkNkpleh",
"Label": "3dTstat",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc",
"Parameters": {},
"Used": [
- "urn:66a1b6d8-088a-4ae0-83f8-e96e5151ae0b"
+ "bids::rm.DP+tlrc"
]
},
{
- "@id": "urn:dd40f1be-ca12-46a1-a52d-5d1f764d8b19",
+ "@id": "urn:1dcat-VxIRgqMS",
"Label": "1dcat",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D",
"Parameters": {},
"Used": [
- "urn:210bf154-81f9-4db1-99d0-871ae70630ab"
+ "bids::X.nocensor.xmat.1D'[3]'"
]
},
{
- "@id": "urn:815e4ca6-6373-4dd2-9391-c5ceca637440",
+ "@id": "urn:1dcat-QBu2vYst",
"Label": "1dcat",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D",
"Parameters": {},
"Used": [
- "urn:b5be0e1d-2eae-4498-ad71-9ee980856337"
+ "bids::X.nocensor.xmat.1D'[4]'"
]
},
{
- "@id": "urn:1f0c4c33-4ba6-430e-a3db-3bf7f03cdf13",
+ "@id": "urn:3dtstat-lCq7pBIS",
"Label": "3dTstat",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"",
"Parameters": {},
"Used": [
- "urn:7b8eadd4-f765-437a-ab0e-4824de937df0"
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:6ebcc108-fd65-49bb-8a39-6353b906a79c",
+ "@id": "urn:1dcat-ZX8bODEi",
"Label": "1dcat",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D",
"Parameters": {},
"Used": [
- "urn:7b8eadd4-f765-437a-ab0e-4824de937df0"
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:689be361-2322-444c-81b5-551d7b16ab70",
+ "@id": "urn:3dfwhmx-Cyw8XHhT",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D",
"Parameters": {},
"Used": [
- "urn:59c7d43f-8ff4-4168-b238-59b4a76e8be2"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:c77d7191-0804-496c-b902-abaed4fcf96c",
+ "@id": "urn:3dfwhmx-gvqns3P7",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D",
"Parameters": {},
"Used": [
- "urn:59c7d43f-8ff4-4168-b238-59b4a76e8be2"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:161541c6-24a8-4a72-a6ca-7fdd2db5f14b",
+ "@id": "urn:3dclusts-tJOYZHF3",
"Label": "3dClustSim",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim",
"Parameters": {},
"Used": [
- "urn:59c7d43f-8ff4-4168-b238-59b4a76e8be2"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:7dcd3f5a-55fd-4255-b6b0-28e323804813",
+ "@id": "urn:genepire-TKiF0wxd",
"Label": "gen_epi_review.py",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD",
"Parameters": {},
"Used": [
- "urn:19376406-be37-4a1b-abdd-6e0af87f6e14"
+ "bids::pb00.$subj.r*.tcat+orig.HEAD"
]
},
{
- "@id": "urn:c40149f1-9ffe-4002-923e-896181a14e31",
+ "@id": "urn:genssrev-nmpXt1CC",
"Label": "gen_ss_review_scripts.py",
- "AssociatedWith": "urn:c405fbed-a681-458f-863a-a4a803fc0543",
+ "AssociatedWith": "urn:afni-vU2XdaEn",
"Command": "gen_ss_review_scripts.py -mot_limit 0.3 -exit0",
"Parameters": {
"-mot_limit": "0.3",
@@ -586,22 +589,22 @@
],
"Entities": [
{
- "@id": "urn:f6b2ac4c-0311-49b6-abf0-b0ea89ecab4c",
+ "@id": "bids::$output_dir",
"Label": "$output_dir",
"AtLocation": "$output_dir",
- "GeneratedBy": "urn:1926242a-0d21-447f-99e9-e5dc8941f48c",
+ "GeneratedBy": "urn:makedire-kHWIFSta",
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}
},
{
- "@id": "urn:00aeec77-58fc-409c-a902-c1a79d93c8a9",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:fcf8088f-b2b9-4a81-a7e0-09c6db3b4aed"
+ "GeneratedBy": "urn:makedire-zchaN5s7"
},
{
- "@id": "urn:ebb97d70-b892-4949-9449-97c5864b16ae",
+ "@id": "bids::afni_cluster_nn3/tone_counting_onset_times.txt",
"Label": "tone_counting_onset_times.txt",
"AtLocation": "./afni_cluster_nn3/tone_counting_onset_times.txt",
"digest": {
@@ -609,7 +612,7 @@
}
},
{
- "@id": "urn:d5506b4c-ab38-46d9-b17a-0e03a202eac8",
+ "@id": "bids::afni_cluster_nn3/tone_counting_probe_duration.txt",
"Label": "tone_counting_probe_duration.txt",
"AtLocation": "./afni_cluster_nn3/tone_counting_probe_duration.txt",
"digest": {
@@ -617,13 +620,13 @@
}
},
{
- "@id": "urn:ca08e7e4-ce9d-43ff-994b-c2be02f6a9f7",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:28047038-52b6-4198-9ecc-50df0c6ad0da"
+ "GeneratedBy": "urn:cp-pJJ01Duo"
},
{
- "@id": "urn:21a3f1b0-7d5f-472c-986d-e69d54815075",
+ "@id": "bids::sub-01_T1w.nii.gz",
"Label": "sub-01_T1w.nii.gz",
"AtLocation": "sub-01_T1w.nii.gz",
"digest": {
@@ -631,13 +634,13 @@
}
},
{
- "@id": "urn:3f6420f5-5f28-44a5-a547-f4a55c2d74a1",
+ "@id": "bids::$output_dir/sub-01_T1w",
"Label": "sub-01_T1w",
"AtLocation": "$output_dir/sub-01_T1w",
- "GeneratedBy": "urn:3f94e5a2-855a-48ed-bcc8-11f9506e1f6f"
+ "GeneratedBy": "urn:3dcopy-CFq8ivQe"
},
{
- "@id": "urn:a899046d-1abd-4476-b24f-bb78675772cd",
+ "@id": "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Label": "sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"digest": {
@@ -645,13 +648,13 @@
}
},
{
- "@id": "urn:49752f72-6a50-440e-abdf-bae073c6dd40",
+ "@id": "bids::$output_dir/pb00.$subj.r01.tcat",
"Label": "pb00.$subj.r01.tcat",
"AtLocation": "$output_dir/pb00.$subj.r01.tcat",
- "GeneratedBy": "urn:bf16fd27-cf3d-4155-9416-ad1c8cbe4fe2"
+ "GeneratedBy": "urn:3dtcat-o4ryHUvB"
},
{
- "@id": "urn:11ebe6d2-2926-485f-90ea-56154c85bab1",
+ "@id": "bids::pb00.$subj.r$run.tcat+orig",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -659,16 +662,16 @@
}
},
{
- "@id": "urn:0930ef3d-25ea-478e-a1e5-c90f4ce8d278",
+ "@id": "bids::outcount.r$run.1D",
"Label": "outcount.r$run.1D",
"AtLocation": "outcount.r$run.1D",
- "GeneratedBy": "urn:1a0347c5-1103-4187-9fe3-2e53100f089c",
+ "GeneratedBy": "urn:3dtoutco-V195mr84",
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},
{
- "@id": "urn:1e4a1da0-955c-4597-81e4-87a8bf71b55f",
+ "@id": "bids::outcount.r*.1D",
"Label": "outcount.r*.1D",
"AtLocation": "outcount.r*.1D",
"digest": {
@@ -676,25 +679,25 @@
}
},
{
- "@id": "urn:da7d2044-3bd8-4f27-88cd-f87a8407fdb0",
+ "@id": "bids::outcount_rall.1D",
"Label": "outcount_rall.1D",
"AtLocation": "outcount_rall.1D",
- "GeneratedBy": "urn:b76ddcb4-bac5-49f8-bccb-e7c55c21b716",
+ "GeneratedBy": "urn:cat-oplZknOp",
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}
},
{
- "@id": "urn:4206f70c-3207-4464-a93b-1094b5e556ce",
+ "@id": "bids::pb01.$subj.r$run.tshift",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift",
- "GeneratedBy": "urn:fcd0434b-5af5-4ca3-a091-42d2f7a8f886",
+ "GeneratedBy": "urn:3dtshift-A8ONAV4i",
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}
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{
- "@id": "urn:4d67debf-04bf-4d39-80b4-3bfaafb9bf08",
+ "@id": "bids::sub-01_T1w+orig",
"Label": "sub-01_T1w",
"AtLocation": "sub-01_T1w+orig",
"digest": {
@@ -702,7 +705,7 @@
}
},
{
- "@id": "urn:9ad800da-5bfa-4f12-b2e5-3028be4f20cf",
+ "@id": "bids::pb01.$subj.r01.tshift+orig",
"Label": "pb01.$subj.r01.tshift",
"AtLocation": "pb01.$subj.r01.tshift+orig",
"digest": {
@@ -710,16 +713,16 @@
}
},
{
- "@id": "urn:00521f64-04c3-462a-b572-daaa10b00fb8",
+ "@id": "bids::_al_junk",
"Label": "_al_junk",
"AtLocation": "_al_junk",
- "GeneratedBy": "urn:592fd391-a562-4f9b-b0be-432c3de0f0a1",
+ "GeneratedBy": "urn:alignepi-FPNGWQ3q",
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}
},
{
- "@id": "urn:64796cac-f8f3-46ff-a608-ec8f2f452bff",
+ "@id": "bids::TT_N27+tlrc",
"Label": "TT_N27",
"AtLocation": "TT_N27+tlrc",
"digest": {
@@ -727,7 +730,7 @@
}
},
{
- "@id": "urn:57519ad5-a5ee-4b54-95a1-995405cbc897",
+ "@id": "bids::sub-01_T1w_ns+orig",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+orig",
"digest": {
@@ -735,7 +738,7 @@
}
},
{
- "@id": "urn:22a28170-7c0e-4430-b02f-0800d1ecf2a4",
+ "@id": "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
"Label": "sub-01_T1w_ns",
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@@ -743,16 +746,16 @@
}
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"AtLocation": "warp.anat.Xat.1D",
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@@ -760,34 +763,34 @@
}
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{
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"AtLocation": "mat.r$run.vr.aff12.1D",
- "GeneratedBy": "urn:fedcd683-f414-4126-b5e2-45ac6fbeb7a6",
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{
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"AtLocation": "rm.epi.all1",
- "GeneratedBy": "urn:91516a9b-26bb-4933-a4e1-563ee506a9b1",
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"AtLocation": "mat.r$run.warp.aff12.1D",
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@@ -795,16 +798,16 @@
}
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{
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@@ -812,16 +815,16 @@
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{
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@@ -829,16 +832,16 @@
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@@ -846,16 +849,16 @@
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@@ -863,16 +866,16 @@
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@@ -880,7 +883,7 @@
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{
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@@ -888,34 +891,42 @@
}
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{
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- "GeneratedBy": "urn:afd5f1ae-2faf-4017-bf1b-0e6bf599fdf2",
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@@ -923,7 +934,7 @@
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@@ -931,7 +942,7 @@
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@@ -939,25 +950,25 @@
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@@ -965,16 +976,16 @@
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@@ -982,16 +993,16 @@
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@@ -999,7 +1010,7 @@
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{
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@@ -1007,7 +1018,7 @@
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{
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@@ -1015,16 +1026,16 @@
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{
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- "GeneratedBy": "urn:63005485-a633-492b-aab2-46783a515b0a",
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@@ -1032,25 +1043,25 @@
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{
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@@ -1058,34 +1069,34 @@
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{
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@@ -1093,25 +1104,25 @@
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@@ -1119,16 +1130,16 @@
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@@ -1136,16 +1147,16 @@
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{
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@@ -1153,7 +1164,7 @@
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"Label": "rm.noise.all",
"AtLocation": "rm.noise.all+tlrc",
"digest": {
@@ -1161,16 +1172,16 @@
}
},
{
- "@id": "urn:1be6efab-9929-4b1e-8bbc-c165cd38270f",
+ "@id": "bids::TSNR.$subj",
"Label": "TSNR.$subj",
"AtLocation": "TSNR.$subj",
- "GeneratedBy": "urn:88d6bd28-7a69-4044-b46a-836e2f61ccd3",
+ "GeneratedBy": "urn:3dcalc-c55gFJ4p",
"digest": {
"sha256": "303f183145a1e295686c08335d3b70753777cf0fa0b3f9628cf8de5471359a00"
}
},
{
- "@id": "urn:035c3970-5a13-491b-a04b-584ca86e8397",
+ "@id": "bids::errts.$%7Bsubj%7D+tlrc",
"Label": "errts.${subj}",
"AtLocation": "errts.${subj}+tlrc",
"digest": {
@@ -1178,25 +1189,25 @@
}
},
{
- "@id": "urn:b1ed202d-bf85-425f-adac-b68fb17b5af0",
+ "@id": "bids::rm.errts.unit",
"Label": "rm.errts.unit",
"AtLocation": "rm.errts.unit",
- "GeneratedBy": "urn:b4680683-ecd5-4088-8bc2-63c2d6c6a59b",
+ "GeneratedBy": "urn:3dtnorm-CGD6UuHs",
"digest": {
"sha256": "03b570ad773a00f51ab7e6cdedfebdeca45f5356de0c25f9e3be44d7bf2c7151"
}
},
{
- "@id": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
+ "@id": "bids::gmean.errts.unit.1D",
"Label": "gmean.errts.unit.1D",
"AtLocation": "gmean.errts.unit.1D",
- "GeneratedBy": "urn:0935d3f6-d3b7-44a9-877c-9e3cc384b111",
+ "GeneratedBy": "urn:3dmaskav-qgH8zcGm",
"digest": {
"sha256": "a35a66cce2e2d487762823c197ca1edc450a9887f46f125826b69c5021662f95"
}
},
{
- "@id": "urn:a9fca6d2-d86c-450d-97a9-50415da048a5",
+ "@id": "bids::out.gcor.1D",
"Label": "out.gcor.1D",
"AtLocation": "out.gcor.1D",
"digest": {
@@ -1204,16 +1215,16 @@
}
},
{
- "@id": "urn:d0b03493-daf8-4372-bd90-a7d591ad03a9",
+ "@id": "urn:uuid:e07f5fa3-47c0-4e8d-b545-c47a7fd0fa16",
"Label": "-",
"AtLocation": "-",
- "GeneratedBy": "urn:153b277a-635d-42c0-a884-4bbfa0c6dd1b",
+ "GeneratedBy": "urn:3dtstat-1aRdzV5C",
"digest": {
"sha256": "dac304c9f20899ca1ef5aa403e565345fd0ff4ed80c35f82007c9b03a68292b3"
}
},
{
- "@id": "urn:ddb15529-6e64-418a-a74b-7a3d384dc0ab",
+ "@id": "bids::rm.errts.unit+tlrc",
"Label": "rm.errts.unit",
"AtLocation": "rm.errts.unit+tlrc",
"digest": {
@@ -1221,16 +1232,16 @@
}
},
{
- "@id": "urn:a4c09a62-cb31-4c2b-ba17-d95d8005b33d",
+ "@id": "bids::rm.DP",
"Label": "rm.DP",
"AtLocation": "rm.DP",
- "GeneratedBy": "urn:b86ebb2d-75c1-4ea3-a50c-aab763d3bc41",
+ "GeneratedBy": "urn:3dcalc-VorpNvMG",
"digest": {
"sha256": "06a0bfbc609c1a06ecf93c479a3288d2911c7f5f3e93cf49c5d26f721c2035ed"
}
},
{
- "@id": "urn:66a1b6d8-088a-4ae0-83f8-e96e5151ae0b",
+ "@id": "bids::rm.DP+tlrc",
"Label": "rm.DP",
"AtLocation": "rm.DP+tlrc",
"digest": {
@@ -1238,16 +1249,16 @@
}
},
{
- "@id": "urn:91ed2886-1c20-431d-9c0f-8f3720ffea22",
+ "@id": "bids::corr_brain",
"Label": "corr_brain",
"AtLocation": "corr_brain",
- "GeneratedBy": "urn:3de44cfa-745b-4bfe-8115-0095c9f923ea",
+ "GeneratedBy": "urn:3dtstat-FkNkpleh",
"digest": {
"sha256": "74e3aeae0da338b871ab5dc9e8859a4e81fcf1b3c0042cd22fe337eb7baf5eae"
}
},
{
- "@id": "urn:210bf154-81f9-4db1-99d0-871ae70630ab",
+ "@id": "bids::X.nocensor.xmat.1D'[3]'",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D'[3]'",
"digest": {
@@ -1255,16 +1266,16 @@
}
},
{
- "@id": "urn:3f07d54e-e55d-4e7e-bc51-9c2e441a58b3",
+ "@id": "bids::ideal_tone_counting.1D",
"Label": "ideal_tone_counting.1D",
"AtLocation": "ideal_tone_counting.1D",
- "GeneratedBy": "urn:dd40f1be-ca12-46a1-a52d-5d1f764d8b19",
+ "GeneratedBy": "urn:1dcat-VxIRgqMS",
"digest": {
"sha256": "9bb1cabac5ce7ca19dffa5cd6336a9bf82d362fea2ce9341978406e421b5333c"
}
},
{
- "@id": "urn:b5be0e1d-2eae-4498-ad71-9ee980856337",
+ "@id": "bids::X.nocensor.xmat.1D'[4]'",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D'[4]'",
"digest": {
@@ -1272,16 +1283,16 @@
}
},
{
- "@id": "urn:50736079-de9a-432b-a2db-79a26b418d57",
+ "@id": "bids::ideal_probe.1D",
"Label": "ideal_probe.1D",
"AtLocation": "ideal_probe.1D",
- "GeneratedBy": "urn:815e4ca6-6373-4dd2-9391-c5ceca637440",
+ "GeneratedBy": "urn:1dcat-QBu2vYst",
"digest": {
"sha256": "705d93afa8b6ded9f4f572db3f967b54e9906942669af51dd8287a9863bb4288"
}
},
{
- "@id": "urn:7b8eadd4-f765-437a-ab0e-4824de937df0",
+ "@id": "bids::X.nocensor.xmat.1D%22[$reg_cols]%22",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D\"[$reg_cols]\"",
"digest": {
@@ -1289,52 +1300,52 @@
}
},
{
- "@id": "urn:969531e6-8e1f-4881-b5cb-ce83fe7ff1ac",
+ "@id": "bids::sum_ideal.1D",
"Label": "sum_ideal.1D",
"AtLocation": "sum_ideal.1D",
- "GeneratedBy": "urn:1f0c4c33-4ba6-430e-a3db-3bf7f03cdf13",
+ "GeneratedBy": "urn:3dtstat-lCq7pBIS",
"digest": {
"sha256": "b2dccadcd84b2d26ec9685c4d1846baf2f11b867f31c36a08748d1c85467b01a"
}
},
{
- "@id": "urn:0fe907b9-525c-451d-b98b-6e4696857b52",
+ "@id": "bids::X.stim.xmat.1D",
"Label": "X.stim.xmat.1D",
"AtLocation": "X.stim.xmat.1D",
- "GeneratedBy": "urn:6ebcc108-fd65-49bb-8a39-6353b906a79c",
+ "GeneratedBy": "urn:1dcat-ZX8bODEi",
"digest": {
"sha256": "7c61b2f4bbb9eb0cecb19f81faa3a79b94d547b7fb4087ed18e368619e0004e6"
}
},
{
- "@id": "urn:30b563bf-fe85-4fb6-bab0-727a4acb3078",
+ "@id": "bids::blur.epits.1D",
"Label": "blur.epits.1D",
"AtLocation": "blur.epits.1D",
- "GeneratedBy": "urn:689be361-2322-444c-81b5-551d7b16ab70",
+ "GeneratedBy": "urn:3dfwhmx-Cyw8XHhT",
"digest": {
"sha256": "623e70a42214e56babc1f1dca156e0b11ba09865dbd6ca9549d54ca2fc601515"
}
},
{
- "@id": "urn:7ac1a591-3185-4ce8-9d34-f3bf695c0fa7",
+ "@id": "bids::blur.errts.1D",
"Label": "blur.errts.1D",
"AtLocation": "blur.errts.1D",
- "GeneratedBy": "urn:c77d7191-0804-496c-b902-abaed4fcf96c",
+ "GeneratedBy": "urn:3dfwhmx-gvqns3P7",
"digest": {
"sha256": "73969700079b5d3275536ac7eaf0e17571d7e74ec49553b6940f90d5718fc800"
}
},
{
- "@id": "urn:08e4f79d-ea4f-4d46-ab8d-c778d5bb066c",
+ "@id": "bids::ClustSim",
"Label": "ClustSim",
"AtLocation": "ClustSim",
- "GeneratedBy": "urn:161541c6-24a8-4a72-a6ca-7fdd2db5f14b",
+ "GeneratedBy": "urn:3dclusts-tJOYZHF3",
"digest": {
"sha256": "2e0cdba2c91902ba12d742a39cb20df66cfd705ba8de767fbf68aae8eb65c6f0"
}
},
{
- "@id": "urn:19376406-be37-4a1b-abdd-6e0af87f6e14",
+ "@id": "bids::pb00.$subj.r*.tcat+orig.HEAD",
"Label": "pb00.$subj.r*.tcat",
"AtLocation": "pb00.$subj.r*.tcat+orig.HEAD",
"digest": {
@@ -1342,10 +1353,10 @@
}
},
{
- "@id": "urn:3629b3b4-6e9a-417f-9924-ee2d75ed4331",
+ "@id": "bids::-exit0",
"Label": "-exit0",
"AtLocation": "-exit0",
- "GeneratedBy": "urn:c40149f1-9ffe-4002-923e-896181a14e31",
+ "GeneratedBy": "urn:genssrev-nmpXt1CC",
"digest": {
"sha256": "871a4d3513ed2924cbb10c1c15a196eac4a46a05bdcc248e3bcdb23327b3ad90"
}
diff --git a/examples/from_parsers/afni/afni_clustconn_26_proc.png b/examples/from_parsers/afni/afni_clustconn_26_proc.png
index d6319b17b..7531d359f 100644
Binary files a/examples/from_parsers/afni/afni_clustconn_26_proc.png and b/examples/from_parsers/afni/afni_clustconn_26_proc.png differ
diff --git a/examples/from_parsers/afni/afni_clustconn_26_proc_block.jsonld b/examples/from_parsers/afni/afni_clustconn_26_proc_block.jsonld
index f3270c4d9..d1a0e4276 100644
--- a/examples/from_parsers/afni/afni_clustconn_26_proc_block.jsonld
+++ b/examples/from_parsers/afni/afni_clustconn_26_proc_block.jsonld
@@ -4,187 +4,189 @@
"Records": {
"Software": [
{
- "@id": "urn:36da7c9a-20bd-4f7a-95e7-c2ed5900e51f",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:afni-reNtbBWO",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
- "Version": "afni24"
+ "Version": "afni24",
+ "AltIdentifier": "RRID:SCR_005927"
}
],
"Activities": [
{
- "@id": "urn:c533bcb1-7df7-4882-b3f7-025f83a992c9",
+ "@id": "urn:autobloc-aS8nTmCG",
"Label": "auto block: setup",
- "AssociatedWith": "urn:36da7c9a-20bd-4f7a-95e7-c2ed5900e51f",
+ "AssociatedWith": "urn:afni-reNtbBWO",
"Command": "mkdir $output_dir; mkdir $output_dir/stimuli; cp ./afni_cluster_nn3/tone_counting_onset_times.txt ./afni_cluster_nn3/tone_counting_probe_duration.txt $output_dir/stimuli; 3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w; ",
"Used": [
- "urn:033018b3-4611-4020-a838-513bb1247ebf",
- "urn:e409a3c1-44eb-47e1-a284-584feffca4ad",
- "urn:b8ec464e-bd05-4efe-a304-d4d6d53fe9a6"
+ "bids::afni_cluster_nn3/tone_counting_onset_times.txt",
+ "bids::afni_cluster_nn3/tone_counting_probe_duration.txt",
+ "bids::sub-01_T1w.nii.gz"
]
},
{
- "@id": "urn:cad734fe-8e50-4457-92ae-2951b1114e43",
+ "@id": "urn:autobloc-ia4ddT4y",
"Label": "auto block: tcat",
- "AssociatedWith": "urn:36da7c9a-20bd-4f7a-95e7-c2ed5900e51f",
+ "AssociatedWith": "urn:afni-reNtbBWO",
"Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ",
"Used": [
- "urn:934935be-608a-4b14-a085-3555a49502b6"
+ "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'"
]
},
{
- "@id": "urn:1170e700-aa59-4aa0-997b-b8f4e38a73d6",
+ "@id": "urn:autobloc-VVyUPAJF",
"Label": "auto block: outcount",
- "AssociatedWith": "urn:36da7c9a-20bd-4f7a-95e7-c2ed5900e51f",
+ "AssociatedWith": "urn:afni-reNtbBWO",
"Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ",
"Used": [
- "urn:56946b2f-aa6b-49de-af5a-1e3a21a7d2df",
- "urn:0e50f3e7-13b7-4552-bab5-d75b2ca8e233"
+ "bids::pb00.$subj.r$run.tcat+orig",
+ "bids::outcount.r*.1D"
]
},
{
- "@id": "urn:de7874b0-8d41-4d13-9f8a-d25dd58b7343",
+ "@id": "urn:tshift-nWUsm1PO",
"Label": "tshift",
- "AssociatedWith": "urn:36da7c9a-20bd-4f7a-95e7-c2ed5900e51f",
+ "AssociatedWith": "urn:afni-reNtbBWO",
"Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ",
"Used": [
- "urn:56946b2f-aa6b-49de-af5a-1e3a21a7d2df"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:80c4a099-d6e8-436f-95e3-7200b12e2428",
+ "@id": "urn:align-Ir8eJ48B",
"Label": "align",
- "AssociatedWith": "urn:36da7c9a-20bd-4f7a-95e7-c2ed5900e51f",
+ "AssociatedWith": "urn:afni-reNtbBWO",
"Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ",
"Used": [
- "urn:144d6d52-57df-46f7-b7fb-819db14165f1",
- "urn:84b79c77-e8eb-471c-9e27-83ae9cd47563"
+ "bids::pb01.$subj.r01.tshift+orig",
+ "bids::sub-01_T1w+orig"
]
},
{
- "@id": "urn:12c1865a-4e4e-43c6-9f86-75748ccc4b69",
+ "@id": "urn:tlrc-3vkBmAg4",
"Label": "tlrc",
- "AssociatedWith": "urn:36da7c9a-20bd-4f7a-95e7-c2ed5900e51f",
+ "AssociatedWith": "urn:afni-reNtbBWO",
"Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ",
"Used": [
- "urn:2766bf06-a141-4e54-9682-cf3964690b32",
- "urn:cd03d6e6-5ca9-4b09-a018-dbd42788847a",
- "urn:e335b461-197f-4383-ba34-1c6e9bde42fe"
+ "bids::TT_N27+tlrc",
+ "bids::sub-01_T1w_ns+orig",
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:283f6a2c-60bd-4445-8863-64da92b4e7ec",
+ "@id": "urn:volreg-6cRFx5Uu",
"Label": "volreg",
- "AssociatedWith": "urn:36da7c9a-20bd-4f7a-95e7-c2ed5900e51f",
+ "AssociatedWith": "urn:afni-reNtbBWO",
"Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig; 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1; cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D; 3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run; 3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run; 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc; cat dfile.r*.1D > dfile_rall.1D; 3dcopy rm.epi.min.r01+tlrc mask_epi_extents; 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg; 3dcopy sub-01_T1w_ns+tlrc anat_final.$subj; 3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped; ",
"Used": [
- "urn:41e363ee-8e6d-4869-9a19-027f02223578",
- "urn:41e363ee-8e6d-4869-9a19-027f02223578",
- "urn:e335b461-197f-4383-ba34-1c6e9bde42fe",
- "urn:41e363ee-8e6d-4869-9a19-027f02223578",
- "urn:8c7ca029-99fa-4b68-83ba-5fa681021c7f",
- "urn:4032004f-469c-4c23-9d84-67b87bd475c3",
- "urn:8c7ca029-99fa-4b68-83ba-5fa681021c7f",
- "urn:bf196f88-6dea-4184-84d9-0017dcb02539",
- "urn:ab0217cf-72be-4734-819d-2ea486fa0aad",
- "urn:9c151f44-34a8-4f40-8b8f-244edc53b37a",
- "urn:0fb9aff5-7a84-418c-b48b-e2ba8ecc3540",
- "urn:7fb86442-2d63-437f-8793-4c6a0429e57b",
- "urn:8c7ca029-99fa-4b68-83ba-5fa681021c7f",
- "urn:c7c84640-688f-48ff-9839-f197cde472eb"
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.epi.all1+orig",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.epi.1.r$run+tlrc",
+ "bids::dfile.r*.1D",
+ "bids::rm.epi.min.r01+tlrc",
+ "bids::mask_epi_extents+tlrc",
+ "bids::rm.epi.nomask.r$run+tlrc",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::anat_final.$subj+tlrc",
+ "bids::warp.anat.Xat.1D"
]
},
{
- "@id": "urn:2fc87508-3c73-46fa-8b6d-1ee5c8e516e5",
+ "@id": "urn:blur-6u7MxnsO",
"Label": "blur",
- "AssociatedWith": "urn:36da7c9a-20bd-4f7a-95e7-c2ed5900e51f",
+ "AssociatedWith": "urn:afni-reNtbBWO",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc; ",
"Used": [
- "urn:338b803b-badc-4a28-a1fe-96893345cd2b",
- "urn:9e815522-5765-4a06-a9d8-89589bf4e78b"
+ "bids::pb02.$subj.r$run.volreg+tlrc",
+ "bids::pb03.$subj.r$run.blur"
]
},
{
- "@id": "urn:fe07b655-f61a-42ab-997a-c3213afad432",
+ "@id": "urn:mask-SiQp3rcH",
"Label": "mask",
- "AssociatedWith": "urn:36da7c9a-20bd-4f7a-95e7-c2ed5900e51f",
+ "AssociatedWith": "urn:afni-reNtbBWO",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc; 3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj; 3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj; 3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt; 3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt; 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group; ",
"Used": [
- "urn:34583576-5b25-413c-887e-259f2c281441",
- "urn:2c613c87-e382-4a3e-931f-f58e2f93f0db",
- "urn:8c7ca029-99fa-4b68-83ba-5fa681021c7f",
- "urn:27dee2a5-d4fd-455a-a7ba-355c85466044",
- "urn:918eddc7-6f84-490a-ac14-1da947842f79",
- "urn:a0d89fab-b0ab-4f2d-9190-54341930a4bb",
- "urn:918eddc7-6f84-490a-ac14-1da947842f79",
- "urn:a0d89fab-b0ab-4f2d-9190-54341930a4bb",
- "urn:2c613c87-e382-4a3e-931f-f58e2f93f0db",
- "urn:c408e374-5f90-48fe-95b2-5f7a05eee2f9",
- "urn:8d7ed096-6eee-46d3-8707-16ad1a94db51"
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.resam.anat+tlrc",
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee",
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee",
+ "bids::/Users/u1591557/abin/TT_N27+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.resam.group+tlrc"
]
},
{
- "@id": "urn:cb76aa60-f974-4049-9756-cd45aff5f484",
+ "@id": "urn:scale-VpuXgWB1",
"Label": "scale",
- "AssociatedWith": "urn:36da7c9a-20bd-4f7a-95e7-c2ed5900e51f",
+ "AssociatedWith": "urn:afni-reNtbBWO",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc; 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale; ",
"Used": [
- "urn:34583576-5b25-413c-887e-259f2c281441",
- "urn:0f745c76-0f78-49c5-8ff9-bccd8ba53898",
- "urn:34583576-5b25-413c-887e-259f2c281441",
- "urn:7fb86442-2d63-437f-8793-4c6a0429e57b"
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::mask_epi_extents+tlrc",
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::rm.mean_r$run+tlrc"
]
},
{
- "@id": "urn:4f3e80fa-50c7-4f8b-8415-92b4b77b380e",
+ "@id": "urn:regress-c23cHR6X",
"Label": "regress",
- "AssociatedWith": "urn:36da7c9a-20bd-4f7a-95e7-c2ed5900e51f",
+ "AssociatedWith": "urn:afni-reNtbBWO",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}; 3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj; 1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt; 3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD; 3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"; 3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"; 3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj; 3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc; 3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D; 3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D; 3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP; 3dTstat -sum -prefix corr_brain rm.DP+tlrc; 1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D; 1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D; 3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"; 1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D; ",
"Used": [
- "urn:84298b0b-a786-45a5-a871-c186fc0ecef3",
- "urn:84298b0b-a786-45a5-a871-c186fc0ecef3",
- "urn:84298b0b-a786-45a5-a871-c186fc0ecef3",
- "urn:1b2b75d0-b3d0-41a6-95d1-205880e86671",
- "urn:1b2b75d0-b3d0-41a6-95d1-205880e86671",
- "urn:a559ffd4-5aeb-4597-9090-066211978da4",
- "urn:2618dc26-6b1b-47a6-bfa4-c219a8a49058",
- "urn:2c613c87-e382-4a3e-931f-f58e2f93f0db",
- "urn:3e2a1065-eb68-42af-8262-c15c24532510",
- "urn:d7059659-eda4-459d-a116-80bc35f12d1f",
- "urn:8e5ab35a-7669-4e51-adee-3f7e416010f6",
- "urn:7ee5385c-09e0-4696-a97c-3cb9e2bbfc83",
- "urn:7ba51dfb-8c22-41d0-8725-26d9c8cac113",
- "urn:46474507-de7a-4299-9f41-3cf6127cb382",
- "urn:8e1c3530-bd73-4ef8-abbd-8e1639bd1b3d",
- "urn:ed38591f-b525-405d-aeda-06e9379f3674",
- "urn:ee7c5123-7690-4489-a1ca-86dc4dbb3813",
- "urn:ee7c5123-7690-4489-a1ca-86dc4dbb3813"
+ "bids::dfile_rall.1D",
+ "bids::dfile_rall.1D",
+ "bids::dfile_rall.1D",
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD",
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD",
+ "bids::all_runs.$subj+tlrc%22[$ktrs]%22",
+ "bids::errts.$%7Bsubj%7D+tlrc%22[$ktrs]%22",
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.noise.all+tlrc",
+ "bids::rm.signal.all+tlrc",
+ "bids::errts.$%7Bsubj%7D+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::out.gcor.1D",
+ "bids::rm.errts.unit+tlrc",
+ "bids::rm.DP+tlrc",
+ "bids::X.nocensor.xmat.1D'[3]'",
+ "bids::X.nocensor.xmat.1D'[4]'",
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22",
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:d3f5c0f9-c276-4ecf-b5e5-7842e1866af6",
+ "@id": "urn:bluresti-qlH4zhL5",
"Label": "blur estimation",
- "AssociatedWith": "urn:36da7c9a-20bd-4f7a-95e7-c2ed5900e51f",
+ "AssociatedWith": "urn:afni-reNtbBWO",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D; 3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D; 3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim; ",
"Used": [
- "urn:2c613c87-e382-4a3e-931f-f58e2f93f0db",
- "urn:2c613c87-e382-4a3e-931f-f58e2f93f0db",
- "urn:2c613c87-e382-4a3e-931f-f58e2f93f0db"
+ "bids::full_mask.$subj+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:a73c178f-c270-4508-803e-75b75a75d3d5",
+ "@id": "urn:autobloc-RIT2DdIu",
"Label": "auto block: generate review scripts",
- "AssociatedWith": "urn:36da7c9a-20bd-4f7a-95e7-c2ed5900e51f",
+ "AssociatedWith": "urn:afni-reNtbBWO",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD; gen_ss_review_scripts.py -mot_limit 0.3 -exit0; ",
"Used": [
- "urn:4b99f7af-3b64-4174-ac3f-cccc60966174"
+ "bids::pb00.$subj.r*.tcat+orig.HEAD"
]
}
],
"Entities": [
{
- "@id": "urn:e409a3c1-44eb-47e1-a284-584feffca4ad",
+ "@id": "bids::afni_cluster_nn3/tone_counting_onset_times.txt",
"Label": "tone_counting_onset_times.txt",
"AtLocation": "./afni_cluster_nn3/tone_counting_onset_times.txt",
"digest": {
@@ -192,7 +194,7 @@
}
},
{
- "@id": "urn:033018b3-4611-4020-a838-513bb1247ebf",
+ "@id": "bids::afni_cluster_nn3/tone_counting_probe_duration.txt",
"Label": "tone_counting_probe_duration.txt",
"AtLocation": "./afni_cluster_nn3/tone_counting_probe_duration.txt",
"digest": {
@@ -200,7 +202,7 @@
}
},
{
- "@id": "urn:b8ec464e-bd05-4efe-a304-d4d6d53fe9a6",
+ "@id": "bids::sub-01_T1w.nii.gz",
"Label": "sub-01_T1w.nii.gz",
"AtLocation": "sub-01_T1w.nii.gz",
"digest": {
@@ -208,34 +210,34 @@
}
},
{
- "@id": "urn:0f7f6c06-a01b-40ab-aef3-0765ceb9612d",
+ "@id": "bids::$output_dir",
"Label": "$output_dir",
"AtLocation": "$output_dir",
- "GeneratedBy": "urn:c533bcb1-7df7-4882-b3f7-025f83a992c9",
+ "GeneratedBy": "urn:autobloc-aS8nTmCG",
"digest": {
"sha256": "9fa4c635e6533ddf2fed54295920052818d948c3ffe97bc753bd7336b453f8cb"
}
},
{
- "@id": "urn:33178c77-5b3e-41fc-aa26-ed92811f912b",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:c533bcb1-7df7-4882-b3f7-025f83a992c9"
+ "GeneratedBy": "urn:autobloc-aS8nTmCG"
},
{
- "@id": "urn:ce01820c-b433-4f27-9aec-66cb4e464837",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:c533bcb1-7df7-4882-b3f7-025f83a992c9"
+ "GeneratedBy": "urn:autobloc-aS8nTmCG"
},
{
- "@id": "urn:94c02812-76a0-4fe5-b8d6-fc317f51ca41",
+ "@id": "bids::$output_dir/sub-01_T1w",
"Label": "sub-01_T1w",
"AtLocation": "$output_dir/sub-01_T1w",
- "GeneratedBy": "urn:c533bcb1-7df7-4882-b3f7-025f83a992c9"
+ "GeneratedBy": "urn:autobloc-aS8nTmCG"
},
{
- "@id": "urn:934935be-608a-4b14-a085-3555a49502b6",
+ "@id": "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Label": "sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"digest": {
@@ -243,13 +245,13 @@
}
},
{
- "@id": "urn:e1b2a3cf-5e2c-46cc-b65d-e2af1525ae24",
+ "@id": "bids::$output_dir/pb00.$subj.r01.tcat",
"Label": "pb00.$subj.r01.tcat",
"AtLocation": "$output_dir/pb00.$subj.r01.tcat",
- "GeneratedBy": "urn:cad734fe-8e50-4457-92ae-2951b1114e43"
+ "GeneratedBy": "urn:autobloc-ia4ddT4y"
},
{
- "@id": "urn:56946b2f-aa6b-49de-af5a-1e3a21a7d2df",
+ "@id": "bids::pb00.$subj.r$run.tcat+orig",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -257,7 +259,7 @@
}
},
{
- "@id": "urn:0e50f3e7-13b7-4552-bab5-d75b2ca8e233",
+ "@id": "bids::outcount.r*.1D",
"Label": "outcount.r*.1D",
"AtLocation": "outcount.r*.1D",
"digest": {
@@ -265,25 +267,25 @@
}
},
{
- "@id": "urn:ffe63744-e200-4a3d-ab0a-e0de9bce6565",
+ "@id": "bids::outcount.r$run.1D",
"Label": "outcount.r$run.1D",
"AtLocation": "outcount.r$run.1D",
- "GeneratedBy": "urn:1170e700-aa59-4aa0-997b-b8f4e38a73d6",
+ "GeneratedBy": "urn:autobloc-VVyUPAJF",
"digest": {
"sha256": "63d9f539e5470badc625d557109f68bc4eecbb02ca2667483739d52f95e5d0dd"
}
},
{
- "@id": "urn:5716b79a-8e82-4d72-99ca-9f76d32cd29c",
+ "@id": "bids::outcount_rall.1D",
"Label": "outcount_rall.1D",
"AtLocation": "outcount_rall.1D",
- "GeneratedBy": "urn:1170e700-aa59-4aa0-997b-b8f4e38a73d6",
+ "GeneratedBy": "urn:autobloc-VVyUPAJF",
"digest": {
"sha256": "cb887fd5e4d5e9acb3a24820d0f7a62ed38a5ffb0fdedd373440ac0219fb186a"
}
},
{
- "@id": "urn:56946b2f-aa6b-49de-af5a-1e3a21a7d2df",
+ "@id": "bids::pb00.$subj.r$run.tcat+orig",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -291,16 +293,16 @@
}
},
{
- "@id": "urn:f92146da-059f-436e-9761-19148ff8a713",
+ "@id": "bids::pb01.$subj.r$run.tshift",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift",
- "GeneratedBy": "urn:de7874b0-8d41-4d13-9f8a-d25dd58b7343",
+ "GeneratedBy": "urn:tshift-nWUsm1PO",
"digest": {
"sha256": "c6bf01cea8d2eac1d7a866f80b865c6e7d4b4e012dbb63d480ac9a8551162d72"
}
},
{
- "@id": "urn:144d6d52-57df-46f7-b7fb-819db14165f1",
+ "@id": "bids::sub-01_T1w+orig",
"Label": "sub-01_T1w",
"AtLocation": "sub-01_T1w+orig",
"digest": {
@@ -308,7 +310,7 @@
}
},
{
- "@id": "urn:84b79c77-e8eb-471c-9e27-83ae9cd47563",
+ "@id": "bids::pb01.$subj.r01.tshift+orig",
"Label": "pb01.$subj.r01.tshift",
"AtLocation": "pb01.$subj.r01.tshift+orig",
"digest": {
@@ -316,16 +318,16 @@
}
},
{
- "@id": "urn:e93ede5a-a9ec-4c73-96ba-d3c0500250c5",
+ "@id": "bids::_al_junk",
"Label": "_al_junk",
"AtLocation": "_al_junk",
- "GeneratedBy": "urn:80c4a099-d6e8-436f-95e3-7200b12e2428",
+ "GeneratedBy": "urn:align-Ir8eJ48B",
"digest": {
"sha256": "bd785a075a4c6446e1e54de9e628913f7f1c814e86b69a9fbfe933209e6d37b5"
}
},
{
- "@id": "urn:cd03d6e6-5ca9-4b09-a018-dbd42788847a",
+ "@id": "bids::TT_N27+tlrc",
"Label": "TT_N27",
"AtLocation": "TT_N27+tlrc",
"digest": {
@@ -333,7 +335,7 @@
}
},
{
- "@id": "urn:2766bf06-a141-4e54-9682-cf3964690b32",
+ "@id": "bids::sub-01_T1w_ns+orig",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+orig",
"digest": {
@@ -341,7 +343,7 @@
}
},
{
- "@id": "urn:e335b461-197f-4383-ba34-1c6e9bde42fe",
+ "@id": "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc::WARP_DATA",
"digest": {
@@ -349,16 +351,16 @@
}
},
{
- "@id": "urn:c7c84640-688f-48ff-9839-f197cde472eb",
+ "@id": "bids::warp.anat.Xat.1D",
"Label": "warp.anat.Xat.1D",
"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:12c1865a-4e4e-43c6-9f86-75748ccc4b69",
+ "GeneratedBy": "urn:tlrc-3vkBmAg4",
"digest": {
"sha256": "800633fb5b4e9be64078bc181c4d5510ffb73fc5cccaf364c7fb6a294aa06728"
}
},
{
- "@id": "urn:e335b461-197f-4383-ba34-1c6e9bde42fe",
+ "@id": "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc::WARP_DATA",
"digest": {
@@ -366,16 +368,16 @@
}
},
{
- "@id": "urn:c7c84640-688f-48ff-9839-f197cde472eb",
+ "@id": "bids::warp.anat.Xat.1D",
"Label": "warp.anat.Xat.1D",
"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:12c1865a-4e4e-43c6-9f86-75748ccc4b69",
+ "GeneratedBy": "urn:tlrc-3vkBmAg4",
"digest": {
"sha256": "800633fb5b4e9be64078bc181c4d5510ffb73fc5cccaf364c7fb6a294aa06728"
}
},
{
- "@id": "urn:41e363ee-8e6d-4869-9a19-027f02223578",
+ "@id": "bids::pb01.$subj.r$run.tshift+orig",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift+orig",
"digest": {
@@ -383,7 +385,7 @@
}
},
{
- "@id": "urn:8c7ca029-99fa-4b68-83ba-5fa681021c7f",
+ "@id": "bids::sub-01_T1w_ns+tlrc",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc",
"digest": {
@@ -391,7 +393,7 @@
}
},
{
- "@id": "urn:4032004f-469c-4c23-9d84-67b87bd475c3",
+ "@id": "bids::rm.epi.all1+orig",
"Label": "rm.epi.all1",
"AtLocation": "rm.epi.all1+orig",
"digest": {
@@ -399,7 +401,7 @@
}
},
{
- "@id": "urn:bf196f88-6dea-4184-84d9-0017dcb02539",
+ "@id": "bids::rm.epi.1.r$run+tlrc",
"Label": "rm.epi.1.r$run",
"AtLocation": "rm.epi.1.r$run+tlrc",
"digest": {
@@ -407,7 +409,7 @@
}
},
{
- "@id": "urn:ab0217cf-72be-4734-819d-2ea486fa0aad",
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@@ -415,7 +417,7 @@
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@@ -423,7 +425,7 @@
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@@ -431,7 +433,7 @@
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@@ -439,97 +441,105 @@
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@@ -537,7 +547,7 @@
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@@ -545,7 +555,7 @@
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@@ -553,7 +563,7 @@
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@@ -561,7 +571,7 @@
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@@ -569,7 +579,7 @@
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@@ -577,7 +587,7 @@
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{
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@@ -585,7 +595,7 @@
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{
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@@ -593,7 +603,7 @@
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{
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@@ -601,7 +611,7 @@
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@@ -609,61 +619,61 @@
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@@ -671,7 +681,7 @@
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@@ -679,7 +689,7 @@
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@@ -687,34 +697,34 @@
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- "GeneratedBy": "urn:cb76aa60-f974-4049-9756-cd45aff5f484",
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@@ -722,7 +732,7 @@
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@@ -730,7 +740,7 @@
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@@ -738,7 +748,7 @@
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@@ -746,7 +756,7 @@
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@@ -754,7 +764,7 @@
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@@ -762,7 +772,7 @@
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@@ -770,7 +780,7 @@
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@@ -778,7 +788,7 @@
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@@ -786,7 +796,7 @@
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@@ -794,7 +804,7 @@
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@@ -802,7 +812,7 @@
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{
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@@ -810,7 +820,7 @@
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{
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@@ -818,133 +828,133 @@
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{
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"AtLocation": "motion_demean.1D",
- "GeneratedBy": "urn:4f3e80fa-50c7-4f8b-8415-92b4b77b380e",
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- "GeneratedBy": "urn:4f3e80fa-50c7-4f8b-8415-92b4b77b380e",
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- "GeneratedBy": "urn:4f3e80fa-50c7-4f8b-8415-92b4b77b380e",
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- "GeneratedBy": "urn:4f3e80fa-50c7-4f8b-8415-92b4b77b380e",
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"sha256": "bda68a16c0afd5e55d4d7415c8c959e61a9aad7898dd456b0f3bb597363dde31"
}
},
{
- "@id": "urn:6b970f51-83db-4286-9ac6-f0639095e34d",
+ "@id": "bids::rm.noise.all",
"Label": "rm.noise.all",
"AtLocation": "rm.noise.all",
- "GeneratedBy": "urn:4f3e80fa-50c7-4f8b-8415-92b4b77b380e",
+ "GeneratedBy": "urn:regress-c23cHR6X",
"digest": {
"sha256": "431314eb75d086ce08373b3a374427969e89414c4a2d607e449c1f6485c547af"
}
},
{
- "@id": "urn:74884da0-1e79-4463-8ba6-1abd595cc3dd",
+ "@id": "bids::TSNR.$subj",
"Label": "TSNR.$subj",
"AtLocation": "TSNR.$subj",
- "GeneratedBy": "urn:4f3e80fa-50c7-4f8b-8415-92b4b77b380e",
+ "GeneratedBy": "urn:regress-c23cHR6X",
"digest": {
"sha256": "303f183145a1e295686c08335d3b70753777cf0fa0b3f9628cf8de5471359a00"
}
},
{
- "@id": "urn:04a712df-9c24-485f-8e45-4df1264e44f8",
+ "@id": "bids::rm.errts.unit",
"Label": "rm.errts.unit",
"AtLocation": "rm.errts.unit",
- "GeneratedBy": "urn:4f3e80fa-50c7-4f8b-8415-92b4b77b380e",
+ "GeneratedBy": "urn:regress-c23cHR6X",
"digest": {
"sha256": "03b570ad773a00f51ab7e6cdedfebdeca45f5356de0c25f9e3be44d7bf2c7151"
}
},
{
- "@id": "urn:65939ac7-7a7a-472d-9da3-5f4823ee8d5b",
+ "@id": "urn:uuid:04745c1c-681d-4ecd-99f5-96d342aae6ed",
"Label": "-",
"AtLocation": "-",
- "GeneratedBy": "urn:4f3e80fa-50c7-4f8b-8415-92b4b77b380e",
+ "GeneratedBy": "urn:regress-c23cHR6X",
"digest": {
"sha256": "dac304c9f20899ca1ef5aa403e565345fd0ff4ed80c35f82007c9b03a68292b3"
}
},
{
- "@id": "urn:f0c9a6c3-06f6-4cf7-8a95-14b8dbdbe664",
+ "@id": "bids::rm.DP",
"Label": "rm.DP",
"AtLocation": "rm.DP",
- "GeneratedBy": "urn:4f3e80fa-50c7-4f8b-8415-92b4b77b380e",
+ "GeneratedBy": "urn:regress-c23cHR6X",
"digest": {
"sha256": "06a0bfbc609c1a06ecf93c479a3288d2911c7f5f3e93cf49c5d26f721c2035ed"
}
},
{
- "@id": "urn:8ae7c2aa-3fc9-45b4-b199-31ac2d6380a1",
+ "@id": "bids::corr_brain",
"Label": "corr_brain",
"AtLocation": "corr_brain",
- "GeneratedBy": "urn:4f3e80fa-50c7-4f8b-8415-92b4b77b380e",
+ "GeneratedBy": "urn:regress-c23cHR6X",
"digest": {
"sha256": "74e3aeae0da338b871ab5dc9e8859a4e81fcf1b3c0042cd22fe337eb7baf5eae"
}
},
{
- "@id": "urn:0da784c9-12e0-4732-b4de-2f7fac3a78b6",
+ "@id": "bids::ideal_tone_counting.1D",
"Label": "ideal_tone_counting.1D",
"AtLocation": "ideal_tone_counting.1D",
- "GeneratedBy": "urn:4f3e80fa-50c7-4f8b-8415-92b4b77b380e",
+ "GeneratedBy": "urn:regress-c23cHR6X",
"digest": {
"sha256": "9bb1cabac5ce7ca19dffa5cd6336a9bf82d362fea2ce9341978406e421b5333c"
}
},
{
- "@id": "urn:b18d15a5-a09a-4c39-b3b2-55e1eb31b5db",
+ "@id": "bids::ideal_probe.1D",
"Label": "ideal_probe.1D",
"AtLocation": "ideal_probe.1D",
- "GeneratedBy": "urn:4f3e80fa-50c7-4f8b-8415-92b4b77b380e",
+ "GeneratedBy": "urn:regress-c23cHR6X",
"digest": {
"sha256": "705d93afa8b6ded9f4f572db3f967b54e9906942669af51dd8287a9863bb4288"
}
},
{
- "@id": "urn:cb2d5117-8e60-42fb-b3fa-2c5ac0a124b9",
+ "@id": "bids::sum_ideal.1D",
"Label": "sum_ideal.1D",
"AtLocation": "sum_ideal.1D",
- "GeneratedBy": "urn:4f3e80fa-50c7-4f8b-8415-92b4b77b380e",
+ "GeneratedBy": "urn:regress-c23cHR6X",
"digest": {
"sha256": "b2dccadcd84b2d26ec9685c4d1846baf2f11b867f31c36a08748d1c85467b01a"
}
},
{
- "@id": "urn:c63d30d7-d415-4bd9-842f-b40abb81097e",
+ "@id": "bids::X.stim.xmat.1D",
"Label": "X.stim.xmat.1D",
"AtLocation": "X.stim.xmat.1D",
- "GeneratedBy": "urn:4f3e80fa-50c7-4f8b-8415-92b4b77b380e",
+ "GeneratedBy": "urn:regress-c23cHR6X",
"digest": {
"sha256": "7c61b2f4bbb9eb0cecb19f81faa3a79b94d547b7fb4087ed18e368619e0004e6"
}
},
{
- "@id": "urn:2c613c87-e382-4a3e-931f-f58e2f93f0db",
+ "@id": "bids::full_mask.$subj+tlrc",
"Label": "full_mask.$subj",
"AtLocation": "full_mask.$subj+tlrc",
"digest": {
@@ -952,34 +962,34 @@
}
},
{
- "@id": "urn:b06f7897-a1fb-4d07-a1da-28a0cb8c1f45",
+ "@id": "bids::blur.epits.1D",
"Label": "blur.epits.1D",
"AtLocation": "blur.epits.1D",
- "GeneratedBy": "urn:d3f5c0f9-c276-4ecf-b5e5-7842e1866af6",
+ "GeneratedBy": "urn:bluresti-qlH4zhL5",
"digest": {
"sha256": "623e70a42214e56babc1f1dca156e0b11ba09865dbd6ca9549d54ca2fc601515"
}
},
{
- "@id": "urn:c8ffc0c2-534a-4b93-b1ca-2e5ab6cc695c",
+ "@id": "bids::blur.errts.1D",
"Label": "blur.errts.1D",
"AtLocation": "blur.errts.1D",
- "GeneratedBy": "urn:d3f5c0f9-c276-4ecf-b5e5-7842e1866af6",
+ "GeneratedBy": "urn:bluresti-qlH4zhL5",
"digest": {
"sha256": "73969700079b5d3275536ac7eaf0e17571d7e74ec49553b6940f90d5718fc800"
}
},
{
- "@id": "urn:168438fa-0542-4538-ad21-d12412acbd5e",
+ "@id": "bids::ClustSim",
"Label": "ClustSim",
"AtLocation": "ClustSim",
- "GeneratedBy": "urn:d3f5c0f9-c276-4ecf-b5e5-7842e1866af6",
+ "GeneratedBy": "urn:bluresti-qlH4zhL5",
"digest": {
"sha256": "2e0cdba2c91902ba12d742a39cb20df66cfd705ba8de767fbf68aae8eb65c6f0"
}
},
{
- "@id": "urn:4b99f7af-3b64-4174-ac3f-cccc60966174",
+ "@id": "bids::pb00.$subj.r*.tcat+orig.HEAD",
"Label": "pb00.$subj.r*.tcat",
"AtLocation": "pb00.$subj.r*.tcat+orig.HEAD",
"digest": {
@@ -987,10 +997,10 @@
}
},
{
- "@id": "urn:96b36d9b-c550-4dcc-a426-16925826d22d",
+ "@id": "bids::-exit0",
"Label": "-exit0",
"AtLocation": "-exit0",
- "GeneratedBy": "urn:a73c178f-c270-4508-803e-75b75a75d3d5",
+ "GeneratedBy": "urn:autobloc-RIT2DdIu",
"digest": {
"sha256": "871a4d3513ed2924cbb10c1c15a196eac4a46a05bdcc248e3bcdb23327b3ad90"
}
diff --git a/examples/from_parsers/afni/afni_clustconn_26_proc_block.png b/examples/from_parsers/afni/afni_clustconn_26_proc_block.png
index b9af50b18..b4aec9b11 100644
Binary files a/examples/from_parsers/afni/afni_clustconn_26_proc_block.png and b/examples/from_parsers/afni/afni_clustconn_26_proc_block.png differ
diff --git a/examples/from_parsers/afni/afni_con_f_proc.jsonld b/examples/from_parsers/afni/afni_con_f_proc.jsonld
index dfa088f5c..851dd4576 100644
--- a/examples/from_parsers/afni/afni_con_f_proc.jsonld
+++ b/examples/from_parsers/afni/afni_con_f_proc.jsonld
@@ -4,578 +4,581 @@
"Records": {
"Software": [
{
- "@id": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:afni-fUbLl1Ef",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
- "Version": "afni24"
+ "Version": "afni24",
+ "AltIdentifier": "RRID:SCR_005927"
}
],
"Activities": [
{
- "@id": "urn:aa96021b-cc85-47e0-afd1-a427861606f0",
+ "@id": "urn:makedire-EjFu5Gzs",
"Label": "Make directory",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "mkdir $output_dir",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:5149ab44-6c94-47ec-9d96-f8a8558e930b",
+ "@id": "urn:makedire-YONHeB75",
"Label": "Make directory",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "mkdir $output_dir/stimuli",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:d191a56c-9c39-409d-a7f3-89bf42f57cc6",
+ "@id": "urn:cp-S3UpI0F6",
"Label": "cp",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "cp ./afni_f_test/tone_counting_onset_times.txt ./afni_f_test/tone_counting_probe_duration.txt $output_dir/stimuli",
"Parameters": {},
"Used": [
- "urn:072360e9-f1eb-43eb-9fa1-b58a93ba009d",
- "urn:1dcfc72d-5ed6-4ff7-a613-c69991b5c517"
+ "bids::afni_f_test/tone_counting_onset_times.txt",
+ "bids::afni_f_test/tone_counting_probe_duration.txt"
]
},
{
- "@id": "urn:d6cbc859-2b90-4245-a5fa-a7da66481e8f",
+ "@id": "urn:3dcopy-wnZoB6GV",
"Label": "3dcopy",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w",
"Parameters": {},
"Used": [
- "urn:b50c1808-e500-4550-966a-e626b6b521f9"
+ "bids::sub-01_T1w.nii.gz"
]
},
{
- "@id": "urn:be39d02a-940a-4437-9d22-c7f954010a48",
+ "@id": "urn:3dtcat-p93OvsNc",
"Label": "3dTcat",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Parameters": {},
"Used": [
- "urn:b75e6167-a56b-47f0-b2b3-f704b2e3f1d1"
+ "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'"
]
},
{
- "@id": "urn:9c952d4e-87cf-4ea6-b03c-4af969fd056b",
+ "@id": "urn:3dtoutco-MaaJHpvs",
"Label": "3dToutcount",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D",
"Parameters": {},
"Used": [
- "urn:b5f66e4e-2342-4065-8f7b-2c21b222d7b8"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:a38e2601-9eb9-4a15-a0b4-bda9d367153f",
+ "@id": "urn:cat-g7cf5SRg",
"Label": "cat",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "cat outcount.r*.1D > outcount_rall.1D",
"Parameters": {},
"Used": [
- "urn:a87b44c4-914f-43e9-8e91-283309980322"
+ "bids::outcount.r*.1D"
]
},
{
- "@id": "urn:678536c5-1572-466a-89e4-3051f34d7755",
+ "@id": "urn:3dtshift-7SbFVAaD",
"Label": "3dTshift",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig",
"Parameters": {},
"Used": [
- "urn:b5f66e4e-2342-4065-8f7b-2c21b222d7b8"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:d3630e97-6933-464a-97bb-ab45131ac706",
+ "@id": "urn:alignepi-enozA4y8",
"Label": "align_epi_anat.py",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off",
"Parameters": {},
"Used": [
- "urn:28a7f0e5-cc3f-4d95-ab33-4effe28cfe77",
- "urn:378c0ea8-a35a-472a-9347-ff979b23f462"
+ "bids::pb01.$subj.r01.tshift+orig",
+ "bids::sub-01_T1w+orig"
]
},
{
- "@id": "urn:1a2225a3-bad6-407b-b80e-b03730489480",
+ "@id": "urn:autotlrc-oduZ40ZK",
"Label": "@auto_tlrc",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss",
"Parameters": {},
"Used": [
- "urn:77377ac8-e94f-47ab-a512-1160810d465d",
- "urn:90d0ad49-8128-44dc-b6d3-40b269bf7e59"
+ "bids::TT_N27+tlrc",
+ "bids::sub-01_T1w_ns+orig"
]
},
{
- "@id": "urn:77295b4e-c8b1-46f6-8adc-7322f4a5361a",
+ "@id": "urn:catmatve-D7J6hS1Y",
"Label": "cat_matvec",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D",
"Parameters": {},
"Used": [
- "urn:333737b2-2884-489a-bd62-8411fc800020"
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:144f0732-ecdf-45a2-a853-842192246329",
+ "@id": "urn:3dvolreg-iMulinnK",
"Label": "3dvolreg",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig",
"Parameters": {},
"Used": [
- "urn:8d51b390-740e-4699-ba32-88d4f25ea861"
+ "bids::pb01.$subj.r$run.tshift+orig"
]
},
{
- "@id": "urn:7cd3c063-0abf-4893-925f-b2b299b0e6f4",
+ "@id": "urn:3dcalc-snZ2MgYQ",
"Label": "3dcalc",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1",
"Parameters": {},
"Used": [
- "urn:8d51b390-740e-4699-ba32-88d4f25ea861"
+ "bids::pb01.$subj.r$run.tshift+orig"
]
},
{
- "@id": "urn:8570c470-01d4-4c71-9c9a-61730f84d797",
+ "@id": "urn:catmatve-Kk6oC6ZE",
"Label": "cat_matvec",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D",
"Parameters": {},
"Used": [
- "urn:333737b2-2884-489a-bd62-8411fc800020"
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:7defd23d-6aca-465e-8cff-5dc88f651245",
+ "@id": "urn:3dalline-EJAmmrdL",
"Label": "3dAllineate",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run",
"Parameters": {},
"Used": [
- "urn:1f2965b4-c815-4bc8-a968-931ff67878fc",
- "urn:4f874d05-1bde-425a-a1e1-afa8043b443b",
- "urn:8d51b390-740e-4699-ba32-88d4f25ea861"
+ "bids::mat.r$run.warp.aff12.1D",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:2e9588bc-42dc-4f81-970f-3c7f63274c6d",
+ "@id": "urn:3dalline-LXY21VdU",
"Label": "3dAllineate",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run",
"Parameters": {},
"Used": [
- "urn:1f2965b4-c815-4bc8-a968-931ff67878fc",
- "urn:4f874d05-1bde-425a-a1e1-afa8043b443b",
- "urn:519d99a7-e9f5-4118-ae26-ce458fd3089b"
+ "bids::mat.r$run.warp.aff12.1D",
+ "bids::rm.epi.all1+orig",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:781e38c2-b867-478d-821b-b7e09975dc14",
+ "@id": "urn:3dtstat-HGyCHkmT",
"Label": "3dTstat",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc",
"Parameters": {},
"Used": [
- "urn:72115625-c8dc-4767-896c-bc1beabd045c"
+ "bids::rm.epi.1.r$run+tlrc"
]
},
{
- "@id": "urn:52ecd782-22ca-4d35-927b-3400bee24e28",
+ "@id": "urn:cat-iFjDMi8K",
"Label": "cat",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "cat dfile.r*.1D > dfile_rall.1D",
"Parameters": {},
"Used": [
- "urn:0bc4025e-062b-4072-a719-c8cac5d631f1"
+ "bids::dfile.r*.1D"
]
},
{
- "@id": "urn:7138a4c9-2a77-46a0-8701-b86b50081572",
+ "@id": "urn:3dcopy-7zdBDXoH",
"Label": "3dcopy",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents",
"Parameters": {},
"Used": [
- "urn:e5dfce3b-8f98-4387-80ab-31507296666f"
+ "bids::rm.epi.min.r01+tlrc"
]
},
{
- "@id": "urn:0eb2e611-6be8-4f49-b918-379168624f99",
+ "@id": "urn:3dcalc-I4FH3Fdh",
"Label": "3dcalc",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg",
"Parameters": {},
"Used": [
- "urn:2e914165-32e7-4df7-b382-59329c255f69",
- "urn:d46bb024-544e-42ee-992c-0379f823de74"
+ "bids::mask_epi_extents+tlrc",
+ "bids::rm.epi.nomask.r$run+tlrc"
]
},
{
- "@id": "urn:ec4eff37-da73-479a-bf55-e1c024f86d2c",
+ "@id": "urn:3dcopy-UjphDPUg",
"Label": "3dcopy",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj",
"Parameters": {},
"Used": [
- "urn:1f2965b4-c815-4bc8-a968-931ff67878fc"
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:c8a4cdcf-f7df-4fbd-ac11-4a8c211692ea",
+ "@id": "urn:3dalline-99Vqvx8a",
"Label": "3dAllineate",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped",
"Parameters": {},
"Used": [
- "urn:df0f0a0c-cfc4-4d8c-b572-856b120846f6"
+ "bids::anat_final.$subj+tlrc",
+ "bids::warp.anat.Xat.1D"
]
},
{
- "@id": "urn:3dee4533-d67a-4b50-8443-b712acd3d6c1",
+ "@id": "urn:3dmerge-1NLLMplG",
"Label": "3dmerge",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc",
"Parameters": {},
"Used": [
- "urn:3bfbbb4a-873e-45e9-9207-d8b0c3667936",
- "urn:66b78379-1541-42a4-ab85-eee1a6eeacf3"
+ "bids::pb02.$subj.r$run.volreg+tlrc",
+ "bids::pb03.$subj.r$run.blur"
]
},
{
- "@id": "urn:c64856a4-70d0-4ee4-823e-ded8d35f52f8",
+ "@id": "urn:3dautoma-ypPBwJMM",
"Label": "3dAutomask",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:344930df-f407-41d1-af01-bd028ff0bbdc"
+ "bids::pb03.$subj.r$run.blur+tlrc"
]
},
{
- "@id": "urn:07ec0c84-5406-43c4-9a02-5abcc5be6fdc",
+ "@id": "urn:3dmaskto-I5XcPV9z",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:6d65e310-6db0-49ad-a1e3-8096780ab290",
+ "@id": "urn:3dresamp-5CCglnUH",
"Label": "3dresample",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat",
"Parameters": {},
"Used": [
- "urn:1f2965b4-c815-4bc8-a968-931ff67878fc",
- "urn:72eaa85b-1d14-43ec-b59b-ba9598401b53"
+ "bids::full_mask.$subj+tlrc",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:ff74b4aa-4b12-49aa-8d16-dc16168bb90e",
+ "@id": "urn:3dmaskto-oB4HfACz",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj",
"Parameters": {},
"Used": [
- "urn:e11beee5-6c6b-453c-8060-fcffbb708e37"
+ "bids::rm.resam.anat+tlrc"
]
},
{
- "@id": "urn:6314e193-6e8a-45e4-8fe3-45ee8c4f8897",
+ "@id": "urn:3dabover-BuBtQnVp",
"Label": "3dABoverlap",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt",
"Parameters": {},
"Used": [
- "urn:1b9fb723-ecb9-4035-9235-b15638d971fd",
- "urn:f8ab6eb6-f5f5-4cec-a58e-20cab6d8bc24"
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee"
]
},
{
- "@id": "urn:aec7aa6f-2588-4bea-bcce-99b4ab634b80",
+ "@id": "urn:3ddot-UX3KoLiE",
"Label": "3ddot",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt",
"Parameters": {},
"Used": [
- "urn:1b9fb723-ecb9-4035-9235-b15638d971fd",
- "urn:f8ab6eb6-f5f5-4cec-a58e-20cab6d8bc24"
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee"
]
},
{
- "@id": "urn:78b95913-a8e5-461c-8c1c-93afbeaae3e2",
+ "@id": "urn:3dresamp-00IhFrmJ",
"Label": "3dresample",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc",
"Parameters": {},
"Used": [
- "urn:6f60d331-157c-4056-a0fe-271a0884e0d9",
- "urn:72eaa85b-1d14-43ec-b59b-ba9598401b53"
+ "bids::/Users/u1591557/abin/TT_N27+tlrc",
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:7ffe4ad5-7d91-48db-ac2a-5f7f443d18b3",
+ "@id": "urn:3dmaskto-YhUONgz0",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group",
"Parameters": {},
"Used": [
- "urn:8f99f1d1-e947-48e1-ba1a-7bd0a656dab0"
+ "bids::rm.resam.group+tlrc"
]
},
{
- "@id": "urn:a28dbf2b-52e6-497a-9a17-f8131d65ccdb",
+ "@id": "urn:3dtstat-2NVb1sut",
"Label": "3dTstat",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:344930df-f407-41d1-af01-bd028ff0bbdc"
+ "bids::pb03.$subj.r$run.blur+tlrc"
]
},
{
- "@id": "urn:d9d77f6b-eeea-42be-bb7f-375ffe0ea710",
+ "@id": "urn:3dcalc-zgipgUrz",
"Label": "3dcalc",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale",
"Parameters": {},
"Used": [
- "urn:344930df-f407-41d1-af01-bd028ff0bbdc",
- "urn:395f5c5b-e9ac-4840-9e36-f7d9f8378081",
- "urn:d46bb024-544e-42ee-992c-0379f823de74"
+ "bids::mask_epi_extents+tlrc",
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::rm.mean_r$run+tlrc"
]
},
{
- "@id": "urn:69393fe9-a34d-43a3-8146-b78f971c8599",
+ "@id": "urn:1dtoolpy-5WTFf33A",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D",
"Parameters": {},
"Used": [
- "urn:a24444a4-a198-4369-9c90-849bd9f58fa9"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:09da4b05-35ba-4775-a31f-b5833a8f2f71",
+ "@id": "urn:1dtoolpy-jER2iZP1",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D",
"Parameters": {},
"Used": [
- "urn:a24444a4-a198-4369-9c90-849bd9f58fa9"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:c0524ec3-3ea6-4e3e-baba-417314d9af3d",
+ "@id": "urn:1dtoolpy-75HvwUVU",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}",
"Parameters": {},
"Used": [
- "urn:a24444a4-a198-4369-9c90-849bd9f58fa9"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:cca9d05c-43fe-47b3-ada3-1c165bea6342",
+ "@id": "urn:3ddeconv-X5zHlyKF",
"Label": "3dDeconvolve",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj",
"Parameters": {},
"Used": [
- "urn:5339cda2-af48-4857-970f-5101e41df618"
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD"
]
},
{
- "@id": "urn:910bccb7-dcd9-4410-83d0-7c955cc2e8db",
+ "@id": "urn:1dtoolpy-cWNMH41s",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt",
"Parameters": {},
"Used": [
- "urn:dbf0bd54-d5d1-45cf-8aa7-b593bd3aacf5"
+ "bids::X.xmat.1D"
]
},
{
- "@id": "urn:441608e5-a5db-483b-988c-f52b353161c6",
+ "@id": "urn:3dtcat-yAzPOFHP",
"Label": "3dTcat",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD",
"Parameters": {},
"Used": [
- "urn:5339cda2-af48-4857-970f-5101e41df618"
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD"
]
},
{
- "@id": "urn:a55793e4-f85a-4ac9-8d63-34f58119f00e",
+ "@id": "urn:3dtstat-F1ly8H7E",
"Label": "3dTstat",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:956a31fd-030a-4e43-8e0b-eb06823cf052"
+ "bids::all_runs.$subj+tlrc%22[$ktrs]%22"
]
},
{
- "@id": "urn:ec9d7980-1d0b-42f4-96b5-51a4ff6c86d0",
+ "@id": "urn:3dtstat-6yntd6Sh",
"Label": "3dTstat",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:f4f9e3cd-9b48-4b47-bb15-6deaeaa2acb0"
+ "bids::errts.$%7Bsubj%7D+tlrc%22[$ktrs]%22"
]
},
{
- "@id": "urn:d401069b-da20-48be-afbb-31e098f3b3b2",
+ "@id": "urn:3dcalc-2Y6jSVAp",
"Label": "3dcalc",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj",
"Parameters": {},
"Used": [
- "urn:0ae21bc4-efb3-434e-a543-eac47f225762",
- "urn:72eaa85b-1d14-43ec-b59b-ba9598401b53",
- "urn:f64a3d35-0ede-4fc7-87a1-edc41e2efc37"
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.noise.all+tlrc",
+ "bids::rm.signal.all+tlrc"
]
},
{
- "@id": "urn:abfb5142-c999-4e6e-ae9e-27cbe9f09a1d",
+ "@id": "urn:3dtnorm-ousknqOT",
"Label": "3dTnorm",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc",
"Parameters": {},
"Used": [
- "urn:94571380-7577-41e6-a488-f0c5ea96db5e"
+ "bids::errts.$%7Bsubj%7D+tlrc"
]
},
{
- "@id": "urn:ae230fff-5fff-4021-9495-434681ac33b1",
+ "@id": "urn:3dmaskav-Sruq3WoS",
"Label": "3dmaskave",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D",
"Parameters": {},
- "Used": []
+ "Used": [
+ "bids::full_mask.$subj+tlrc"
+ ]
},
{
- "@id": "urn:95dbbb1a-af6d-4133-8620-a928beb28b2c",
+ "@id": "urn:3dtstat-pms0xbvC",
"Label": "3dTstat",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D",
"Parameters": {},
"Used": [
- "urn:00d2cbcd-88c4-495d-a56c-9c436669c375"
+ "bids::out.gcor.1D"
]
},
{
- "@id": "urn:f219d288-e9d1-4f13-9536-893d46332f3b",
+ "@id": "urn:3dcalc-56JypSy4",
"Label": "3dcalc",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP",
"Parameters": {},
"Used": [
- "urn:4414d31d-9eaf-4d18-b375-04f3314a1039",
- "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c"
+ "bids::gmean.errts.unit.1D",
+ "bids::rm.errts.unit+tlrc"
]
},
{
- "@id": "urn:605488b5-e8b5-43a7-a87e-6bf4673c8dbd",
+ "@id": "urn:3dtstat-QXdZP1fq",
"Label": "3dTstat",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc",
"Parameters": {},
"Used": [
- "urn:92dd3a7a-0a15-443b-b85f-3201f38e7d41"
+ "bids::rm.DP+tlrc"
]
},
{
- "@id": "urn:7fe5640e-c1ac-41e2-a390-5cfb10ed270c",
+ "@id": "urn:1dcat-ad96m6UQ",
"Label": "1dcat",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D",
"Parameters": {},
"Used": [
- "urn:362a9b21-aaf4-43be-8ae2-e9676da61333"
+ "bids::X.nocensor.xmat.1D'[3]'"
]
},
{
- "@id": "urn:71033977-c543-4f01-b2cf-9b47a1244aae",
+ "@id": "urn:1dcat-2K9ekGxY",
"Label": "1dcat",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D",
"Parameters": {},
"Used": [
- "urn:19c392b8-27a2-4289-8244-b4873e9ca58f"
+ "bids::X.nocensor.xmat.1D'[4]'"
]
},
{
- "@id": "urn:c5644168-63b9-4e5f-b32b-354c7481a6b3",
+ "@id": "urn:3dtstat-eAA6J8hu",
"Label": "3dTstat",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"",
"Parameters": {},
"Used": [
- "urn:ea004d6b-2e31-45db-b3b4-7b0e08b96791"
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:5ea48616-c75d-40df-8da5-ecbca08599d0",
+ "@id": "urn:1dcat-GlOIdXgH",
"Label": "1dcat",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D",
"Parameters": {},
"Used": [
- "urn:ea004d6b-2e31-45db-b3b4-7b0e08b96791"
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:9597a3cc-fad1-4121-b2ff-551c158e1486",
+ "@id": "urn:3dfwhmx-DtOKeO5X",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D",
"Parameters": {},
"Used": [
- "urn:72eaa85b-1d14-43ec-b59b-ba9598401b53"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:54fe14f2-f486-4eb3-8300-f2e9a0b704e8",
+ "@id": "urn:3dfwhmx-sWc6Z41Y",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D",
"Parameters": {},
"Used": [
- "urn:72eaa85b-1d14-43ec-b59b-ba9598401b53"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:0eebfdde-bdc5-40d0-bb8d-4c6bcb1afb9a",
+ "@id": "urn:3dclusts-1uLxHtpf",
"Label": "3dClustSim",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim",
"Parameters": {},
"Used": [
- "urn:72eaa85b-1d14-43ec-b59b-ba9598401b53"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:a06e91f3-8542-4272-a179-a66a7156b03a",
+ "@id": "urn:genepire-dgvg4PFX",
"Label": "gen_epi_review.py",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD",
"Parameters": {},
"Used": [
- "urn:47e324b7-183c-44e8-9f43-dc1008b8693a"
+ "bids::pb00.$subj.r*.tcat+orig.HEAD"
]
},
{
- "@id": "urn:2e5f2dfb-470a-43c5-95a0-5dbecb68ecd6",
+ "@id": "urn:genssrev-Ap2cZwro",
"Label": "gen_ss_review_scripts.py",
- "AssociatedWith": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "AssociatedWith": "urn:afni-fUbLl1Ef",
"Command": "gen_ss_review_scripts.py -mot_limit 0.3 -exit0",
"Parameters": {
"-mot_limit": "0.3",
@@ -586,22 +589,22 @@
],
"Entities": [
{
- "@id": "urn:50667222-e5a1-489b-b422-5627eca72bc6",
+ "@id": "bids::$output_dir",
"Label": "$output_dir",
"AtLocation": "$output_dir",
- "GeneratedBy": "urn:aa96021b-cc85-47e0-afd1-a427861606f0",
+ "GeneratedBy": "urn:makedire-EjFu5Gzs",
"digest": {
"sha256": "9fa4c635e6533ddf2fed54295920052818d948c3ffe97bc753bd7336b453f8cb"
}
},
{
- "@id": "urn:fc2beb3a-0ddd-4657-a687-4409efff62b4",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:5149ab44-6c94-47ec-9d96-f8a8558e930b"
+ "GeneratedBy": "urn:makedire-YONHeB75"
},
{
- "@id": "urn:072360e9-f1eb-43eb-9fa1-b58a93ba009d",
+ "@id": "bids::afni_f_test/tone_counting_onset_times.txt",
"Label": "tone_counting_onset_times.txt",
"AtLocation": "./afni_f_test/tone_counting_onset_times.txt",
"digest": {
@@ -609,7 +612,7 @@
}
},
{
- "@id": "urn:1dcfc72d-5ed6-4ff7-a613-c69991b5c517",
+ "@id": "bids::afni_f_test/tone_counting_probe_duration.txt",
"Label": "tone_counting_probe_duration.txt",
"AtLocation": "./afni_f_test/tone_counting_probe_duration.txt",
"digest": {
@@ -617,13 +620,13 @@
}
},
{
- "@id": "urn:162eba86-ca6b-40ce-90b8-82fc8a8aee10",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:d191a56c-9c39-409d-a7f3-89bf42f57cc6"
+ "GeneratedBy": "urn:cp-S3UpI0F6"
},
{
- "@id": "urn:b50c1808-e500-4550-966a-e626b6b521f9",
+ "@id": "bids::sub-01_T1w.nii.gz",
"Label": "sub-01_T1w.nii.gz",
"AtLocation": "sub-01_T1w.nii.gz",
"digest": {
@@ -631,13 +634,13 @@
}
},
{
- "@id": "urn:0f978606-b24a-49bb-bc30-6419c648087e",
+ "@id": "bids::$output_dir/sub-01_T1w",
"Label": "sub-01_T1w",
"AtLocation": "$output_dir/sub-01_T1w",
- "GeneratedBy": "urn:d6cbc859-2b90-4245-a5fa-a7da66481e8f"
+ "GeneratedBy": "urn:3dcopy-wnZoB6GV"
},
{
- "@id": "urn:b75e6167-a56b-47f0-b2b3-f704b2e3f1d1",
+ "@id": "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Label": "sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"digest": {
@@ -645,13 +648,13 @@
}
},
{
- "@id": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "@id": "bids::$output_dir/pb00.$subj.r01.tcat",
"Label": "pb00.$subj.r01.tcat",
"AtLocation": "$output_dir/pb00.$subj.r01.tcat",
- "GeneratedBy": "urn:be39d02a-940a-4437-9d22-c7f954010a48"
+ "GeneratedBy": "urn:3dtcat-p93OvsNc"
},
{
- "@id": "urn:b5f66e4e-2342-4065-8f7b-2c21b222d7b8",
+ "@id": "bids::pb00.$subj.r$run.tcat+orig",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -659,16 +662,16 @@
}
},
{
- "@id": "urn:7cd6ecd7-6511-4f63-9962-952ebad0dcdb",
+ "@id": "bids::outcount.r$run.1D",
"Label": "outcount.r$run.1D",
"AtLocation": "outcount.r$run.1D",
- "GeneratedBy": "urn:9c952d4e-87cf-4ea6-b03c-4af969fd056b",
+ "GeneratedBy": "urn:3dtoutco-MaaJHpvs",
"digest": {
"sha256": "63d9f539e5470badc625d557109f68bc4eecbb02ca2667483739d52f95e5d0dd"
}
},
{
- "@id": "urn:a87b44c4-914f-43e9-8e91-283309980322",
+ "@id": "bids::outcount.r*.1D",
"Label": "outcount.r*.1D",
"AtLocation": "outcount.r*.1D",
"digest": {
@@ -676,25 +679,25 @@
}
},
{
- "@id": "urn:dbbefaf5-b5c5-45f4-9193-b68b19b71729",
+ "@id": "bids::outcount_rall.1D",
"Label": "outcount_rall.1D",
"AtLocation": "outcount_rall.1D",
- "GeneratedBy": "urn:a38e2601-9eb9-4a15-a0b4-bda9d367153f",
+ "GeneratedBy": "urn:cat-g7cf5SRg",
"digest": {
"sha256": "cb887fd5e4d5e9acb3a24820d0f7a62ed38a5ffb0fdedd373440ac0219fb186a"
}
},
{
- "@id": "urn:1943f1bb-e353-4a4a-a8d8-371ad6ae2b30",
+ "@id": "bids::pb01.$subj.r$run.tshift",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift",
- "GeneratedBy": "urn:678536c5-1572-466a-89e4-3051f34d7755",
+ "GeneratedBy": "urn:3dtshift-7SbFVAaD",
"digest": {
"sha256": "c6bf01cea8d2eac1d7a866f80b865c6e7d4b4e012dbb63d480ac9a8551162d72"
}
},
{
- "@id": "urn:28a7f0e5-cc3f-4d95-ab33-4effe28cfe77",
+ "@id": "bids::sub-01_T1w+orig",
"Label": "sub-01_T1w",
"AtLocation": "sub-01_T1w+orig",
"digest": {
@@ -702,7 +705,7 @@
}
},
{
- "@id": "urn:378c0ea8-a35a-472a-9347-ff979b23f462",
+ "@id": "bids::pb01.$subj.r01.tshift+orig",
"Label": "pb01.$subj.r01.tshift",
"AtLocation": "pb01.$subj.r01.tshift+orig",
"digest": {
@@ -710,16 +713,16 @@
}
},
{
- "@id": "urn:2b05ded6-ada3-4741-91ef-c43d763b40ca",
+ "@id": "bids::_al_junk",
"Label": "_al_junk",
"AtLocation": "_al_junk",
- "GeneratedBy": "urn:d3630e97-6933-464a-97bb-ab45131ac706",
+ "GeneratedBy": "urn:alignepi-enozA4y8",
"digest": {
"sha256": "bd785a075a4c6446e1e54de9e628913f7f1c814e86b69a9fbfe933209e6d37b5"
}
},
{
- "@id": "urn:77377ac8-e94f-47ab-a512-1160810d465d",
+ "@id": "bids::TT_N27+tlrc",
"Label": "TT_N27",
"AtLocation": "TT_N27+tlrc",
"digest": {
@@ -727,7 +730,7 @@
}
},
{
- "@id": "urn:90d0ad49-8128-44dc-b6d3-40b269bf7e59",
+ "@id": "bids::sub-01_T1w_ns+orig",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+orig",
"digest": {
@@ -735,7 +738,7 @@
}
},
{
- "@id": "urn:333737b2-2884-489a-bd62-8411fc800020",
+ "@id": "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc::WARP_DATA",
"digest": {
@@ -743,16 +746,16 @@
}
},
{
- "@id": "urn:df0f0a0c-cfc4-4d8c-b572-856b120846f6",
+ "@id": "bids::warp.anat.Xat.1D",
"Label": "warp.anat.Xat.1D",
"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:77295b4e-c8b1-46f6-8adc-7322f4a5361a",
+ "GeneratedBy": "urn:catmatve-D7J6hS1Y",
"digest": {
"sha256": "800633fb5b4e9be64078bc181c4d5510ffb73fc5cccaf364c7fb6a294aa06728"
}
},
{
- "@id": "urn:8d51b390-740e-4699-ba32-88d4f25ea861",
+ "@id": "bids::pb01.$subj.r$run.tshift+orig",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift+orig",
"digest": {
@@ -760,34 +763,34 @@
}
},
{
- "@id": "urn:6a09ed66-56d8-45c8-baab-c2417d274efe",
+ "@id": "bids::mat.r$run.vr.aff12.1D",
"Label": "mat.r$run.vr.aff12.1D",
"AtLocation": "mat.r$run.vr.aff12.1D",
- "GeneratedBy": "urn:144f0732-ecdf-45a2-a853-842192246329",
+ "GeneratedBy": "urn:3dvolreg-iMulinnK",
"digest": {
"sha256": "2e6e6c2ce8089cfa3c6e11dc72fca0cc8497f7a55faae2ced402de4867466c91"
}
},
{
- "@id": "urn:4c7e0766-bcb2-4baa-b971-d4766f468d5c",
+ "@id": "bids::rm.epi.all1",
"Label": "rm.epi.all1",
"AtLocation": "rm.epi.all1",
- "GeneratedBy": "urn:7cd3c063-0abf-4893-925f-b2b299b0e6f4",
+ "GeneratedBy": "urn:3dcalc-snZ2MgYQ",
"digest": {
"sha256": "1023e3c16cecdbdc73ea456bcf33c2e5bb4f1e07094b73d29022d651e5fa3f85"
}
},
{
- "@id": "urn:4f874d05-1bde-425a-a1e1-afa8043b443b",
+ "@id": "bids::mat.r$run.warp.aff12.1D",
"Label": "mat.r$run.warp.aff12.1D",
"AtLocation": "mat.r$run.warp.aff12.1D",
- "GeneratedBy": "urn:8570c470-01d4-4c71-9c9a-61730f84d797",
+ "GeneratedBy": "urn:catmatve-Kk6oC6ZE",
"digest": {
"sha256": "7c536b6f582a067c718f9e5ea2566cb535c73b43b4e15116c4c46045734d6eee"
}
},
{
- "@id": "urn:1f2965b4-c815-4bc8-a968-931ff67878fc",
+ "@id": "bids::sub-01_T1w_ns+tlrc",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc",
"digest": {
@@ -795,16 +798,16 @@
}
},
{
- "@id": "urn:3ee51032-c8a7-4052-bb8f-7ea83a1e6e4e",
+ "@id": "bids::rm.epi.nomask.r$run",
"Label": "rm.epi.nomask.r$run",
"AtLocation": "rm.epi.nomask.r$run",
- "GeneratedBy": "urn:7defd23d-6aca-465e-8cff-5dc88f651245",
+ "GeneratedBy": "urn:3dalline-EJAmmrdL",
"digest": {
"sha256": "03d6cba0426c5545e350e6b63a19b0e46f8dfa2223fd08691753e8914a479e36"
}
},
{
- "@id": "urn:519d99a7-e9f5-4118-ae26-ce458fd3089b",
+ "@id": "bids::rm.epi.all1+orig",
"Label": "rm.epi.all1",
"AtLocation": "rm.epi.all1+orig",
"digest": {
@@ -812,16 +815,16 @@
}
},
{
- "@id": "urn:8ed3b907-e504-4144-82fb-7de3b75a166e",
+ "@id": "bids::rm.epi.1.r$run",
"Label": "rm.epi.1.r$run",
"AtLocation": "rm.epi.1.r$run",
- "GeneratedBy": "urn:2e9588bc-42dc-4f81-970f-3c7f63274c6d",
+ "GeneratedBy": "urn:3dalline-LXY21VdU",
"digest": {
"sha256": "b1b9128c103ea246625db1a35e6f474a221ca6c1105a30df38aefdc4d5421e84"
}
},
{
- "@id": "urn:72115625-c8dc-4767-896c-bc1beabd045c",
+ "@id": "bids::rm.epi.1.r$run+tlrc",
"Label": "rm.epi.1.r$run",
"AtLocation": "rm.epi.1.r$run+tlrc",
"digest": {
@@ -829,16 +832,16 @@
}
},
{
- "@id": "urn:c6a8b859-d3e4-4464-8b39-609f871f7964",
+ "@id": "bids::rm.epi.min.r$run",
"Label": "rm.epi.min.r$run",
"AtLocation": "rm.epi.min.r$run",
- "GeneratedBy": "urn:781e38c2-b867-478d-821b-b7e09975dc14",
+ "GeneratedBy": "urn:3dtstat-HGyCHkmT",
"digest": {
"sha256": "b4418a96ddbbf25afdfd01ed0506ddebe009011ba18aed10137f994260fd1a66"
}
},
{
- "@id": "urn:0bc4025e-062b-4072-a719-c8cac5d631f1",
+ "@id": "bids::dfile.r*.1D",
"Label": "dfile.r*.1D",
"AtLocation": "dfile.r*.1D",
"digest": {
@@ -846,16 +849,16 @@
}
},
{
- "@id": "urn:a24444a4-a198-4369-9c90-849bd9f58fa9",
+ "@id": "bids::dfile_rall.1D",
"Label": "dfile_rall.1D",
"AtLocation": "dfile_rall.1D",
- "GeneratedBy": "urn:52ecd782-22ca-4d35-927b-3400bee24e28",
+ "GeneratedBy": "urn:cat-iFjDMi8K",
"digest": {
"sha256": "011e7296870a1ac7e15377fb0d529ed68710bb16b138bef6aeb6c645f437dcf2"
}
},
{
- "@id": "urn:e5dfce3b-8f98-4387-80ab-31507296666f",
+ "@id": "bids::rm.epi.min.r01+tlrc",
"Label": "rm.epi.min.r01",
"AtLocation": "rm.epi.min.r01+tlrc",
"digest": {
@@ -863,16 +866,16 @@
}
},
{
- "@id": "urn:bbca53c8-51f0-4ec5-b50a-b3285b733beb",
+ "@id": "bids::mask_epi_extents",
"Label": "mask_epi_extents",
"AtLocation": "mask_epi_extents",
- "GeneratedBy": "urn:7138a4c9-2a77-46a0-8701-b86b50081572",
+ "GeneratedBy": "urn:3dcopy-7zdBDXoH",
"digest": {
"sha256": "a69dd71209516ec24e2b3364072ed54adff16619459b1c369866210ec642e987"
}
},
{
- "@id": "urn:2e914165-32e7-4df7-b382-59329c255f69",
+ "@id": "bids::rm.epi.nomask.r$run+tlrc",
"Label": "rm.epi.nomask.r$run",
"AtLocation": "rm.epi.nomask.r$run+tlrc",
"digest": {
@@ -880,7 +883,7 @@
}
},
{
- "@id": "urn:d46bb024-544e-42ee-992c-0379f823de74",
+ "@id": "bids::mask_epi_extents+tlrc",
"Label": "mask_epi_extents",
"AtLocation": "mask_epi_extents+tlrc",
"digest": {
@@ -888,34 +891,42 @@
}
},
{
- "@id": "urn:850535a6-7f6f-45a4-8cef-8772dba02348",
+ "@id": "bids::pb02.$subj.r$run.volreg",
"Label": "pb02.$subj.r$run.volreg",
"AtLocation": "pb02.$subj.r$run.volreg",
- "GeneratedBy": "urn:0eb2e611-6be8-4f49-b918-379168624f99",
+ "GeneratedBy": "urn:3dcalc-I4FH3Fdh",
"digest": {
"sha256": "8821927190ac1b3f8f9d9a5ec74f6468ae6c1cb736e58e5de2cdbe3543d5cc0c"
}
},
{
- "@id": "urn:958c36f5-1558-4804-ac95-4066e11d6a08",
+ "@id": "bids::anat_final.$subj",
"Label": "anat_final.$subj",
"AtLocation": "anat_final.$subj",
- "GeneratedBy": "urn:ec4eff37-da73-479a-bf55-e1c024f86d2c",
+ "GeneratedBy": "urn:3dcopy-UjphDPUg",
"digest": {
"sha256": "69b750d004bdba337de0b4ffa683bd92bc8f34b854d320327839ad264b28c4c5"
}
},
{
- "@id": "urn:f66e8613-ecf6-4721-ac49-842ee0aa7526",
+ "@id": "bids::anat_final.$subj+tlrc",
+ "Label": "anat_final.$subj",
+ "AtLocation": "anat_final.$subj+tlrc",
+ "digest": {
+ "sha256": "94eb1853614cc085b22772c011f119f6a0ad7ec06cba2850587762e7f1a6eae6"
+ }
+ },
+ {
+ "@id": "bids::anat_w_skull_warped",
"Label": "anat_w_skull_warped",
"AtLocation": "anat_w_skull_warped",
- "GeneratedBy": "urn:c8a4cdcf-f7df-4fbd-ac11-4a8c211692ea",
+ "GeneratedBy": "urn:3dalline-99Vqvx8a",
"digest": {
"sha256": "462fdb8cd2b882e250fee3c6adb7acf0b0b9a9edb3e1cadf9d45d16180871105"
}
},
{
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@@ -923,7 +934,7 @@
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@@ -931,7 +942,7 @@
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@@ -939,25 +950,25 @@
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@@ -965,16 +976,16 @@
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@@ -982,16 +993,16 @@
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@@ -999,7 +1010,7 @@
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@@ -1007,7 +1018,7 @@
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@@ -1015,16 +1026,16 @@
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@@ -1032,25 +1043,25 @@
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@@ -1058,34 +1069,34 @@
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@@ -1093,25 +1104,25 @@
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@@ -1119,16 +1130,16 @@
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@@ -1136,16 +1147,16 @@
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@@ -1153,7 +1164,7 @@
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@@ -1161,16 +1172,16 @@
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@@ -1178,25 +1189,25 @@
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@@ -1204,16 +1215,16 @@
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@@ -1221,16 +1232,16 @@
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@@ -1238,16 +1249,16 @@
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@@ -1255,16 +1266,16 @@
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@@ -1272,16 +1283,16 @@
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@@ -1289,52 +1300,52 @@
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@@ -1342,10 +1353,10 @@
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+ "@id": "bids::-exit0",
"Label": "-exit0",
"AtLocation": "-exit0",
- "GeneratedBy": "urn:2e5f2dfb-470a-43c5-95a0-5dbecb68ecd6",
+ "GeneratedBy": "urn:genssrev-Ap2cZwro",
"digest": {
"sha256": "871a4d3513ed2924cbb10c1c15a196eac4a46a05bdcc248e3bcdb23327b3ad90"
}
diff --git a/examples/from_parsers/afni/afni_con_f_proc.png b/examples/from_parsers/afni/afni_con_f_proc.png
index 7756f371c..584e3d9ad 100644
Binary files a/examples/from_parsers/afni/afni_con_f_proc.png and b/examples/from_parsers/afni/afni_con_f_proc.png differ
diff --git a/examples/from_parsers/afni/afni_con_f_proc_block.jsonld b/examples/from_parsers/afni/afni_con_f_proc_block.jsonld
index dc9d21d53..378989d5e 100644
--- a/examples/from_parsers/afni/afni_con_f_proc_block.jsonld
+++ b/examples/from_parsers/afni/afni_con_f_proc_block.jsonld
@@ -4,187 +4,189 @@
"Records": {
"Software": [
{
- "@id": "urn:3b9828af-25bc-4463-b18a-2b842e1f91ff",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:afni-JCuJkKkJ",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
- "Version": "afni24"
+ "Version": "afni24",
+ "AltIdentifier": "RRID:SCR_005927"
}
],
"Activities": [
{
- "@id": "urn:7a7a59ec-2b5e-4f2f-a800-99af492f869c",
+ "@id": "urn:autobloc-gx5Gs1iF",
"Label": "auto block: setup",
- "AssociatedWith": "urn:3b9828af-25bc-4463-b18a-2b842e1f91ff",
+ "AssociatedWith": "urn:afni-JCuJkKkJ",
"Command": "mkdir $output_dir; mkdir $output_dir/stimuli; cp ./afni_f_test/tone_counting_onset_times.txt ./afni_f_test/tone_counting_probe_duration.txt $output_dir/stimuli; 3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w; ",
"Used": [
- "urn:30f2c87d-f28f-4a74-8d93-0c761ca96317",
- "urn:6b4c40e2-9e63-4713-84af-081da9537ef3",
- "urn:3a79788e-4c74-4a65-b4c6-27115e8884d6"
+ "bids::afni_f_test/tone_counting_onset_times.txt",
+ "bids::afni_f_test/tone_counting_probe_duration.txt",
+ "bids::sub-01_T1w.nii.gz"
]
},
{
- "@id": "urn:b1c281e2-c739-46f8-a194-514e241747b2",
+ "@id": "urn:autobloc-aWD77U1W",
"Label": "auto block: tcat",
- "AssociatedWith": "urn:3b9828af-25bc-4463-b18a-2b842e1f91ff",
+ "AssociatedWith": "urn:afni-JCuJkKkJ",
"Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ",
"Used": [
- "urn:4d37d4cb-b4a6-442a-b3a5-39d657df0ece"
+ "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'"
]
},
{
- "@id": "urn:2e3df101-cb1e-445d-ab72-61377537503d",
+ "@id": "urn:autobloc-ItX0hSbT",
"Label": "auto block: outcount",
- "AssociatedWith": "urn:3b9828af-25bc-4463-b18a-2b842e1f91ff",
+ "AssociatedWith": "urn:afni-JCuJkKkJ",
"Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ",
"Used": [
- "urn:b096695f-7087-450e-9140-ce73eb052e67",
- "urn:4a199e13-d903-4746-8a05-4c28d3f24786"
+ "bids::pb00.$subj.r$run.tcat+orig",
+ "bids::outcount.r*.1D"
]
},
{
- "@id": "urn:60d56e93-faf4-4101-be8b-18f457793b62",
+ "@id": "urn:tshift-qJQPUAmK",
"Label": "tshift",
- "AssociatedWith": "urn:3b9828af-25bc-4463-b18a-2b842e1f91ff",
+ "AssociatedWith": "urn:afni-JCuJkKkJ",
"Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ",
"Used": [
- "urn:b096695f-7087-450e-9140-ce73eb052e67"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:1f988b1a-d24f-425f-a9ae-e63df25e13c1",
+ "@id": "urn:align-2yy5MCs2",
"Label": "align",
- "AssociatedWith": "urn:3b9828af-25bc-4463-b18a-2b842e1f91ff",
+ "AssociatedWith": "urn:afni-JCuJkKkJ",
"Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ",
"Used": [
- "urn:c9a633f5-e6cf-4a7a-8473-0e1b99164061",
- "urn:e7e293a9-eed8-4907-8a4f-271b2c2e77d0"
+ "bids::pb01.$subj.r01.tshift+orig",
+ "bids::sub-01_T1w+orig"
]
},
{
- "@id": "urn:fa0fcc24-2f99-4ce4-b71a-6fc34570f7cc",
+ "@id": "urn:tlrc-LkdaOXQO",
"Label": "tlrc",
- "AssociatedWith": "urn:3b9828af-25bc-4463-b18a-2b842e1f91ff",
+ "AssociatedWith": "urn:afni-JCuJkKkJ",
"Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ",
"Used": [
- "urn:eb856fcf-6bbd-4aca-b994-a5f4f046b424",
- "urn:ff64e210-7ac9-4c70-add6-986f2c290fcd",
- "urn:e02a94c5-0f0d-4ae7-b811-f3e501ab6750"
+ "bids::TT_N27+tlrc",
+ "bids::sub-01_T1w_ns+orig",
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:07715c6d-a301-48f9-b7e1-a44f5c4aec34",
+ "@id": "urn:volreg-QjASoC7j",
"Label": "volreg",
- "AssociatedWith": "urn:3b9828af-25bc-4463-b18a-2b842e1f91ff",
+ "AssociatedWith": "urn:afni-JCuJkKkJ",
"Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig; 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1; cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D; 3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run; 3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run; 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc; cat dfile.r*.1D > dfile_rall.1D; 3dcopy rm.epi.min.r01+tlrc mask_epi_extents; 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg; 3dcopy sub-01_T1w_ns+tlrc anat_final.$subj; 3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped; ",
"Used": [
- "urn:8576faad-35a6-4007-baae-031b625be042",
- "urn:8576faad-35a6-4007-baae-031b625be042",
- "urn:e02a94c5-0f0d-4ae7-b811-f3e501ab6750",
- "urn:8576faad-35a6-4007-baae-031b625be042",
- "urn:bae96fa9-f172-4a9c-bbe4-5d029f4dcd50",
- "urn:55c204fc-4ef2-4bab-b845-fd5c543a7a0b",
- "urn:bae96fa9-f172-4a9c-bbe4-5d029f4dcd50",
- "urn:9c283eeb-3683-4f35-966a-6cee22e62921",
- "urn:e5955845-059f-4888-9f31-10a84ecd3afd",
- "urn:dcd9b6d5-0d6c-44a8-b2a4-20746f3bf451",
- "urn:3bbde2e2-3198-4f5e-a405-3dc2859a814d",
- "urn:b0e85dbd-3264-414a-aad3-bded58a631c6",
- "urn:bae96fa9-f172-4a9c-bbe4-5d029f4dcd50",
- "urn:318d11c1-328d-4b91-827d-74de938fd19b"
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.epi.all1+orig",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.epi.1.r$run+tlrc",
+ "bids::dfile.r*.1D",
+ "bids::rm.epi.min.r01+tlrc",
+ "bids::mask_epi_extents+tlrc",
+ "bids::rm.epi.nomask.r$run+tlrc",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::anat_final.$subj+tlrc",
+ "bids::warp.anat.Xat.1D"
]
},
{
- "@id": "urn:32257d53-8603-40db-b02f-6002a5d6ee1a",
+ "@id": "urn:blur-RHUHuJ7U",
"Label": "blur",
- "AssociatedWith": "urn:3b9828af-25bc-4463-b18a-2b842e1f91ff",
+ "AssociatedWith": "urn:afni-JCuJkKkJ",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc; ",
"Used": [
- "urn:1cf6abc0-28b4-47b1-8241-d2e415806801",
- "urn:40c7b3b1-aa1b-41ef-b09f-423be7a6600a"
+ "bids::pb02.$subj.r$run.volreg+tlrc",
+ "bids::pb03.$subj.r$run.blur"
]
},
{
- "@id": "urn:84089e16-6209-4d72-ba0a-c9003f234966",
+ "@id": "urn:mask-veDX9g76",
"Label": "mask",
- "AssociatedWith": "urn:3b9828af-25bc-4463-b18a-2b842e1f91ff",
+ "AssociatedWith": "urn:afni-JCuJkKkJ",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc; 3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj; 3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj; 3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt; 3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt; 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group; ",
"Used": [
- "urn:7cdabd60-f015-462a-9a04-a3e21053d633",
- "urn:b17cce80-9f35-4a8d-88e0-e1d81c9b0c87",
- "urn:bae96fa9-f172-4a9c-bbe4-5d029f4dcd50",
- "urn:57c66382-57aa-4906-b4b8-d0fdd4b367d8",
- "urn:0e402105-a625-4b0d-aabb-84565733d38a",
- "urn:96e34fde-acd7-4ce9-bcbd-bfb3b267f717",
- "urn:0e402105-a625-4b0d-aabb-84565733d38a",
- "urn:96e34fde-acd7-4ce9-bcbd-bfb3b267f717",
- "urn:b17cce80-9f35-4a8d-88e0-e1d81c9b0c87",
- "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
- "urn:ea12cbb8-ae5f-4a2e-b17f-47c484ceeaaa"
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.resam.anat+tlrc",
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee",
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee",
+ "bids::/Users/u1591557/abin/TT_N27+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.resam.group+tlrc"
]
},
{
- "@id": "urn:75b192c7-da14-488c-93e9-6b6390ee73a9",
+ "@id": "urn:scale-TZk2BHod",
"Label": "scale",
- "AssociatedWith": "urn:3b9828af-25bc-4463-b18a-2b842e1f91ff",
+ "AssociatedWith": "urn:afni-JCuJkKkJ",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc; 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale; ",
"Used": [
- "urn:7cdabd60-f015-462a-9a04-a3e21053d633",
- "urn:7189312d-f5ce-4082-86ae-5e98af99708a",
- "urn:7cdabd60-f015-462a-9a04-a3e21053d633",
- "urn:b0e85dbd-3264-414a-aad3-bded58a631c6"
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::mask_epi_extents+tlrc",
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::rm.mean_r$run+tlrc"
]
},
{
- "@id": "urn:e1481f5e-884b-4430-8ff3-ec696a5999d9",
+ "@id": "urn:regress-VfuA197y",
"Label": "regress",
- "AssociatedWith": "urn:3b9828af-25bc-4463-b18a-2b842e1f91ff",
+ "AssociatedWith": "urn:afni-JCuJkKkJ",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}; 3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj; 1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt; 3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD; 3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"; 3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"; 3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj; 3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc; 3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D; 3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D; 3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP; 3dTstat -sum -prefix corr_brain rm.DP+tlrc; 1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D; 1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D; 3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"; 1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D; ",
"Used": [
- "urn:b624270f-a3c2-46c6-a27c-89d37f792539",
- "urn:b624270f-a3c2-46c6-a27c-89d37f792539",
- "urn:b624270f-a3c2-46c6-a27c-89d37f792539",
- "urn:bb99cab8-a1c8-42d2-b619-b0e8b124d0ee",
- "urn:bb99cab8-a1c8-42d2-b619-b0e8b124d0ee",
- "urn:6ef2fa60-155f-45b3-8ea3-cfcd906b43b9",
- "urn:0dd0e641-9d9b-44e8-b602-7a0ea3ba1b56",
- "urn:48f9cdad-094a-41e9-bacd-4d5e0a8d9639",
- "urn:a7ffb8df-7cfd-4716-9d41-1790b26e57c7",
- "urn:b17cce80-9f35-4a8d-88e0-e1d81c9b0c87",
- "urn:e72dcc3e-adcd-4dbe-8641-3498938eeada",
- "urn:b540995f-3dce-433c-9c41-c68e3df4d976",
- "urn:b89b4e42-4d72-4ccf-aec4-9ac21339fc1c",
- "urn:30b89792-f8a9-4f81-8734-f482347fb96d",
- "urn:2925e014-5c3f-4f83-bf81-5437b7478cba",
- "urn:238ee357-9664-4341-89fe-87da449145ba",
- "urn:64f3a5a9-a8b3-4de3-9b4c-89e46e6bdf39",
- "urn:64f3a5a9-a8b3-4de3-9b4c-89e46e6bdf39"
+ "bids::dfile_rall.1D",
+ "bids::dfile_rall.1D",
+ "bids::dfile_rall.1D",
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD",
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD",
+ "bids::all_runs.$subj+tlrc%22[$ktrs]%22",
+ "bids::errts.$%7Bsubj%7D+tlrc%22[$ktrs]%22",
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.noise.all+tlrc",
+ "bids::rm.signal.all+tlrc",
+ "bids::errts.$%7Bsubj%7D+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::out.gcor.1D",
+ "bids::rm.errts.unit+tlrc",
+ "bids::rm.DP+tlrc",
+ "bids::X.nocensor.xmat.1D'[3]'",
+ "bids::X.nocensor.xmat.1D'[4]'",
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22",
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:8a07fb2b-8782-48d7-8ff0-81e6a9ad26ed",
+ "@id": "urn:bluresti-Qz0unv2Z",
"Label": "blur estimation",
- "AssociatedWith": "urn:3b9828af-25bc-4463-b18a-2b842e1f91ff",
+ "AssociatedWith": "urn:afni-JCuJkKkJ",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D; 3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D; 3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim; ",
"Used": [
- "urn:b17cce80-9f35-4a8d-88e0-e1d81c9b0c87",
- "urn:b17cce80-9f35-4a8d-88e0-e1d81c9b0c87",
- "urn:b17cce80-9f35-4a8d-88e0-e1d81c9b0c87"
+ "bids::full_mask.$subj+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:758476e6-7d68-4c13-968c-da2ed9657bd8",
+ "@id": "urn:autobloc-2RxNDsvi",
"Label": "auto block: generate review scripts",
- "AssociatedWith": "urn:3b9828af-25bc-4463-b18a-2b842e1f91ff",
+ "AssociatedWith": "urn:afni-JCuJkKkJ",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD; gen_ss_review_scripts.py -mot_limit 0.3 -exit0; ",
"Used": [
- "urn:218ffa82-8cd0-4624-9995-7d9b9da621f0"
+ "bids::pb00.$subj.r*.tcat+orig.HEAD"
]
}
],
"Entities": [
{
- "@id": "urn:30f2c87d-f28f-4a74-8d93-0c761ca96317",
+ "@id": "bids::afni_f_test/tone_counting_onset_times.txt",
"Label": "tone_counting_onset_times.txt",
"AtLocation": "./afni_f_test/tone_counting_onset_times.txt",
"digest": {
@@ -192,7 +194,7 @@
}
},
{
- "@id": "urn:6b4c40e2-9e63-4713-84af-081da9537ef3",
+ "@id": "bids::afni_f_test/tone_counting_probe_duration.txt",
"Label": "tone_counting_probe_duration.txt",
"AtLocation": "./afni_f_test/tone_counting_probe_duration.txt",
"digest": {
@@ -200,7 +202,7 @@
}
},
{
- "@id": "urn:3a79788e-4c74-4a65-b4c6-27115e8884d6",
+ "@id": "bids::sub-01_T1w.nii.gz",
"Label": "sub-01_T1w.nii.gz",
"AtLocation": "sub-01_T1w.nii.gz",
"digest": {
@@ -208,34 +210,34 @@
}
},
{
- "@id": "urn:6c839333-833f-49bb-a38e-fde96e9ae7f0",
+ "@id": "bids::$output_dir",
"Label": "$output_dir",
"AtLocation": "$output_dir",
- "GeneratedBy": "urn:7a7a59ec-2b5e-4f2f-a800-99af492f869c",
+ "GeneratedBy": "urn:autobloc-gx5Gs1iF",
"digest": {
"sha256": "9fa4c635e6533ddf2fed54295920052818d948c3ffe97bc753bd7336b453f8cb"
}
},
{
- "@id": "urn:a39d779d-35f9-4d5b-bd4e-775ab902dd6a",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:7a7a59ec-2b5e-4f2f-a800-99af492f869c"
+ "GeneratedBy": "urn:autobloc-gx5Gs1iF"
},
{
- "@id": "urn:5e81132b-0af3-47d9-a5e3-016da536af9c",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:7a7a59ec-2b5e-4f2f-a800-99af492f869c"
+ "GeneratedBy": "urn:autobloc-gx5Gs1iF"
},
{
- "@id": "urn:c2ff4c68-2abb-4b70-908a-6844e3ed2b58",
+ "@id": "bids::$output_dir/sub-01_T1w",
"Label": "sub-01_T1w",
"AtLocation": "$output_dir/sub-01_T1w",
- "GeneratedBy": "urn:7a7a59ec-2b5e-4f2f-a800-99af492f869c"
+ "GeneratedBy": "urn:autobloc-gx5Gs1iF"
},
{
- "@id": "urn:4d37d4cb-b4a6-442a-b3a5-39d657df0ece",
+ "@id": "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Label": "sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"digest": {
@@ -243,13 +245,13 @@
}
},
{
- "@id": "urn:12ac620f-52b9-4e67-9ca4-2c6ed0706ca2",
+ "@id": "bids::$output_dir/pb00.$subj.r01.tcat",
"Label": "pb00.$subj.r01.tcat",
"AtLocation": "$output_dir/pb00.$subj.r01.tcat",
- "GeneratedBy": "urn:b1c281e2-c739-46f8-a194-514e241747b2"
+ "GeneratedBy": "urn:autobloc-aWD77U1W"
},
{
- "@id": "urn:b096695f-7087-450e-9140-ce73eb052e67",
+ "@id": "bids::pb00.$subj.r$run.tcat+orig",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -257,7 +259,7 @@
}
},
{
- "@id": "urn:4a199e13-d903-4746-8a05-4c28d3f24786",
+ "@id": "bids::outcount.r*.1D",
"Label": "outcount.r*.1D",
"AtLocation": "outcount.r*.1D",
"digest": {
@@ -265,25 +267,25 @@
}
},
{
- "@id": "urn:5fd5670b-c661-4d9f-852f-fdb5238e0773",
+ "@id": "bids::outcount.r$run.1D",
"Label": "outcount.r$run.1D",
"AtLocation": "outcount.r$run.1D",
- "GeneratedBy": "urn:2e3df101-cb1e-445d-ab72-61377537503d",
+ "GeneratedBy": "urn:autobloc-ItX0hSbT",
"digest": {
"sha256": "63d9f539e5470badc625d557109f68bc4eecbb02ca2667483739d52f95e5d0dd"
}
},
{
- "@id": "urn:315774d8-d488-4729-b1f0-85284457a2e3",
+ "@id": "bids::outcount_rall.1D",
"Label": "outcount_rall.1D",
"AtLocation": "outcount_rall.1D",
- "GeneratedBy": "urn:2e3df101-cb1e-445d-ab72-61377537503d",
+ "GeneratedBy": "urn:autobloc-ItX0hSbT",
"digest": {
"sha256": "cb887fd5e4d5e9acb3a24820d0f7a62ed38a5ffb0fdedd373440ac0219fb186a"
}
},
{
- "@id": "urn:b096695f-7087-450e-9140-ce73eb052e67",
+ "@id": "bids::pb00.$subj.r$run.tcat+orig",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -291,16 +293,16 @@
}
},
{
- "@id": "urn:7a85b1cc-2bb2-4767-a505-0472b5801790",
+ "@id": "bids::pb01.$subj.r$run.tshift",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift",
- "GeneratedBy": "urn:60d56e93-faf4-4101-be8b-18f457793b62",
+ "GeneratedBy": "urn:tshift-qJQPUAmK",
"digest": {
"sha256": "c6bf01cea8d2eac1d7a866f80b865c6e7d4b4e012dbb63d480ac9a8551162d72"
}
},
{
- "@id": "urn:e7e293a9-eed8-4907-8a4f-271b2c2e77d0",
+ "@id": "bids::sub-01_T1w+orig",
"Label": "sub-01_T1w",
"AtLocation": "sub-01_T1w+orig",
"digest": {
@@ -308,7 +310,7 @@
}
},
{
- "@id": "urn:c9a633f5-e6cf-4a7a-8473-0e1b99164061",
+ "@id": "bids::pb01.$subj.r01.tshift+orig",
"Label": "pb01.$subj.r01.tshift",
"AtLocation": "pb01.$subj.r01.tshift+orig",
"digest": {
@@ -316,16 +318,16 @@
}
},
{
- "@id": "urn:76213b1a-bbf3-4212-a463-8865023f1bda",
+ "@id": "bids::_al_junk",
"Label": "_al_junk",
"AtLocation": "_al_junk",
- "GeneratedBy": "urn:1f988b1a-d24f-425f-a9ae-e63df25e13c1",
+ "GeneratedBy": "urn:align-2yy5MCs2",
"digest": {
"sha256": "bd785a075a4c6446e1e54de9e628913f7f1c814e86b69a9fbfe933209e6d37b5"
}
},
{
- "@id": "urn:eb856fcf-6bbd-4aca-b994-a5f4f046b424",
+ "@id": "bids::TT_N27+tlrc",
"Label": "TT_N27",
"AtLocation": "TT_N27+tlrc",
"digest": {
@@ -333,7 +335,7 @@
}
},
{
- "@id": "urn:ff64e210-7ac9-4c70-add6-986f2c290fcd",
+ "@id": "bids::sub-01_T1w_ns+orig",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+orig",
"digest": {
@@ -341,7 +343,7 @@
}
},
{
- "@id": "urn:e02a94c5-0f0d-4ae7-b811-f3e501ab6750",
+ "@id": "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc::WARP_DATA",
"digest": {
@@ -349,16 +351,16 @@
}
},
{
- "@id": "urn:318d11c1-328d-4b91-827d-74de938fd19b",
+ "@id": "bids::warp.anat.Xat.1D",
"Label": "warp.anat.Xat.1D",
"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:fa0fcc24-2f99-4ce4-b71a-6fc34570f7cc",
+ "GeneratedBy": "urn:tlrc-LkdaOXQO",
"digest": {
"sha256": "800633fb5b4e9be64078bc181c4d5510ffb73fc5cccaf364c7fb6a294aa06728"
}
},
{
- "@id": "urn:e02a94c5-0f0d-4ae7-b811-f3e501ab6750",
+ "@id": "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc::WARP_DATA",
"digest": {
@@ -366,16 +368,16 @@
}
},
{
- "@id": "urn:318d11c1-328d-4b91-827d-74de938fd19b",
+ "@id": "bids::warp.anat.Xat.1D",
"Label": "warp.anat.Xat.1D",
"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:fa0fcc24-2f99-4ce4-b71a-6fc34570f7cc",
+ "GeneratedBy": "urn:tlrc-LkdaOXQO",
"digest": {
"sha256": "800633fb5b4e9be64078bc181c4d5510ffb73fc5cccaf364c7fb6a294aa06728"
}
},
{
- "@id": "urn:8576faad-35a6-4007-baae-031b625be042",
+ "@id": "bids::pb01.$subj.r$run.tshift+orig",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift+orig",
"digest": {
@@ -383,7 +385,7 @@
}
},
{
- "@id": "urn:bae96fa9-f172-4a9c-bbe4-5d029f4dcd50",
+ "@id": "bids::sub-01_T1w_ns+tlrc",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc",
"digest": {
@@ -391,7 +393,7 @@
}
},
{
- "@id": "urn:55c204fc-4ef2-4bab-b845-fd5c543a7a0b",
+ "@id": "bids::rm.epi.all1+orig",
"Label": "rm.epi.all1",
"AtLocation": "rm.epi.all1+orig",
"digest": {
@@ -399,7 +401,7 @@
}
},
{
- "@id": "urn:9c283eeb-3683-4f35-966a-6cee22e62921",
+ "@id": "bids::rm.epi.1.r$run+tlrc",
"Label": "rm.epi.1.r$run",
"AtLocation": "rm.epi.1.r$run+tlrc",
"digest": {
@@ -407,7 +409,7 @@
}
},
{
- "@id": "urn:e5955845-059f-4888-9f31-10a84ecd3afd",
+ "@id": "bids::dfile.r*.1D",
"Label": "dfile.r*.1D",
"AtLocation": "dfile.r*.1D",
"digest": {
@@ -415,7 +417,7 @@
}
},
{
- "@id": "urn:dcd9b6d5-0d6c-44a8-b2a4-20746f3bf451",
+ "@id": "bids::rm.epi.min.r01+tlrc",
"Label": "rm.epi.min.r01",
"AtLocation": "rm.epi.min.r01+tlrc",
"digest": {
@@ -423,7 +425,7 @@
}
},
{
- "@id": "urn:3bbde2e2-3198-4f5e-a405-3dc2859a814d",
+ "@id": "bids::rm.epi.nomask.r$run+tlrc",
"Label": "rm.epi.nomask.r$run",
"AtLocation": "rm.epi.nomask.r$run+tlrc",
"digest": {
@@ -431,7 +433,7 @@
}
},
{
- "@id": "urn:b0e85dbd-3264-414a-aad3-bded58a631c6",
+ "@id": "bids::mask_epi_extents+tlrc",
"Label": "mask_epi_extents",
"AtLocation": "mask_epi_extents+tlrc",
"digest": {
@@ -439,97 +441,105 @@
}
},
{
- "@id": "urn:a7eb83f1-3b46-4769-a8da-f910ed4bef65",
+ "@id": "bids::anat_final.$subj+tlrc",
+ "Label": "anat_final.$subj",
+ "AtLocation": "anat_final.$subj+tlrc",
+ "digest": {
+ "sha256": "94eb1853614cc085b22772c011f119f6a0ad7ec06cba2850587762e7f1a6eae6"
+ }
+ },
+ {
+ "@id": "bids::mat.r$run.vr.aff12.1D",
"Label": "mat.r$run.vr.aff12.1D",
"AtLocation": "mat.r$run.vr.aff12.1D",
- "GeneratedBy": "urn:07715c6d-a301-48f9-b7e1-a44f5c4aec34",
+ "GeneratedBy": "urn:volreg-QjASoC7j",
"digest": {
"sha256": "2e6e6c2ce8089cfa3c6e11dc72fca0cc8497f7a55faae2ced402de4867466c91"
}
},
{
- "@id": "urn:c3ea95c6-89ba-4b96-9a86-b4b166b94a52",
+ "@id": "bids::rm.epi.all1",
"Label": "rm.epi.all1",
"AtLocation": "rm.epi.all1",
- "GeneratedBy": "urn:07715c6d-a301-48f9-b7e1-a44f5c4aec34",
+ "GeneratedBy": "urn:volreg-QjASoC7j",
"digest": {
"sha256": "1023e3c16cecdbdc73ea456bcf33c2e5bb4f1e07094b73d29022d651e5fa3f85"
}
},
{
- "@id": "urn:6a5a682c-1df7-48eb-93e1-b320e412ec2e",
+ "@id": "bids::rm.epi.nomask.r$run",
"Label": "rm.epi.nomask.r$run",
"AtLocation": "rm.epi.nomask.r$run",
- "GeneratedBy": "urn:07715c6d-a301-48f9-b7e1-a44f5c4aec34",
+ "GeneratedBy": "urn:volreg-QjASoC7j",
"digest": {
"sha256": "03d6cba0426c5545e350e6b63a19b0e46f8dfa2223fd08691753e8914a479e36"
}
},
{
- "@id": "urn:d4a83aff-fe1a-478a-8c0b-3fdf85f08262",
+ "@id": "bids::rm.epi.1.r$run",
"Label": "rm.epi.1.r$run",
"AtLocation": "rm.epi.1.r$run",
- "GeneratedBy": "urn:07715c6d-a301-48f9-b7e1-a44f5c4aec34",
+ "GeneratedBy": "urn:volreg-QjASoC7j",
"digest": {
"sha256": "b1b9128c103ea246625db1a35e6f474a221ca6c1105a30df38aefdc4d5421e84"
}
},
{
- "@id": "urn:6bbd0a71-c593-4f62-a7b7-4d10f75aaf00",
+ "@id": "bids::rm.epi.min.r$run",
"Label": "rm.epi.min.r$run",
"AtLocation": "rm.epi.min.r$run",
- "GeneratedBy": "urn:07715c6d-a301-48f9-b7e1-a44f5c4aec34",
+ "GeneratedBy": "urn:volreg-QjASoC7j",
"digest": {
"sha256": "b4418a96ddbbf25afdfd01ed0506ddebe009011ba18aed10137f994260fd1a66"
}
},
{
- "@id": "urn:b624270f-a3c2-46c6-a27c-89d37f792539",
+ "@id": "bids::dfile_rall.1D",
"Label": "dfile_rall.1D",
"AtLocation": "dfile_rall.1D",
- "GeneratedBy": "urn:07715c6d-a301-48f9-b7e1-a44f5c4aec34",
+ "GeneratedBy": "urn:volreg-QjASoC7j",
"digest": {
"sha256": "011e7296870a1ac7e15377fb0d529ed68710bb16b138bef6aeb6c645f437dcf2"
}
},
{
- "@id": "urn:a68d7d7d-2892-4c73-8931-cb493bf3664b",
+ "@id": "bids::mask_epi_extents",
"Label": "mask_epi_extents",
"AtLocation": "mask_epi_extents",
- "GeneratedBy": "urn:07715c6d-a301-48f9-b7e1-a44f5c4aec34",
+ "GeneratedBy": "urn:volreg-QjASoC7j",
"digest": {
"sha256": "a69dd71209516ec24e2b3364072ed54adff16619459b1c369866210ec642e987"
}
},
{
- "@id": "urn:d8e5489f-a3db-414f-b726-91d2578e169f",
+ "@id": "bids::pb02.$subj.r$run.volreg",
"Label": "pb02.$subj.r$run.volreg",
"AtLocation": "pb02.$subj.r$run.volreg",
- "GeneratedBy": "urn:07715c6d-a301-48f9-b7e1-a44f5c4aec34",
+ "GeneratedBy": "urn:volreg-QjASoC7j",
"digest": {
"sha256": "8821927190ac1b3f8f9d9a5ec74f6468ae6c1cb736e58e5de2cdbe3543d5cc0c"
}
},
{
- "@id": "urn:21696db2-7995-4ed0-b49a-cf12853936ea",
+ "@id": "bids::anat_final.$subj",
"Label": "anat_final.$subj",
"AtLocation": "anat_final.$subj",
- "GeneratedBy": "urn:07715c6d-a301-48f9-b7e1-a44f5c4aec34",
+ "GeneratedBy": "urn:volreg-QjASoC7j",
"digest": {
"sha256": "69b750d004bdba337de0b4ffa683bd92bc8f34b854d320327839ad264b28c4c5"
}
},
{
- "@id": "urn:a8a1a9f6-ef1a-480d-bdea-a1be759db9ea",
+ "@id": "bids::anat_w_skull_warped",
"Label": "anat_w_skull_warped",
"AtLocation": "anat_w_skull_warped",
- "GeneratedBy": "urn:07715c6d-a301-48f9-b7e1-a44f5c4aec34",
+ "GeneratedBy": "urn:volreg-QjASoC7j",
"digest": {
"sha256": "462fdb8cd2b882e250fee3c6adb7acf0b0b9a9edb3e1cadf9d45d16180871105"
}
},
{
- "@id": "urn:1cf6abc0-28b4-47b1-8241-d2e415806801",
+ "@id": "bids::pb03.$subj.r$run.blur",
"Label": "pb03.$subj.r$run.blur",
"AtLocation": "pb03.$subj.r$run.blur",
"digest": {
@@ -537,7 +547,7 @@
}
},
{
- "@id": "urn:40c7b3b1-aa1b-41ef-b09f-423be7a6600a",
+ "@id": "bids::pb02.$subj.r$run.volreg+tlrc",
"Label": "pb02.$subj.r$run.volreg",
"AtLocation": "pb02.$subj.r$run.volreg+tlrc",
"digest": {
@@ -545,7 +555,7 @@
}
},
{
- "@id": "urn:bae96fa9-f172-4a9c-bbe4-5d029f4dcd50",
+ "@id": "bids::sub-01_T1w_ns+tlrc",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc",
"digest": {
@@ -553,7 +563,7 @@
}
},
{
- "@id": "urn:7cdabd60-f015-462a-9a04-a3e21053d633",
+ "@id": "bids::pb03.$subj.r$run.blur+tlrc",
"Label": "pb03.$subj.r$run.blur",
"AtLocation": "pb03.$subj.r$run.blur+tlrc",
"digest": {
@@ -561,7 +571,7 @@
}
},
{
- "@id": "urn:b17cce80-9f35-4a8d-88e0-e1d81c9b0c87",
+ "@id": "bids::full_mask.$subj+tlrc",
"Label": "full_mask.$subj",
"AtLocation": "full_mask.$subj+tlrc",
"digest": {
@@ -569,7 +579,7 @@
}
},
{
- "@id": "urn:57c66382-57aa-4906-b4b8-d0fdd4b367d8",
+ "@id": "bids::rm.resam.anat+tlrc",
"Label": "rm.resam.anat",
"AtLocation": "rm.resam.anat+tlrc",
"digest": {
@@ -577,7 +587,7 @@
}
},
{
- "@id": "urn:0e402105-a625-4b0d-aabb-84565733d38a",
+ "@id": "bids::mask_anat.$subj+tlrc",
"Label": "mask_anat.$subj",
"AtLocation": "mask_anat.$subj+tlrc",
"digest": {
@@ -585,7 +595,7 @@
}
},
{
- "@id": "urn:96e34fde-acd7-4ce9-bcbd-bfb3b267f717",
+ "@id": "bids::tee",
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"AtLocation": "tee",
"digest": {
@@ -593,7 +603,7 @@
}
},
{
- "@id": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "@id": "bids::/Users/u1591557/abin/TT_N27+tlrc",
"Label": "TT_N27",
"AtLocation": "/Users/u1591557/abin/TT_N27+tlrc",
"digest": {
@@ -601,7 +611,7 @@
}
},
{
- "@id": "urn:ea12cbb8-ae5f-4a2e-b17f-47c484ceeaaa",
+ "@id": "bids::rm.resam.group+tlrc",
"Label": "rm.resam.group",
"AtLocation": "rm.resam.group+tlrc",
"digest": {
@@ -609,61 +619,61 @@
}
},
{
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{
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@@ -671,7 +681,7 @@
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{
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@@ -679,7 +689,7 @@
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{
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@@ -687,34 +697,34 @@
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{
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{
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{
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@@ -722,7 +732,7 @@
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@@ -730,7 +740,7 @@
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{
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@@ -738,7 +748,7 @@
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@@ -746,7 +756,7 @@
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@@ -754,7 +764,7 @@
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@@ -762,7 +772,7 @@
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@@ -770,7 +780,7 @@
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@@ -778,7 +788,7 @@
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@@ -786,7 +796,7 @@
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@@ -794,7 +804,7 @@
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{
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@@ -802,7 +812,7 @@
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{
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@@ -810,7 +820,7 @@
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{
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@@ -818,133 +828,133 @@
}
},
{
- "@id": "urn:cd4eb98c-0ee8-4e24-bcf5-30ca3bb9157b",
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"AtLocation": "motion_demean.1D",
- "GeneratedBy": "urn:e1481f5e-884b-4430-8ff3-ec696a5999d9",
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"AtLocation": "motion_deriv.1D",
- "GeneratedBy": "urn:e1481f5e-884b-4430-8ff3-ec696a5999d9",
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{
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{
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{
- "@id": "urn:766cf6f0-051b-45c6-8451-c590708c3122",
+ "@id": "bids::TSNR.$subj",
"Label": "TSNR.$subj",
"AtLocation": "TSNR.$subj",
- "GeneratedBy": "urn:e1481f5e-884b-4430-8ff3-ec696a5999d9",
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{
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{
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"Label": "-",
"AtLocation": "-",
- "GeneratedBy": "urn:e1481f5e-884b-4430-8ff3-ec696a5999d9",
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{
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{
- "@id": "urn:1aae6267-2647-4471-be32-eedcaaf44213",
+ "@id": "bids::corr_brain",
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"AtLocation": "corr_brain",
- "GeneratedBy": "urn:e1481f5e-884b-4430-8ff3-ec696a5999d9",
+ "GeneratedBy": "urn:regress-VfuA197y",
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{
- "@id": "urn:1ac2c87f-eeb1-4e78-95d3-ea9b816d6ba5",
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"AtLocation": "ideal_tone_counting.1D",
- "GeneratedBy": "urn:e1481f5e-884b-4430-8ff3-ec696a5999d9",
+ "GeneratedBy": "urn:regress-VfuA197y",
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{
- "@id": "urn:94015072-e745-45a1-8944-c5e62523e8fb",
+ "@id": "bids::ideal_probe.1D",
"Label": "ideal_probe.1D",
"AtLocation": "ideal_probe.1D",
- "GeneratedBy": "urn:e1481f5e-884b-4430-8ff3-ec696a5999d9",
+ "GeneratedBy": "urn:regress-VfuA197y",
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{
- "@id": "urn:81320ff0-3c04-46f5-82a0-2096247086bc",
+ "@id": "bids::sum_ideal.1D",
"Label": "sum_ideal.1D",
"AtLocation": "sum_ideal.1D",
- "GeneratedBy": "urn:e1481f5e-884b-4430-8ff3-ec696a5999d9",
+ "GeneratedBy": "urn:regress-VfuA197y",
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{
- "@id": "urn:0057116e-ac2f-4b31-a958-78f2eae0e582",
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"AtLocation": "X.stim.xmat.1D",
- "GeneratedBy": "urn:e1481f5e-884b-4430-8ff3-ec696a5999d9",
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+ "@id": "bids::full_mask.$subj+tlrc",
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@@ -952,34 +962,34 @@
}
},
{
- "@id": "urn:85a7e7b5-430c-4e81-b113-e540bfe5e48d",
+ "@id": "bids::blur.epits.1D",
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"AtLocation": "blur.epits.1D",
- "GeneratedBy": "urn:8a07fb2b-8782-48d7-8ff0-81e6a9ad26ed",
+ "GeneratedBy": "urn:bluresti-Qz0unv2Z",
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{
- "@id": "urn:7cdfe3ab-fac6-4fc5-88cf-6f8b3dfcd272",
+ "@id": "bids::blur.errts.1D",
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"AtLocation": "blur.errts.1D",
- "GeneratedBy": "urn:8a07fb2b-8782-48d7-8ff0-81e6a9ad26ed",
+ "GeneratedBy": "urn:bluresti-Qz0unv2Z",
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{
- "@id": "urn:457e2c3b-290a-4d49-b677-77424fc164e0",
+ "@id": "bids::ClustSim",
"Label": "ClustSim",
"AtLocation": "ClustSim",
- "GeneratedBy": "urn:8a07fb2b-8782-48d7-8ff0-81e6a9ad26ed",
+ "GeneratedBy": "urn:bluresti-Qz0unv2Z",
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{
- "@id": "urn:218ffa82-8cd0-4624-9995-7d9b9da621f0",
+ "@id": "bids::pb00.$subj.r*.tcat+orig.HEAD",
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"digest": {
@@ -987,10 +997,10 @@
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{
- "@id": "urn:02fa4dac-b13e-47ef-8390-9b5f37135c15",
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- "GeneratedBy": "urn:758476e6-7d68-4c13-968c-da2ed9657bd8",
+ "GeneratedBy": "urn:autobloc-2RxNDsvi",
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diff --git a/examples/from_parsers/afni/afni_con_f_proc_block.png b/examples/from_parsers/afni/afni_con_f_proc_block.png
index 3e465eb0d..66e528a35 100644
Binary files a/examples/from_parsers/afni/afni_con_f_proc_block.png and b/examples/from_parsers/afni/afni_con_f_proc_block.png differ
diff --git a/examples/from_parsers/afni/afni_default_proc.jsonld b/examples/from_parsers/afni/afni_default_proc.jsonld
index ec807f148..78eca316f 100644
--- a/examples/from_parsers/afni/afni_default_proc.jsonld
+++ b/examples/from_parsers/afni/afni_default_proc.jsonld
@@ -4,578 +4,581 @@
"Records": {
"Software": [
{
- "@id": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:afni-J4qIgUS6",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
- "Version": "afni24"
+ "Version": "afni24",
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}
],
"Activities": [
{
- "@id": "urn:b88af698-494b-4523-94e7-fa097b7f8c7f",
+ "@id": "urn:makedire-GKieyNlP",
"Label": "Make directory",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "mkdir $output_dir",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:aa3da46b-70ce-43e9-9884-20dfe3b086b0",
+ "@id": "urn:makedire-UVm2hYna",
"Label": "Make directory",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "mkdir $output_dir/stimuli",
"Parameters": {},
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},
{
- "@id": "urn:f904d8c4-e34a-440f-a647-465fa6a4caab",
+ "@id": "urn:cp-fMIzX1pE",
"Label": "cp",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "cp ./afni_voxelwise_p0001/tone_counting_onset_times.txt ./afni_voxelwise_p0001/tone_counting_probe_duration.txt $output_dir/stimuli",
"Parameters": {},
"Used": [
- "urn:1ac4c5b6-5db5-4e90-bff5-46c18e816b01",
- "urn:4f135819-17e3-44e5-bf60-cfa7e579b316"
+ "bids::afni_voxelwise_p0001/tone_counting_onset_times.txt",
+ "bids::afni_voxelwise_p0001/tone_counting_probe_duration.txt"
]
},
{
- "@id": "urn:0960d74a-45cf-420e-b77a-4d7caf1ea1c6",
+ "@id": "urn:3dcopy-TNNinI1i",
"Label": "3dcopy",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "3dcopy ./afni_voxelwise_p0001/sub-01_T1w.nii.gz $output_dir/sub-01_T1w",
"Parameters": {},
"Used": [
- "urn:2064b37b-01ad-4872-a0c7-e6672efda5ac"
+ "bids::afni_voxelwise_p0001/sub-01_T1w.nii.gz"
]
},
{
- "@id": "urn:b22cc2ec-cee6-480d-97f4-1904f26a4605",
+ "@id": "urn:3dtcat-dwXz4e0G",
"Label": "3dTcat",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat ./afni_voxelwise_p0001/sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Parameters": {},
"Used": [
- "urn:d56b4f90-3293-4027-990f-c954c816480a"
+ "bids::afni_voxelwise_p0001/sub-01_task-tonecounting_bold.nii.gz'[0..$]'"
]
},
{
- "@id": "urn:ffe0f216-4a97-48d6-b019-8d8dfb3306fc",
+ "@id": "urn:3dtoutco-Bm38cl8G",
"Label": "3dToutcount",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D",
"Parameters": {},
"Used": [
- "urn:8b2d5380-3323-4471-a93a-b69b4275bd30"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:fdfb15e4-17f6-48f7-b24e-edf1e2394938",
+ "@id": "urn:cat-DjwBZT3w",
"Label": "cat",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "cat outcount.r*.1D > outcount_rall.1D",
"Parameters": {},
"Used": [
- "urn:f0455c3c-ef14-4009-bd6d-60d1f8f07081"
+ "bids::outcount.r*.1D"
]
},
{
- "@id": "urn:c12f783b-27ea-44e4-aaab-d818c36d5272",
+ "@id": "urn:3dtshift-TjxbHsNe",
"Label": "3dTshift",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig",
"Parameters": {},
"Used": [
- "urn:8b2d5380-3323-4471-a93a-b69b4275bd30"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:54d4205c-2755-4b93-8703-c1d55bea28be",
+ "@id": "urn:alignepi-qzMviOnv",
"Label": "align_epi_anat.py",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off",
"Parameters": {},
"Used": [
- "urn:52b454bd-7e81-4ee7-ac1e-efe736cdd46c",
- "urn:7735b3ca-2f92-43b2-ae95-4ef18acc796b"
+ "bids::pb01.$subj.r01.tshift+orig",
+ "bids::sub-01_T1w+orig"
]
},
{
- "@id": "urn:91a99f75-a4b5-434e-b5fc-cd05fae1fad9",
+ "@id": "urn:autotlrc-Ye1q2rYP",
"Label": "@auto_tlrc",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss",
"Parameters": {},
"Used": [
- "urn:a094dcca-d44d-4beb-bdac-576804c53c44",
- "urn:d5fc324a-1aa6-4bb9-bf50-5348c8468ba1"
+ "bids::TT_N27+tlrc",
+ "bids::sub-01_T1w_ns+orig"
]
},
{
- "@id": "urn:530372d1-1692-44c6-8880-08936c1e3afc",
+ "@id": "urn:catmatve-terER4Y4",
"Label": "cat_matvec",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D",
"Parameters": {},
"Used": [
- "urn:3aa79963-75fc-45c4-838b-653210bd3857"
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:81eb387a-a9f4-404a-89ac-8eb8bd0c328d",
+ "@id": "urn:3dvolreg-tS8mWkCy",
"Label": "3dvolreg",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig",
"Parameters": {},
"Used": [
- "urn:f7c6d767-3954-45c5-8bc2-d4090610d584"
+ "bids::pb01.$subj.r$run.tshift+orig"
]
},
{
- "@id": "urn:dfde6c8e-d119-4215-b337-145bb3eef5f1",
+ "@id": "urn:3dcalc-lVv6vmhn",
"Label": "3dcalc",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1",
"Parameters": {},
"Used": [
- "urn:f7c6d767-3954-45c5-8bc2-d4090610d584"
+ "bids::pb01.$subj.r$run.tshift+orig"
]
},
{
- "@id": "urn:606c5072-51fb-4143-a52a-2b73db9adcb5",
+ "@id": "urn:catmatve-YaBZGpgm",
"Label": "cat_matvec",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D",
"Parameters": {},
"Used": [
- "urn:3aa79963-75fc-45c4-838b-653210bd3857"
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:41ef447f-fccd-4aff-ae40-399d14ad3aa0",
+ "@id": "urn:3dalline-mAEHSFbA",
"Label": "3dAllineate",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run",
"Parameters": {},
"Used": [
- "urn:51ee2018-45e8-49ce-a6ac-8202b01a4902",
- "urn:ef1d1588-ae65-4d09-9c2f-4e241eed532c",
- "urn:f7c6d767-3954-45c5-8bc2-d4090610d584"
+ "bids::mat.r$run.warp.aff12.1D",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:294e434c-6bd8-47c2-ae75-bb719ea79b78",
+ "@id": "urn:3dalline-oSNVZLhS",
"Label": "3dAllineate",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run",
"Parameters": {},
"Used": [
- "urn:51ee2018-45e8-49ce-a6ac-8202b01a4902",
- "urn:ef1d1588-ae65-4d09-9c2f-4e241eed532c",
- "urn:f06804b1-350d-4114-a036-23dd4599b121"
+ "bids::mat.r$run.warp.aff12.1D",
+ "bids::rm.epi.all1+orig",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:9c18c3d4-999e-4e35-af52-a2ab367c9566",
+ "@id": "urn:3dtstat-sybsb09m",
"Label": "3dTstat",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc",
"Parameters": {},
"Used": [
- "urn:a4052ff6-ac0e-4709-8ccf-096142900064"
+ "bids::rm.epi.1.r$run+tlrc"
]
},
{
- "@id": "urn:8b2f63d1-861e-4b43-97e4-6bbbff470320",
+ "@id": "urn:cat-2fz5ttpF",
"Label": "cat",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "cat dfile.r*.1D > dfile_rall.1D",
"Parameters": {},
"Used": [
- "urn:d6806031-87b7-40be-b276-bf0ebc9c7440"
+ "bids::dfile.r*.1D"
]
},
{
- "@id": "urn:9f7852ef-9692-4835-816e-224e3152c46a",
+ "@id": "urn:3dcopy-6anXD3J3",
"Label": "3dcopy",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents",
"Parameters": {},
"Used": [
- "urn:800cb0d4-2427-4684-a00f-3cb9d52a9925"
+ "bids::rm.epi.min.r01+tlrc"
]
},
{
- "@id": "urn:fb6b516a-fe10-4c47-b3d3-71d602d8b389",
+ "@id": "urn:3dcalc-aAV2PGan",
"Label": "3dcalc",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg",
"Parameters": {},
"Used": [
- "urn:6506f02f-3be9-4a1a-af00-dec6938acd6f",
- "urn:84d71315-bdad-41e8-bc26-b0cc204b972d"
+ "bids::mask_epi_extents+tlrc",
+ "bids::rm.epi.nomask.r$run+tlrc"
]
},
{
- "@id": "urn:f1b89e77-c3d4-4079-82fb-6a16163b9421",
+ "@id": "urn:3dcopy-4bzRrv4x",
"Label": "3dcopy",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj",
"Parameters": {},
"Used": [
- "urn:ef1d1588-ae65-4d09-9c2f-4e241eed532c"
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:4846c2a0-8a5e-452e-8445-48caead091df",
+ "@id": "urn:3dalline-14yOSmwP",
"Label": "3dAllineate",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped",
"Parameters": {},
"Used": [
- "urn:f237b0b8-0b29-478c-ac7f-2dc18976a994"
+ "bids::anat_final.$subj+tlrc",
+ "bids::warp.anat.Xat.1D"
]
},
{
- "@id": "urn:953da91d-fdcc-4eb3-8b57-5f3f17727bc0",
+ "@id": "urn:3dmerge-dro1prKM",
"Label": "3dmerge",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc",
"Parameters": {},
"Used": [
- "urn:9887c94f-91b2-4240-a36a-eadb5aa3c924",
- "urn:b08e3d70-dd9a-40fe-b019-685761dbc4b9"
+ "bids::pb02.$subj.r$run.volreg+tlrc",
+ "bids::pb03.$subj.r$run.blur"
]
},
{
- "@id": "urn:6a61799d-2599-4916-80ef-4883143bc617",
+ "@id": "urn:3dautoma-bcOPYTPN",
"Label": "3dAutomask",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:8cf5d2ac-cc2a-44e7-8eb2-c32e0dbb77df"
+ "bids::pb03.$subj.r$run.blur+tlrc"
]
},
{
- "@id": "urn:97cd560d-ae4f-434c-a666-628134b605a4",
+ "@id": "urn:3dmaskto-mSRxvjzr",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:933a06df-d189-4d77-8890-8ccf53fd1c0f",
+ "@id": "urn:3dresamp-ZosW2ivc",
"Label": "3dresample",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat",
"Parameters": {},
"Used": [
- "urn:ef1d1588-ae65-4d09-9c2f-4e241eed532c",
- "urn:f412f5d1-816b-440b-9539-e4500dd9a7f4"
+ "bids::full_mask.$subj+tlrc",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:50bf7294-d26c-4351-b726-0037e3bc30b4",
+ "@id": "urn:3dmaskto-XYoCnOGa",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj",
"Parameters": {},
"Used": [
- "urn:761d8304-1910-4af4-9bcc-748950048e05"
+ "bids::rm.resam.anat+tlrc"
]
},
{
- "@id": "urn:c52ab986-0721-4976-918f-518822d8df32",
+ "@id": "urn:3dabover-1842EkJd",
"Label": "3dABoverlap",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt",
"Parameters": {},
"Used": [
- "urn:1b6c722e-cdaa-4c88-b3a6-87c65a37554a",
- "urn:ae9dab48-a818-43a0-be2b-28a9a4d076da"
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee"
]
},
{
- "@id": "urn:7bfc174d-9b61-4f39-a8f4-e8760740f100",
+ "@id": "urn:3ddot-mS7k1Zi6",
"Label": "3ddot",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt",
"Parameters": {},
"Used": [
- "urn:1b6c722e-cdaa-4c88-b3a6-87c65a37554a",
- "urn:ae9dab48-a818-43a0-be2b-28a9a4d076da"
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee"
]
},
{
- "@id": "urn:0381843b-eb04-4177-9a55-a98f65fb3262",
+ "@id": "urn:3dresamp-jEcqiAZS",
"Label": "3dresample",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc",
"Parameters": {},
"Used": [
- "urn:5092984f-5d20-4ec0-817f-5992ffdcb2c9",
- "urn:f412f5d1-816b-440b-9539-e4500dd9a7f4"
+ "bids::/Users/u1591557/abin/TT_N27+tlrc",
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:c87a3172-8501-4620-87eb-5dfa686b2f8b",
+ "@id": "urn:3dmaskto-Fp5LFGAY",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group",
"Parameters": {},
"Used": [
- "urn:599f48e7-16cb-41c8-9af7-3e9523a18a89"
+ "bids::rm.resam.group+tlrc"
]
},
{
- "@id": "urn:507a8da5-9f2f-4616-ad3e-679eaad090d9",
+ "@id": "urn:3dtstat-1LKfPoWn",
"Label": "3dTstat",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:8cf5d2ac-cc2a-44e7-8eb2-c32e0dbb77df"
+ "bids::pb03.$subj.r$run.blur+tlrc"
]
},
{
- "@id": "urn:4f7198d4-27d5-4774-a8be-0493629b20c4",
+ "@id": "urn:3dcalc-Gkx96YT7",
"Label": "3dcalc",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale",
"Parameters": {},
"Used": [
- "urn:01c533ac-888f-4efc-a3c7-9a21bb0032c9",
- "urn:84d71315-bdad-41e8-bc26-b0cc204b972d",
- "urn:8cf5d2ac-cc2a-44e7-8eb2-c32e0dbb77df"
+ "bids::mask_epi_extents+tlrc",
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::rm.mean_r$run+tlrc"
]
},
{
- "@id": "urn:783f0bfe-bc17-4fd3-86e4-5265722f4f3f",
+ "@id": "urn:1dtoolpy-nkvl2lAw",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D",
"Parameters": {},
"Used": [
- "urn:aa64aea4-5eb2-4c2d-b8fb-dd510fa63edb"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:8e7d0070-8079-4c57-aede-ac31ab3d2c61",
+ "@id": "urn:1dtoolpy-XEzwoJee",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D",
"Parameters": {},
"Used": [
- "urn:aa64aea4-5eb2-4c2d-b8fb-dd510fa63edb"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:e69f4098-08d3-44bb-a7eb-cae49508103f",
+ "@id": "urn:1dtoolpy-s3Oil2R1",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}",
"Parameters": {},
"Used": [
- "urn:aa64aea4-5eb2-4c2d-b8fb-dd510fa63edb"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:21ac6c9a-3333-4923-9186-c9e5020afcb9",
+ "@id": "urn:3ddeconv-7obQPDKT",
"Label": "3dDeconvolve",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj",
"Parameters": {},
"Used": [
- "urn:ae6c30bd-7165-4aa1-bb31-3af82ba212fa"
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD"
]
},
{
- "@id": "urn:96c4c10a-78de-41e9-819c-cee215f36d3c",
+ "@id": "urn:1dtoolpy-UGmO4TdG",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt",
"Parameters": {},
"Used": [
- "urn:6f8300aa-44d9-4384-99b3-e51129ac29ab"
+ "bids::X.xmat.1D"
]
},
{
- "@id": "urn:0eb349a3-d1f9-4176-87bb-ee9a8f7163f1",
+ "@id": "urn:3dtcat-KMmrJrK3",
"Label": "3dTcat",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD",
"Parameters": {},
"Used": [
- "urn:ae6c30bd-7165-4aa1-bb31-3af82ba212fa"
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD"
]
},
{
- "@id": "urn:ed752a0c-4414-4ed9-9dec-4e4f5fcff34d",
+ "@id": "urn:3dtstat-byrkkVkB",
"Label": "3dTstat",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:e16d69a9-cb22-4fa6-93e3-3f382186da83"
+ "bids::all_runs.$subj+tlrc%22[$ktrs]%22"
]
},
{
- "@id": "urn:b50d8309-9587-4c3d-8b68-eafea4254b96",
+ "@id": "urn:3dtstat-VI3XkDVU",
"Label": "3dTstat",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:04745c1c-681d-4ecd-99f5-96d342aae6ed"
+ "bids::errts.$%7Bsubj%7D+tlrc%22[$ktrs]%22"
]
},
{
- "@id": "urn:92d3b2a1-dba6-4edc-93c6-11c3082b306f",
+ "@id": "urn:3dcalc-roPISxqF",
"Label": "3dcalc",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj",
"Parameters": {},
"Used": [
- "urn:63f6635e-d42e-4729-93ce-219e08306297",
- "urn:8dd263d5-5ca0-470a-b2ea-56225b421ea3",
- "urn:f412f5d1-816b-440b-9539-e4500dd9a7f4"
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.noise.all+tlrc",
+ "bids::rm.signal.all+tlrc"
]
},
{
- "@id": "urn:6ca79a28-ccba-4ed7-9c3e-b723a3384c43",
+ "@id": "urn:3dtnorm-nfo0JwJ6",
"Label": "3dTnorm",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc",
"Parameters": {},
"Used": [
- "urn:3f992f36-31d9-44ae-802b-5d8e0bf192cf"
+ "bids::errts.$%7Bsubj%7D+tlrc"
]
},
{
- "@id": "urn:44e6ae47-f94d-4f63-b751-deb9963deff6",
+ "@id": "urn:3dmaskav-nm5FLxqI",
"Label": "3dmaskave",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D",
"Parameters": {},
- "Used": []
+ "Used": [
+ "bids::full_mask.$subj+tlrc"
+ ]
},
{
- "@id": "urn:b8bea1b6-d3a6-4051-98f1-1a65f739b6f3",
+ "@id": "urn:3dtstat-UQVvH69i",
"Label": "3dTstat",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D",
"Parameters": {},
"Used": [
- "urn:27316f60-9bb2-44a4-92e3-10550fd887e9"
+ "bids::out.gcor.1D"
]
},
{
- "@id": "urn:0ab3aafa-76ca-4e3a-8379-e94368eed76a",
+ "@id": "urn:3dcalc-dd4aneC8",
"Label": "3dcalc",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP",
"Parameters": {},
"Used": [
- "urn:29be423e-dd92-4371-8292-a47c133dbab8",
- "urn:a2ad449d-4882-4dec-90e8-1a9f300f1dbd"
+ "bids::gmean.errts.unit.1D",
+ "bids::rm.errts.unit+tlrc"
]
},
{
- "@id": "urn:f3689c31-ae2f-4947-a2cf-9b34744341b9",
+ "@id": "urn:3dtstat-Un5JiITd",
"Label": "3dTstat",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc",
"Parameters": {},
"Used": [
- "urn:e31fdb15-9bb3-4157-8090-92da89cfac7e"
+ "bids::rm.DP+tlrc"
]
},
{
- "@id": "urn:193bd4ee-4468-4ce5-af56-994791c02d2e",
+ "@id": "urn:1dcat-eyAicARn",
"Label": "1dcat",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D",
"Parameters": {},
"Used": [
- "urn:2aa858d0-c72e-4263-aa8f-f09a66258e4c"
+ "bids::X.nocensor.xmat.1D'[3]'"
]
},
{
- "@id": "urn:2ece99e1-6677-4796-a80a-3775f3199700",
+ "@id": "urn:1dcat-6OiK19Zo",
"Label": "1dcat",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D",
"Parameters": {},
"Used": [
- "urn:bf214b29-acb3-4c15-bf07-61fae1e0c4bc"
+ "bids::X.nocensor.xmat.1D'[4]'"
]
},
{
- "@id": "urn:d0ff6f02-8181-41b5-909b-f0b23781c1f9",
+ "@id": "urn:3dtstat-m1M13vmy",
"Label": "3dTstat",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"",
"Parameters": {},
"Used": [
- "urn:f7b23cf4-c8f9-4b58-9b0e-e0e62ffbccb7"
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:c4fc115a-6e43-47e8-8064-cf6a59c5d9dc",
+ "@id": "urn:1dcat-A6WOvFVZ",
"Label": "1dcat",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D",
"Parameters": {},
"Used": [
- "urn:f7b23cf4-c8f9-4b58-9b0e-e0e62ffbccb7"
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:7708af65-3664-4ba3-b0eb-852b1312c3eb",
+ "@id": "urn:3dfwhmx-Eild0vbL",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D",
"Parameters": {},
"Used": [
- "urn:f412f5d1-816b-440b-9539-e4500dd9a7f4"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:50600ca9-626c-462a-a065-e43145b94a63",
+ "@id": "urn:3dfwhmx-6itTOS0r",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D",
"Parameters": {},
"Used": [
- "urn:f412f5d1-816b-440b-9539-e4500dd9a7f4"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:593ce871-0708-4cde-bd2a-be90a20aad38",
+ "@id": "urn:3dclusts-owXwdfFv",
"Label": "3dClustSim",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim",
"Parameters": {},
"Used": [
- "urn:f412f5d1-816b-440b-9539-e4500dd9a7f4"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:bb3b9fe4-d9bb-456f-b15e-532108af5130",
+ "@id": "urn:genepire-NvZnjQj9",
"Label": "gen_epi_review.py",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD",
"Parameters": {},
"Used": [
- "urn:d1bbf2f0-8f57-4537-8e7d-a4f1f2046f1c"
+ "bids::pb00.$subj.r*.tcat+orig.HEAD"
]
},
{
- "@id": "urn:8c4c3b13-4c9e-41e0-a695-b0506ea60e3a",
+ "@id": "urn:genssrev-XsBgNJCx",
"Label": "gen_ss_review_scripts.py",
- "AssociatedWith": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
+ "AssociatedWith": "urn:afni-J4qIgUS6",
"Command": "gen_ss_review_scripts.py -mot_limit 0.3 -exit0",
"Parameters": {
"-mot_limit": "0.3",
@@ -586,22 +589,22 @@
],
"Entities": [
{
- "@id": "urn:2cb93a0c-4c77-4b4e-a8c5-a1f6c46df8fc",
+ "@id": "bids::$output_dir",
"Label": "$output_dir",
"AtLocation": "$output_dir",
- "GeneratedBy": "urn:b88af698-494b-4523-94e7-fa097b7f8c7f",
+ "GeneratedBy": "urn:makedire-GKieyNlP",
"digest": {
"sha256": "9fa4c635e6533ddf2fed54295920052818d948c3ffe97bc753bd7336b453f8cb"
}
},
{
- "@id": "urn:38fb1c54-00fb-4ac6-a9dc-26c81c1cb409",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:aa3da46b-70ce-43e9-9884-20dfe3b086b0"
+ "GeneratedBy": "urn:makedire-UVm2hYna"
},
{
- "@id": "urn:4f135819-17e3-44e5-bf60-cfa7e579b316",
+ "@id": "bids::afni_voxelwise_p0001/tone_counting_onset_times.txt",
"Label": "tone_counting_onset_times.txt",
"AtLocation": "./afni_voxelwise_p0001/tone_counting_onset_times.txt",
"digest": {
@@ -609,7 +612,7 @@
}
},
{
- "@id": "urn:1ac4c5b6-5db5-4e90-bff5-46c18e816b01",
+ "@id": "bids::afni_voxelwise_p0001/tone_counting_probe_duration.txt",
"Label": "tone_counting_probe_duration.txt",
"AtLocation": "./afni_voxelwise_p0001/tone_counting_probe_duration.txt",
"digest": {
@@ -617,13 +620,13 @@
}
},
{
- "@id": "urn:ffb56926-83e5-458a-881d-6174e5768f9f",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:f904d8c4-e34a-440f-a647-465fa6a4caab"
+ "GeneratedBy": "urn:cp-fMIzX1pE"
},
{
- "@id": "urn:2064b37b-01ad-4872-a0c7-e6672efda5ac",
+ "@id": "bids::afni_voxelwise_p0001/sub-01_T1w.nii.gz",
"Label": "sub-01_T1w.nii.gz",
"AtLocation": "./afni_voxelwise_p0001/sub-01_T1w.nii.gz",
"digest": {
@@ -631,13 +634,13 @@
}
},
{
- "@id": "urn:3dfd4a56-f366-4bd7-b140-c5252318e0cb",
+ "@id": "bids::$output_dir/sub-01_T1w",
"Label": "sub-01_T1w",
"AtLocation": "$output_dir/sub-01_T1w",
- "GeneratedBy": "urn:0960d74a-45cf-420e-b77a-4d7caf1ea1c6"
+ "GeneratedBy": "urn:3dcopy-TNNinI1i"
},
{
- "@id": "urn:d56b4f90-3293-4027-990f-c954c816480a",
+ "@id": "bids::afni_voxelwise_p0001/sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Label": "sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "./afni_voxelwise_p0001/sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"digest": {
@@ -645,13 +648,13 @@
}
},
{
- "@id": "urn:b3730248-9b2b-49ed-9dee-45be3b2efa5d",
+ "@id": "bids::$output_dir/pb00.$subj.r01.tcat",
"Label": "pb00.$subj.r01.tcat",
"AtLocation": "$output_dir/pb00.$subj.r01.tcat",
- "GeneratedBy": "urn:b22cc2ec-cee6-480d-97f4-1904f26a4605"
+ "GeneratedBy": "urn:3dtcat-dwXz4e0G"
},
{
- "@id": "urn:8b2d5380-3323-4471-a93a-b69b4275bd30",
+ "@id": "bids::pb00.$subj.r$run.tcat+orig",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -659,16 +662,16 @@
}
},
{
- "@id": "urn:7b6220b4-8027-423d-a314-287932253b51",
+ "@id": "bids::outcount.r$run.1D",
"Label": "outcount.r$run.1D",
"AtLocation": "outcount.r$run.1D",
- "GeneratedBy": "urn:ffe0f216-4a97-48d6-b019-8d8dfb3306fc",
+ "GeneratedBy": "urn:3dtoutco-Bm38cl8G",
"digest": {
"sha256": "63d9f539e5470badc625d557109f68bc4eecbb02ca2667483739d52f95e5d0dd"
}
},
{
- "@id": "urn:f0455c3c-ef14-4009-bd6d-60d1f8f07081",
+ "@id": "bids::outcount.r*.1D",
"Label": "outcount.r*.1D",
"AtLocation": "outcount.r*.1D",
"digest": {
@@ -676,25 +679,25 @@
}
},
{
- "@id": "urn:8a659019-84c1-4c8e-9f06-1f02d1b401dd",
+ "@id": "bids::outcount_rall.1D",
"Label": "outcount_rall.1D",
"AtLocation": "outcount_rall.1D",
- "GeneratedBy": "urn:fdfb15e4-17f6-48f7-b24e-edf1e2394938",
+ "GeneratedBy": "urn:cat-DjwBZT3w",
"digest": {
"sha256": "cb887fd5e4d5e9acb3a24820d0f7a62ed38a5ffb0fdedd373440ac0219fb186a"
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{
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"AtLocation": "pb01.$subj.r$run.tshift",
- "GeneratedBy": "urn:c12f783b-27ea-44e4-aaab-d818c36d5272",
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{
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"digest": {
@@ -702,7 +705,7 @@
}
},
{
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"digest": {
@@ -710,16 +713,16 @@
}
},
{
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+ "@id": "bids::_al_junk",
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"AtLocation": "_al_junk",
- "GeneratedBy": "urn:54d4205c-2755-4b93-8703-c1d55bea28be",
+ "GeneratedBy": "urn:alignepi-qzMviOnv",
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}
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{
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"digest": {
@@ -727,7 +730,7 @@
}
},
{
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+ "@id": "bids::sub-01_T1w_ns+orig",
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"digest": {
@@ -735,7 +738,7 @@
}
},
{
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+ "@id": "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
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"digest": {
@@ -743,16 +746,16 @@
}
},
{
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+ "@id": "bids::warp.anat.Xat.1D",
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"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:530372d1-1692-44c6-8880-08936c1e3afc",
+ "GeneratedBy": "urn:catmatve-terER4Y4",
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{
- "@id": "urn:f7c6d767-3954-45c5-8bc2-d4090610d584",
+ "@id": "bids::pb01.$subj.r$run.tshift+orig",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift+orig",
"digest": {
@@ -760,34 +763,34 @@
}
},
{
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+ "@id": "bids::mat.r$run.vr.aff12.1D",
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"AtLocation": "mat.r$run.vr.aff12.1D",
- "GeneratedBy": "urn:81eb387a-a9f4-404a-89ac-8eb8bd0c328d",
+ "GeneratedBy": "urn:3dvolreg-tS8mWkCy",
"digest": {
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}
},
{
- "@id": "urn:a8b54658-54ec-4979-b35f-12f9dd86de95",
+ "@id": "bids::rm.epi.all1",
"Label": "rm.epi.all1",
"AtLocation": "rm.epi.all1",
- "GeneratedBy": "urn:dfde6c8e-d119-4215-b337-145bb3eef5f1",
+ "GeneratedBy": "urn:3dcalc-lVv6vmhn",
"digest": {
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}
},
{
- "@id": "urn:51ee2018-45e8-49ce-a6ac-8202b01a4902",
+ "@id": "bids::mat.r$run.warp.aff12.1D",
"Label": "mat.r$run.warp.aff12.1D",
"AtLocation": "mat.r$run.warp.aff12.1D",
- "GeneratedBy": "urn:606c5072-51fb-4143-a52a-2b73db9adcb5",
+ "GeneratedBy": "urn:catmatve-YaBZGpgm",
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}
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{
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+ "@id": "bids::sub-01_T1w_ns+tlrc",
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"AtLocation": "sub-01_T1w_ns+tlrc",
"digest": {
@@ -795,16 +798,16 @@
}
},
{
- "@id": "urn:7f98f463-6009-4719-8115-5e8ed110f410",
+ "@id": "bids::rm.epi.nomask.r$run",
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"AtLocation": "rm.epi.nomask.r$run",
- "GeneratedBy": "urn:41ef447f-fccd-4aff-ae40-399d14ad3aa0",
+ "GeneratedBy": "urn:3dalline-mAEHSFbA",
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{
- "@id": "urn:f06804b1-350d-4114-a036-23dd4599b121",
+ "@id": "bids::rm.epi.all1+orig",
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"digest": {
@@ -812,16 +815,16 @@
}
},
{
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+ "@id": "bids::rm.epi.1.r$run",
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"AtLocation": "rm.epi.1.r$run",
- "GeneratedBy": "urn:294e434c-6bd8-47c2-ae75-bb719ea79b78",
+ "GeneratedBy": "urn:3dalline-oSNVZLhS",
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{
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+ "@id": "bids::rm.epi.1.r$run+tlrc",
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@@ -829,16 +832,16 @@
}
},
{
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+ "@id": "bids::rm.epi.min.r$run",
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"AtLocation": "rm.epi.min.r$run",
- "GeneratedBy": "urn:9c18c3d4-999e-4e35-af52-a2ab367c9566",
+ "GeneratedBy": "urn:3dtstat-sybsb09m",
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{
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+ "@id": "bids::dfile.r*.1D",
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"digest": {
@@ -846,16 +849,16 @@
}
},
{
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+ "@id": "bids::dfile_rall.1D",
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- "GeneratedBy": "urn:8b2f63d1-861e-4b43-97e4-6bbbff470320",
+ "GeneratedBy": "urn:cat-2fz5ttpF",
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{
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+ "@id": "bids::rm.epi.min.r01+tlrc",
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"digest": {
@@ -863,16 +866,16 @@
}
},
{
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+ "@id": "bids::mask_epi_extents",
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"AtLocation": "mask_epi_extents",
- "GeneratedBy": "urn:9f7852ef-9692-4835-816e-224e3152c46a",
+ "GeneratedBy": "urn:3dcopy-6anXD3J3",
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{
- "@id": "urn:6506f02f-3be9-4a1a-af00-dec6938acd6f",
+ "@id": "bids::rm.epi.nomask.r$run+tlrc",
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"digest": {
@@ -880,7 +883,7 @@
}
},
{
- "@id": "urn:84d71315-bdad-41e8-bc26-b0cc204b972d",
+ "@id": "bids::mask_epi_extents+tlrc",
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"digest": {
@@ -888,34 +891,42 @@
}
},
{
- "@id": "urn:5cefbcb6-8854-49cd-9e25-46649309344b",
+ "@id": "bids::pb02.$subj.r$run.volreg",
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"AtLocation": "pb02.$subj.r$run.volreg",
- "GeneratedBy": "urn:fb6b516a-fe10-4c47-b3d3-71d602d8b389",
+ "GeneratedBy": "urn:3dcalc-aAV2PGan",
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}
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{
- "@id": "urn:70d45a51-a443-48f7-82c8-3542f0071288",
+ "@id": "bids::anat_final.$subj",
"Label": "anat_final.$subj",
"AtLocation": "anat_final.$subj",
- "GeneratedBy": "urn:f1b89e77-c3d4-4079-82fb-6a16163b9421",
+ "GeneratedBy": "urn:3dcopy-4bzRrv4x",
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},
{
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+ "@id": "bids::anat_final.$subj+tlrc",
+ "Label": "anat_final.$subj",
+ "AtLocation": "anat_final.$subj+tlrc",
+ "digest": {
+ "sha256": "94eb1853614cc085b22772c011f119f6a0ad7ec06cba2850587762e7f1a6eae6"
+ }
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+ {
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"AtLocation": "anat_w_skull_warped",
- "GeneratedBy": "urn:4846c2a0-8a5e-452e-8445-48caead091df",
+ "GeneratedBy": "urn:3dalline-14yOSmwP",
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{
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+ "@id": "bids::pb03.$subj.r$run.blur",
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"digest": {
@@ -923,7 +934,7 @@
}
},
{
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@@ -931,7 +942,7 @@
}
},
{
- "@id": "urn:8cf5d2ac-cc2a-44e7-8eb2-c32e0dbb77df",
+ "@id": "bids::pb03.$subj.r$run.blur+tlrc",
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"digest": {
@@ -939,25 +950,25 @@
}
},
{
- "@id": "urn:53016baa-c6e5-4905-972c-da0a4f944e2c",
+ "@id": "bids::rm.mask_r$run",
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- "GeneratedBy": "urn:6a61799d-2599-4916-80ef-4883143bc617",
+ "GeneratedBy": "urn:3dautoma-bcOPYTPN",
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{
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+ "@id": "bids::full_mask.$subj",
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- "GeneratedBy": "urn:97cd560d-ae4f-434c-a666-628134b605a4",
+ "GeneratedBy": "urn:3dmaskto-mSRxvjzr",
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{
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@@ -965,16 +976,16 @@
}
},
{
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+ "@id": "bids::rm.resam.anat",
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- "GeneratedBy": "urn:933a06df-d189-4d77-8890-8ccf53fd1c0f",
+ "GeneratedBy": "urn:3dresamp-ZosW2ivc",
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{
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"digest": {
@@ -982,16 +993,16 @@
}
},
{
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- "GeneratedBy": "urn:50bf7294-d26c-4351-b726-0037e3bc30b4",
+ "GeneratedBy": "urn:3dmaskto-XYoCnOGa",
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}
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{
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"digest": {
@@ -999,7 +1010,7 @@
}
},
{
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+ "@id": "bids::tee",
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@@ -1007,7 +1018,7 @@
}
},
{
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+ "@id": "bids::/Users/u1591557/abin/TT_N27+tlrc",
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"AtLocation": "/Users/u1591557/abin/TT_N27+tlrc",
"digest": {
@@ -1015,16 +1026,16 @@
}
},
{
- "@id": "urn:934d1d17-8270-4333-8f7f-2a939728bcea",
+ "@id": "bids::rm.resam.group",
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"AtLocation": "./rm.resam.group",
- "GeneratedBy": "urn:0381843b-eb04-4177-9a55-a98f65fb3262",
+ "GeneratedBy": "urn:3dresamp-jEcqiAZS",
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},
{
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+ "@id": "bids::rm.resam.group+tlrc",
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"digest": {
@@ -1032,25 +1043,25 @@
}
},
{
- "@id": "urn:ae057ca4-c2cc-4fd9-8c26-73e9f56c8b0d",
+ "@id": "bids::mask_group",
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"AtLocation": "mask_group",
- "GeneratedBy": "urn:c87a3172-8501-4620-87eb-5dfa686b2f8b",
+ "GeneratedBy": "urn:3dmaskto-Fp5LFGAY",
"digest": {
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}
},
{
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+ "@id": "bids::rm.mean_r$run",
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"AtLocation": "rm.mean_r$run",
- "GeneratedBy": "urn:507a8da5-9f2f-4616-ad3e-679eaad090d9",
+ "GeneratedBy": "urn:3dtstat-1LKfPoWn",
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{
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+ "@id": "bids::rm.mean_r$run+tlrc",
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"digest": {
@@ -1058,34 +1069,34 @@
}
},
{
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+ "@id": "bids::pb04.$subj.r$run.scale",
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"AtLocation": "pb04.$subj.r$run.scale",
- "GeneratedBy": "urn:4f7198d4-27d5-4774-a8be-0493629b20c4",
+ "GeneratedBy": "urn:3dcalc-Gkx96YT7",
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}
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{
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+ "@id": "bids::motion_demean.1D",
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"AtLocation": "motion_demean.1D",
- "GeneratedBy": "urn:783f0bfe-bc17-4fd3-86e4-5265722f4f3f",
+ "GeneratedBy": "urn:1dtoolpy-nkvl2lAw",
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}
},
{
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+ "@id": "bids::motion_deriv.1D",
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- "GeneratedBy": "urn:8e7d0070-8079-4c57-aede-ac31ab3d2c61",
+ "GeneratedBy": "urn:1dtoolpy-XEzwoJee",
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},
{
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"digest": {
@@ -1093,25 +1104,25 @@
}
},
{
- "@id": "urn:6f8300aa-44d9-4384-99b3-e51129ac29ab",
+ "@id": "bids::X.xmat.1D",
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- "GeneratedBy": "urn:21ac6c9a-3333-4923-9186-c9e5020afcb9",
+ "GeneratedBy": "urn:3ddeconv-7obQPDKT",
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{
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- "GeneratedBy": "urn:0eb349a3-d1f9-4176-87bb-ee9a8f7163f1",
+ "GeneratedBy": "urn:3dtcat-KMmrJrK3",
"digest": {
"sha256": "bcf27fc2e339e751d0ea9bba931674c21fd9d434ff411330f4df55f872a8cc7e"
}
},
{
- "@id": "urn:e16d69a9-cb22-4fa6-93e3-3f382186da83",
+ "@id": "bids::all_runs.$subj+tlrc%22[$ktrs]%22",
"Label": "all_runs.$subj",
"AtLocation": "all_runs.$subj+tlrc\"[$ktrs]\"",
"digest": {
@@ -1119,16 +1130,16 @@
}
},
{
- "@id": "urn:2a1e7f2d-b460-4777-ac63-055b665855d2",
+ "@id": "bids::rm.signal.all",
"Label": "rm.signal.all",
"AtLocation": "rm.signal.all",
- "GeneratedBy": "urn:ed752a0c-4414-4ed9-9dec-4e4f5fcff34d",
+ "GeneratedBy": "urn:3dtstat-byrkkVkB",
"digest": {
"sha256": "bda68a16c0afd5e55d4d7415c8c959e61a9aad7898dd456b0f3bb597363dde31"
}
},
{
- "@id": "urn:04745c1c-681d-4ecd-99f5-96d342aae6ed",
+ "@id": "bids::errts.$%7Bsubj%7D+tlrc%22[$ktrs]%22",
"Label": "errts.${subj}",
"AtLocation": "errts.${subj}+tlrc\"[$ktrs]\"",
"digest": {
@@ -1136,16 +1147,16 @@
}
},
{
- "@id": "urn:e8f6b5c8-2fca-43dd-bd0f-121ec5da6cce",
+ "@id": "bids::rm.noise.all",
"Label": "rm.noise.all",
"AtLocation": "rm.noise.all",
- "GeneratedBy": "urn:b50d8309-9587-4c3d-8b68-eafea4254b96",
+ "GeneratedBy": "urn:3dtstat-VI3XkDVU",
"digest": {
"sha256": "431314eb75d086ce08373b3a374427969e89414c4a2d607e449c1f6485c547af"
}
},
{
- "@id": "urn:63f6635e-d42e-4729-93ce-219e08306297",
+ "@id": "bids::rm.signal.all+tlrc",
"Label": "rm.signal.all",
"AtLocation": "rm.signal.all+tlrc",
"digest": {
@@ -1153,7 +1164,7 @@
}
},
{
- "@id": "urn:8dd263d5-5ca0-470a-b2ea-56225b421ea3",
+ "@id": "bids::rm.noise.all+tlrc",
"Label": "rm.noise.all",
"AtLocation": "rm.noise.all+tlrc",
"digest": {
@@ -1161,16 +1172,16 @@
}
},
{
- "@id": "urn:b1f4fe7b-5e69-4b1f-8a3c-256fe2edb512",
+ "@id": "bids::TSNR.$subj",
"Label": "TSNR.$subj",
"AtLocation": "TSNR.$subj",
- "GeneratedBy": "urn:92d3b2a1-dba6-4edc-93c6-11c3082b306f",
+ "GeneratedBy": "urn:3dcalc-roPISxqF",
"digest": {
"sha256": "303f183145a1e295686c08335d3b70753777cf0fa0b3f9628cf8de5471359a00"
}
},
{
- "@id": "urn:3f992f36-31d9-44ae-802b-5d8e0bf192cf",
+ "@id": "bids::errts.$%7Bsubj%7D+tlrc",
"Label": "errts.${subj}",
"AtLocation": "errts.${subj}+tlrc",
"digest": {
@@ -1178,25 +1189,25 @@
}
},
{
- "@id": "urn:3ed0a019-09cf-43fc-8a4d-a3b823fc25ad",
+ "@id": "bids::rm.errts.unit",
"Label": "rm.errts.unit",
"AtLocation": "rm.errts.unit",
- "GeneratedBy": "urn:6ca79a28-ccba-4ed7-9c3e-b723a3384c43",
+ "GeneratedBy": "urn:3dtnorm-nfo0JwJ6",
"digest": {
"sha256": "03b570ad773a00f51ab7e6cdedfebdeca45f5356de0c25f9e3be44d7bf2c7151"
}
},
{
- "@id": "urn:29be423e-dd92-4371-8292-a47c133dbab8",
+ "@id": "bids::gmean.errts.unit.1D",
"Label": "gmean.errts.unit.1D",
"AtLocation": "gmean.errts.unit.1D",
- "GeneratedBy": "urn:44e6ae47-f94d-4f63-b751-deb9963deff6",
+ "GeneratedBy": "urn:3dmaskav-nm5FLxqI",
"digest": {
"sha256": "a35a66cce2e2d487762823c197ca1edc450a9887f46f125826b69c5021662f95"
}
},
{
- "@id": "urn:27316f60-9bb2-44a4-92e3-10550fd887e9",
+ "@id": "bids::out.gcor.1D",
"Label": "out.gcor.1D",
"AtLocation": "out.gcor.1D",
"digest": {
@@ -1204,16 +1215,16 @@
}
},
{
- "@id": "urn:b48cd1d1-d2be-4825-a90d-7b235addb099",
+ "@id": "urn:uuid:e0b55535-1ed2-485c-afc5-1a0f64f8d8fe",
"Label": "-",
"AtLocation": "-",
- "GeneratedBy": "urn:b8bea1b6-d3a6-4051-98f1-1a65f739b6f3",
+ "GeneratedBy": "urn:3dtstat-UQVvH69i",
"digest": {
"sha256": "dac304c9f20899ca1ef5aa403e565345fd0ff4ed80c35f82007c9b03a68292b3"
}
},
{
- "@id": "urn:a2ad449d-4882-4dec-90e8-1a9f300f1dbd",
+ "@id": "bids::rm.errts.unit+tlrc",
"Label": "rm.errts.unit",
"AtLocation": "rm.errts.unit+tlrc",
"digest": {
@@ -1221,16 +1232,16 @@
}
},
{
- "@id": "urn:4aa8a051-839e-42db-9cd2-590565abf862",
+ "@id": "bids::rm.DP",
"Label": "rm.DP",
"AtLocation": "rm.DP",
- "GeneratedBy": "urn:0ab3aafa-76ca-4e3a-8379-e94368eed76a",
+ "GeneratedBy": "urn:3dcalc-dd4aneC8",
"digest": {
"sha256": "06a0bfbc609c1a06ecf93c479a3288d2911c7f5f3e93cf49c5d26f721c2035ed"
}
},
{
- "@id": "urn:e31fdb15-9bb3-4157-8090-92da89cfac7e",
+ "@id": "bids::rm.DP+tlrc",
"Label": "rm.DP",
"AtLocation": "rm.DP+tlrc",
"digest": {
@@ -1238,16 +1249,16 @@
}
},
{
- "@id": "urn:ddf90615-d0eb-4158-8692-b9628e86d510",
+ "@id": "bids::corr_brain",
"Label": "corr_brain",
"AtLocation": "corr_brain",
- "GeneratedBy": "urn:f3689c31-ae2f-4947-a2cf-9b34744341b9",
+ "GeneratedBy": "urn:3dtstat-Un5JiITd",
"digest": {
"sha256": "74e3aeae0da338b871ab5dc9e8859a4e81fcf1b3c0042cd22fe337eb7baf5eae"
}
},
{
- "@id": "urn:2aa858d0-c72e-4263-aa8f-f09a66258e4c",
+ "@id": "bids::X.nocensor.xmat.1D'[3]'",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D'[3]'",
"digest": {
@@ -1255,16 +1266,16 @@
}
},
{
- "@id": "urn:99750f1a-7d7d-4c62-8dbb-d96f90fce621",
+ "@id": "bids::ideal_tone_counting.1D",
"Label": "ideal_tone_counting.1D",
"AtLocation": "ideal_tone_counting.1D",
- "GeneratedBy": "urn:193bd4ee-4468-4ce5-af56-994791c02d2e",
+ "GeneratedBy": "urn:1dcat-eyAicARn",
"digest": {
"sha256": "9bb1cabac5ce7ca19dffa5cd6336a9bf82d362fea2ce9341978406e421b5333c"
}
},
{
- "@id": "urn:bf214b29-acb3-4c15-bf07-61fae1e0c4bc",
+ "@id": "bids::X.nocensor.xmat.1D'[4]'",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D'[4]'",
"digest": {
@@ -1272,16 +1283,16 @@
}
},
{
- "@id": "urn:a9cb952e-31b9-43a4-817f-3dc1683dc1e8",
+ "@id": "bids::ideal_probe.1D",
"Label": "ideal_probe.1D",
"AtLocation": "ideal_probe.1D",
- "GeneratedBy": "urn:2ece99e1-6677-4796-a80a-3775f3199700",
+ "GeneratedBy": "urn:1dcat-6OiK19Zo",
"digest": {
"sha256": "705d93afa8b6ded9f4f572db3f967b54e9906942669af51dd8287a9863bb4288"
}
},
{
- "@id": "urn:f7b23cf4-c8f9-4b58-9b0e-e0e62ffbccb7",
+ "@id": "bids::X.nocensor.xmat.1D%22[$reg_cols]%22",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D\"[$reg_cols]\"",
"digest": {
@@ -1289,52 +1300,52 @@
}
},
{
- "@id": "urn:6583ee61-642d-4fcc-a076-a3935f48dfa0",
+ "@id": "bids::sum_ideal.1D",
"Label": "sum_ideal.1D",
"AtLocation": "sum_ideal.1D",
- "GeneratedBy": "urn:d0ff6f02-8181-41b5-909b-f0b23781c1f9",
+ "GeneratedBy": "urn:3dtstat-m1M13vmy",
"digest": {
"sha256": "b2dccadcd84b2d26ec9685c4d1846baf2f11b867f31c36a08748d1c85467b01a"
}
},
{
- "@id": "urn:d39efdca-98e2-420d-9c11-781542369bd7",
+ "@id": "bids::X.stim.xmat.1D",
"Label": "X.stim.xmat.1D",
"AtLocation": "X.stim.xmat.1D",
- "GeneratedBy": "urn:c4fc115a-6e43-47e8-8064-cf6a59c5d9dc",
+ "GeneratedBy": "urn:1dcat-A6WOvFVZ",
"digest": {
"sha256": "7c61b2f4bbb9eb0cecb19f81faa3a79b94d547b7fb4087ed18e368619e0004e6"
}
},
{
- "@id": "urn:67122f30-c4c7-48e5-a243-57daecc964c3",
+ "@id": "bids::blur.epits.1D",
"Label": "blur.epits.1D",
"AtLocation": "blur.epits.1D",
- "GeneratedBy": "urn:7708af65-3664-4ba3-b0eb-852b1312c3eb",
+ "GeneratedBy": "urn:3dfwhmx-Eild0vbL",
"digest": {
"sha256": "623e70a42214e56babc1f1dca156e0b11ba09865dbd6ca9549d54ca2fc601515"
}
},
{
- "@id": "urn:08f73c1c-6be9-45f3-a4d7-396d919f2879",
+ "@id": "bids::blur.errts.1D",
"Label": "blur.errts.1D",
"AtLocation": "blur.errts.1D",
- "GeneratedBy": "urn:50600ca9-626c-462a-a065-e43145b94a63",
+ "GeneratedBy": "urn:3dfwhmx-6itTOS0r",
"digest": {
"sha256": "73969700079b5d3275536ac7eaf0e17571d7e74ec49553b6940f90d5718fc800"
}
},
{
- "@id": "urn:1988764e-c779-4ef3-84d9-06844656fb70",
+ "@id": "bids::ClustSim",
"Label": "ClustSim",
"AtLocation": "ClustSim",
- "GeneratedBy": "urn:593ce871-0708-4cde-bd2a-be90a20aad38",
+ "GeneratedBy": "urn:3dclusts-owXwdfFv",
"digest": {
"sha256": "2e0cdba2c91902ba12d742a39cb20df66cfd705ba8de767fbf68aae8eb65c6f0"
}
},
{
- "@id": "urn:d1bbf2f0-8f57-4537-8e7d-a4f1f2046f1c",
+ "@id": "bids::pb00.$subj.r*.tcat+orig.HEAD",
"Label": "pb00.$subj.r*.tcat",
"AtLocation": "pb00.$subj.r*.tcat+orig.HEAD",
"digest": {
@@ -1342,10 +1353,10 @@
}
},
{
- "@id": "urn:41e319a6-a2f0-471e-8f54-2328f979e712",
+ "@id": "bids::-exit0",
"Label": "-exit0",
"AtLocation": "-exit0",
- "GeneratedBy": "urn:8c4c3b13-4c9e-41e0-a695-b0506ea60e3a",
+ "GeneratedBy": "urn:genssrev-XsBgNJCx",
"digest": {
"sha256": "871a4d3513ed2924cbb10c1c15a196eac4a46a05bdcc248e3bcdb23327b3ad90"
}
diff --git a/examples/from_parsers/afni/afni_default_proc.png b/examples/from_parsers/afni/afni_default_proc.png
index e4ec69fb1..560357f4e 100644
Binary files a/examples/from_parsers/afni/afni_default_proc.png and b/examples/from_parsers/afni/afni_default_proc.png differ
diff --git a/examples/from_parsers/afni/afni_default_proc_block.jsonld b/examples/from_parsers/afni/afni_default_proc_block.jsonld
index fe67fd24d..e7c08c809 100644
--- a/examples/from_parsers/afni/afni_default_proc_block.jsonld
+++ b/examples/from_parsers/afni/afni_default_proc_block.jsonld
@@ -4,187 +4,189 @@
"Records": {
"Software": [
{
- "@id": "urn:388ac5f3-9da0-4574-8860-bc4c4ef8e2cf",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:afni-kOck4tYs",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
- "Version": "afni24"
+ "Version": "afni24",
+ "AltIdentifier": "RRID:SCR_005927"
}
],
"Activities": [
{
- "@id": "urn:fabaa16a-39fb-4f22-b9eb-5137541ebe91",
+ "@id": "urn:autobloc-YPIV47Dx",
"Label": "auto block: setup",
- "AssociatedWith": "urn:388ac5f3-9da0-4574-8860-bc4c4ef8e2cf",
+ "AssociatedWith": "urn:afni-kOck4tYs",
"Command": "mkdir $output_dir; mkdir $output_dir/stimuli; cp ./afni_voxelwise_p0001/tone_counting_onset_times.txt ./afni_voxelwise_p0001/tone_counting_probe_duration.txt $output_dir/stimuli; 3dcopy ./afni_voxelwise_p0001/sub-01_T1w.nii.gz $output_dir/sub-01_T1w; ",
"Used": [
- "urn:5ac4155b-5684-4290-ab9b-2b6ad1bce005",
- "urn:61514613-573b-4097-a192-839256f4ebb0",
- "urn:4f3078c7-5d97-44be-a167-6b52a4ed4792"
+ "bids::afni_voxelwise_p0001/tone_counting_onset_times.txt",
+ "bids::afni_voxelwise_p0001/tone_counting_probe_duration.txt",
+ "bids::afni_voxelwise_p0001/sub-01_T1w.nii.gz"
]
},
{
- "@id": "urn:9afb0d8c-87de-47ba-8300-b53136b969a7",
+ "@id": "urn:autobloc-jOINcnrz",
"Label": "auto block: tcat",
- "AssociatedWith": "urn:388ac5f3-9da0-4574-8860-bc4c4ef8e2cf",
+ "AssociatedWith": "urn:afni-kOck4tYs",
"Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat ./afni_voxelwise_p0001/sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ",
"Used": [
- "urn:b273314b-3ae2-4b37-a7b6-bb52403036c0"
+ "bids::afni_voxelwise_p0001/sub-01_task-tonecounting_bold.nii.gz'[0..$]'"
]
},
{
- "@id": "urn:6c751afa-da20-46ef-88be-683cd5a1c123",
+ "@id": "urn:autobloc-oMmfgA8Z",
"Label": "auto block: outcount",
- "AssociatedWith": "urn:388ac5f3-9da0-4574-8860-bc4c4ef8e2cf",
+ "AssociatedWith": "urn:afni-kOck4tYs",
"Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ",
"Used": [
- "urn:a6d9a96a-ea47-4d15-865a-199226d68c20",
- "urn:d879f59d-06b6-498b-8909-23c195a04bbd"
+ "bids::pb00.$subj.r$run.tcat+orig",
+ "bids::outcount.r*.1D"
]
},
{
- "@id": "urn:4209a343-3884-4554-9ebc-7ec0df1f26f7",
+ "@id": "urn:tshift-1y89hpW4",
"Label": "tshift",
- "AssociatedWith": "urn:388ac5f3-9da0-4574-8860-bc4c4ef8e2cf",
+ "AssociatedWith": "urn:afni-kOck4tYs",
"Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ",
"Used": [
- "urn:a6d9a96a-ea47-4d15-865a-199226d68c20"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:8f5db629-7053-4922-b9f0-6bdf5a81ae52",
+ "@id": "urn:align-59hUVXxz",
"Label": "align",
- "AssociatedWith": "urn:388ac5f3-9da0-4574-8860-bc4c4ef8e2cf",
+ "AssociatedWith": "urn:afni-kOck4tYs",
"Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ",
"Used": [
- "urn:e02b2957-be9a-46ac-992e-79c7f1221e7f",
- "urn:eaff5bc3-be66-4128-b4f4-91fd52a52863"
+ "bids::pb01.$subj.r01.tshift+orig",
+ "bids::sub-01_T1w+orig"
]
},
{
- "@id": "urn:4a912de4-b861-4bd1-82bb-5147dcb9be43",
+ "@id": "urn:tlrc-Djxy7vcJ",
"Label": "tlrc",
- "AssociatedWith": "urn:388ac5f3-9da0-4574-8860-bc4c4ef8e2cf",
+ "AssociatedWith": "urn:afni-kOck4tYs",
"Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ",
"Used": [
- "urn:94ace730-8e53-4c79-9410-23f84d5d6ed5",
- "urn:bc517e2d-3c97-4bc8-a4cc-2065b5e47f88",
- "urn:b8ffcea9-b44b-4358-88db-1ac5e5ed7993"
+ "bids::TT_N27+tlrc",
+ "bids::sub-01_T1w_ns+orig",
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:34b6df30-bd5a-4398-9342-1874c1deb96d",
+ "@id": "urn:volreg-l63WyLnA",
"Label": "volreg",
- "AssociatedWith": "urn:388ac5f3-9da0-4574-8860-bc4c4ef8e2cf",
+ "AssociatedWith": "urn:afni-kOck4tYs",
"Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig; 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1; cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D; 3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run; 3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run; 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc; cat dfile.r*.1D > dfile_rall.1D; 3dcopy rm.epi.min.r01+tlrc mask_epi_extents; 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg; 3dcopy sub-01_T1w_ns+tlrc anat_final.$subj; 3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped; ",
"Used": [
- "urn:47db8c78-61a9-4483-973d-7008bea38376",
- "urn:47db8c78-61a9-4483-973d-7008bea38376",
- "urn:b8ffcea9-b44b-4358-88db-1ac5e5ed7993",
- "urn:47db8c78-61a9-4483-973d-7008bea38376",
- "urn:7e922751-88ef-48e2-b7b0-91a6d51a8754",
- "urn:7e922751-88ef-48e2-b7b0-91a6d51a8754",
- "urn:a3d059b2-541c-4a68-800c-cfca807651ea",
- "urn:c290da90-9494-48c5-822f-947f1168f274",
- "urn:fe0dab03-b97b-4c4e-920c-ec29d36e0707",
- "urn:63af4367-07e3-4e07-bc18-42a97c68ef60",
- "urn:19c0d5bd-aa50-40b0-9902-bd71567b0b67",
- "urn:c16ff10b-d98c-4f4d-b98e-7bd72518b8a2",
- "urn:7e922751-88ef-48e2-b7b0-91a6d51a8754",
- "urn:06c49393-1ec2-46da-aae3-d9277627d38f"
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.epi.all1+orig",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.epi.1.r$run+tlrc",
+ "bids::dfile.r*.1D",
+ "bids::rm.epi.min.r01+tlrc",
+ "bids::mask_epi_extents+tlrc",
+ "bids::rm.epi.nomask.r$run+tlrc",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::anat_final.$subj+tlrc",
+ "bids::warp.anat.Xat.1D"
]
},
{
- "@id": "urn:40f4de67-872c-4eb2-aa1b-fcd9d510265a",
+ "@id": "urn:blur-aro2m421",
"Label": "blur",
- "AssociatedWith": "urn:388ac5f3-9da0-4574-8860-bc4c4ef8e2cf",
+ "AssociatedWith": "urn:afni-kOck4tYs",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc; ",
"Used": [
- "urn:6fceeca3-6d78-41c5-80ac-ea5d354ca5da",
- "urn:f1285616-769b-4a07-ba5b-dd3b362ceada"
+ "bids::pb02.$subj.r$run.volreg+tlrc",
+ "bids::pb03.$subj.r$run.blur"
]
},
{
- "@id": "urn:3cbb8f84-a9e2-44ca-8654-65448f05f932",
+ "@id": "urn:mask-ljR4ulK8",
"Label": "mask",
- "AssociatedWith": "urn:388ac5f3-9da0-4574-8860-bc4c4ef8e2cf",
+ "AssociatedWith": "urn:afni-kOck4tYs",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc; 3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj; 3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj; 3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt; 3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt; 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group; ",
"Used": [
- "urn:891c9e64-aa58-40ac-ab51-a4591ef98f3d",
- "urn:438c9f67-4c05-49df-bc1d-5321f4d5e6d4",
- "urn:7e922751-88ef-48e2-b7b0-91a6d51a8754",
- "urn:ee7e472a-0fd8-46e5-84aa-d9c56df36337",
- "urn:c2d998a1-f944-487f-852a-87a2d18c487e",
- "urn:c7c86089-eaa4-4a18-8530-49a201b46d44",
- "urn:c2d998a1-f944-487f-852a-87a2d18c487e",
- "urn:c7c86089-eaa4-4a18-8530-49a201b46d44",
- "urn:438c9f67-4c05-49df-bc1d-5321f4d5e6d4",
- "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
- "urn:3256a338-3396-4916-bb29-dc788cf16b91"
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.resam.anat+tlrc",
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee",
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee",
+ "bids::/Users/u1591557/abin/TT_N27+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.resam.group+tlrc"
]
},
{
- "@id": "urn:b59ccf17-52ef-44e6-8967-572a84fccdb9",
+ "@id": "urn:scale-ruEsLOtV",
"Label": "scale",
- "AssociatedWith": "urn:388ac5f3-9da0-4574-8860-bc4c4ef8e2cf",
+ "AssociatedWith": "urn:afni-kOck4tYs",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc; 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale; ",
"Used": [
- "urn:891c9e64-aa58-40ac-ab51-a4591ef98f3d",
- "urn:001bda1e-4507-43fa-a69e-407a63862dba",
- "urn:891c9e64-aa58-40ac-ab51-a4591ef98f3d",
- "urn:c16ff10b-d98c-4f4d-b98e-7bd72518b8a2"
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::mask_epi_extents+tlrc",
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::rm.mean_r$run+tlrc"
]
},
{
- "@id": "urn:86bc592c-d2ec-4194-95e3-3ac6b1a98412",
+ "@id": "urn:regress-uKPvbnOr",
"Label": "regress",
- "AssociatedWith": "urn:388ac5f3-9da0-4574-8860-bc4c4ef8e2cf",
+ "AssociatedWith": "urn:afni-kOck4tYs",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}; 3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj; 1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt; 3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD; 3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"; 3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"; 3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj; 3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc; 3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D; 3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D; 3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP; 3dTstat -sum -prefix corr_brain rm.DP+tlrc; 1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D; 1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D; 3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"; 1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D; ",
"Used": [
- "urn:ba739902-3b6e-4bcb-8e1c-1a6b65555274",
- "urn:ba739902-3b6e-4bcb-8e1c-1a6b65555274",
- "urn:ba739902-3b6e-4bcb-8e1c-1a6b65555274",
- "urn:d1335ad7-52c8-4e1f-b59e-17bd7ba6b484",
- "urn:d1335ad7-52c8-4e1f-b59e-17bd7ba6b484",
- "urn:223b5f50-2b03-45d3-b424-40d1fa650516",
- "urn:efc86a01-5f01-4b48-9380-fdb30ecd01b2",
- "urn:2865335c-14e3-4c09-91ec-1c2ce71c403a",
- "urn:438c9f67-4c05-49df-bc1d-5321f4d5e6d4",
- "urn:a0b9bd52-1f4c-449a-a30b-716616d3920b",
- "urn:a41cf029-3f2e-42b7-bdbf-e8d710365518",
- "urn:99999a49-6cab-4a7e-98b1-7839f9f69243",
- "urn:ceeead2a-ad34-47d3-90e6-938a3309d894",
- "urn:fbc5b261-27ad-48b2-8d9d-f0abc6a2f421",
- "urn:2b92b353-7620-4afd-871b-bfa460def5c6",
- "urn:1c76f216-0aa4-4f8e-85f7-bfbced813d7d",
- "urn:a1818c62-2095-4959-86e3-ffb15482055e",
- "urn:a1818c62-2095-4959-86e3-ffb15482055e"
+ "bids::dfile_rall.1D",
+ "bids::dfile_rall.1D",
+ "bids::dfile_rall.1D",
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD",
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD",
+ "bids::all_runs.$subj+tlrc%22[$ktrs]%22",
+ "bids::errts.$%7Bsubj%7D+tlrc%22[$ktrs]%22",
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.noise.all+tlrc",
+ "bids::rm.signal.all+tlrc",
+ "bids::errts.$%7Bsubj%7D+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::out.gcor.1D",
+ "bids::rm.errts.unit+tlrc",
+ "bids::rm.DP+tlrc",
+ "bids::X.nocensor.xmat.1D'[3]'",
+ "bids::X.nocensor.xmat.1D'[4]'",
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22",
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:f92f1112-5e5e-475a-a057-1dffee538eca",
+ "@id": "urn:bluresti-UQl2sHWq",
"Label": "blur estimation",
- "AssociatedWith": "urn:388ac5f3-9da0-4574-8860-bc4c4ef8e2cf",
+ "AssociatedWith": "urn:afni-kOck4tYs",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D; 3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D; 3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim; ",
"Used": [
- "urn:438c9f67-4c05-49df-bc1d-5321f4d5e6d4",
- "urn:438c9f67-4c05-49df-bc1d-5321f4d5e6d4",
- "urn:438c9f67-4c05-49df-bc1d-5321f4d5e6d4"
+ "bids::full_mask.$subj+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:380501ca-17d2-4ef6-b735-bdd2502c1fd6",
+ "@id": "urn:autobloc-52StQ3NA",
"Label": "auto block: generate review scripts",
- "AssociatedWith": "urn:388ac5f3-9da0-4574-8860-bc4c4ef8e2cf",
+ "AssociatedWith": "urn:afni-kOck4tYs",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD; gen_ss_review_scripts.py -mot_limit 0.3 -exit0; ",
"Used": [
- "urn:5f936fa4-b3cf-47d1-99ed-f6ed17e7d2e9"
+ "bids::pb00.$subj.r*.tcat+orig.HEAD"
]
}
],
"Entities": [
{
- "@id": "urn:61514613-573b-4097-a192-839256f4ebb0",
+ "@id": "bids::afni_voxelwise_p0001/tone_counting_onset_times.txt",
"Label": "tone_counting_onset_times.txt",
"AtLocation": "./afni_voxelwise_p0001/tone_counting_onset_times.txt",
"digest": {
@@ -192,7 +194,7 @@
}
},
{
- "@id": "urn:5ac4155b-5684-4290-ab9b-2b6ad1bce005",
+ "@id": "bids::afni_voxelwise_p0001/tone_counting_probe_duration.txt",
"Label": "tone_counting_probe_duration.txt",
"AtLocation": "./afni_voxelwise_p0001/tone_counting_probe_duration.txt",
"digest": {
@@ -200,7 +202,7 @@
}
},
{
- "@id": "urn:4f3078c7-5d97-44be-a167-6b52a4ed4792",
+ "@id": "bids::afni_voxelwise_p0001/sub-01_T1w.nii.gz",
"Label": "sub-01_T1w.nii.gz",
"AtLocation": "./afni_voxelwise_p0001/sub-01_T1w.nii.gz",
"digest": {
@@ -208,34 +210,34 @@
}
},
{
- "@id": "urn:6499cebe-6d01-4f19-8bbe-be298f1d4514",
+ "@id": "bids::$output_dir",
"Label": "$output_dir",
"AtLocation": "$output_dir",
- "GeneratedBy": "urn:fabaa16a-39fb-4f22-b9eb-5137541ebe91",
+ "GeneratedBy": "urn:autobloc-YPIV47Dx",
"digest": {
"sha256": "9fa4c635e6533ddf2fed54295920052818d948c3ffe97bc753bd7336b453f8cb"
}
},
{
- "@id": "urn:13e5b321-4fa2-4564-981e-90497af02801",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:fabaa16a-39fb-4f22-b9eb-5137541ebe91"
+ "GeneratedBy": "urn:autobloc-YPIV47Dx"
},
{
- "@id": "urn:937d9c30-01a1-49e2-9455-91173deffec6",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:fabaa16a-39fb-4f22-b9eb-5137541ebe91"
+ "GeneratedBy": "urn:autobloc-YPIV47Dx"
},
{
- "@id": "urn:8cc05d68-b8ed-4279-a47d-6f0555931cf8",
+ "@id": "bids::$output_dir/sub-01_T1w",
"Label": "sub-01_T1w",
"AtLocation": "$output_dir/sub-01_T1w",
- "GeneratedBy": "urn:fabaa16a-39fb-4f22-b9eb-5137541ebe91"
+ "GeneratedBy": "urn:autobloc-YPIV47Dx"
},
{
- "@id": "urn:b273314b-3ae2-4b37-a7b6-bb52403036c0",
+ "@id": "bids::afni_voxelwise_p0001/sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Label": "sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "./afni_voxelwise_p0001/sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"digest": {
@@ -243,13 +245,13 @@
}
},
{
- "@id": "urn:1fb60e81-b476-46e6-b75d-ded62428c57d",
+ "@id": "bids::$output_dir/pb00.$subj.r01.tcat",
"Label": "pb00.$subj.r01.tcat",
"AtLocation": "$output_dir/pb00.$subj.r01.tcat",
- "GeneratedBy": "urn:9afb0d8c-87de-47ba-8300-b53136b969a7"
+ "GeneratedBy": "urn:autobloc-jOINcnrz"
},
{
- "@id": "urn:a6d9a96a-ea47-4d15-865a-199226d68c20",
+ "@id": "bids::pb00.$subj.r$run.tcat+orig",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -257,7 +259,7 @@
}
},
{
- "@id": "urn:d879f59d-06b6-498b-8909-23c195a04bbd",
+ "@id": "bids::outcount.r*.1D",
"Label": "outcount.r*.1D",
"AtLocation": "outcount.r*.1D",
"digest": {
@@ -265,25 +267,25 @@
}
},
{
- "@id": "urn:37fcb1c9-0771-4bf1-8b00-2944fb5a8404",
+ "@id": "bids::outcount.r$run.1D",
"Label": "outcount.r$run.1D",
"AtLocation": "outcount.r$run.1D",
- "GeneratedBy": "urn:6c751afa-da20-46ef-88be-683cd5a1c123",
+ "GeneratedBy": "urn:autobloc-oMmfgA8Z",
"digest": {
"sha256": "63d9f539e5470badc625d557109f68bc4eecbb02ca2667483739d52f95e5d0dd"
}
},
{
- "@id": "urn:6b16e55b-00bb-442a-9f61-c8499f354a37",
+ "@id": "bids::outcount_rall.1D",
"Label": "outcount_rall.1D",
"AtLocation": "outcount_rall.1D",
- "GeneratedBy": "urn:6c751afa-da20-46ef-88be-683cd5a1c123",
+ "GeneratedBy": "urn:autobloc-oMmfgA8Z",
"digest": {
"sha256": "cb887fd5e4d5e9acb3a24820d0f7a62ed38a5ffb0fdedd373440ac0219fb186a"
}
},
{
- "@id": "urn:a6d9a96a-ea47-4d15-865a-199226d68c20",
+ "@id": "bids::pb00.$subj.r$run.tcat+orig",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -291,16 +293,16 @@
}
},
{
- "@id": "urn:5776b9bf-181e-425a-94de-eb6c4a20ceb8",
+ "@id": "bids::pb01.$subj.r$run.tshift",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift",
- "GeneratedBy": "urn:4209a343-3884-4554-9ebc-7ec0df1f26f7",
+ "GeneratedBy": "urn:tshift-1y89hpW4",
"digest": {
"sha256": "c6bf01cea8d2eac1d7a866f80b865c6e7d4b4e012dbb63d480ac9a8551162d72"
}
},
{
- "@id": "urn:eaff5bc3-be66-4128-b4f4-91fd52a52863",
+ "@id": "bids::sub-01_T1w+orig",
"Label": "sub-01_T1w",
"AtLocation": "sub-01_T1w+orig",
"digest": {
@@ -308,7 +310,7 @@
}
},
{
- "@id": "urn:e02b2957-be9a-46ac-992e-79c7f1221e7f",
+ "@id": "bids::pb01.$subj.r01.tshift+orig",
"Label": "pb01.$subj.r01.tshift",
"AtLocation": "pb01.$subj.r01.tshift+orig",
"digest": {
@@ -316,16 +318,16 @@
}
},
{
- "@id": "urn:9716b1e7-3548-4f7f-bdf7-c312f447a21a",
+ "@id": "bids::_al_junk",
"Label": "_al_junk",
"AtLocation": "_al_junk",
- "GeneratedBy": "urn:8f5db629-7053-4922-b9f0-6bdf5a81ae52",
+ "GeneratedBy": "urn:align-59hUVXxz",
"digest": {
"sha256": "bd785a075a4c6446e1e54de9e628913f7f1c814e86b69a9fbfe933209e6d37b5"
}
},
{
- "@id": "urn:bc517e2d-3c97-4bc8-a4cc-2065b5e47f88",
+ "@id": "bids::TT_N27+tlrc",
"Label": "TT_N27",
"AtLocation": "TT_N27+tlrc",
"digest": {
@@ -333,7 +335,7 @@
}
},
{
- "@id": "urn:94ace730-8e53-4c79-9410-23f84d5d6ed5",
+ "@id": "bids::sub-01_T1w_ns+orig",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+orig",
"digest": {
@@ -341,7 +343,7 @@
}
},
{
- "@id": "urn:b8ffcea9-b44b-4358-88db-1ac5e5ed7993",
+ "@id": "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc::WARP_DATA",
"digest": {
@@ -349,16 +351,16 @@
}
},
{
- "@id": "urn:06c49393-1ec2-46da-aae3-d9277627d38f",
+ "@id": "bids::warp.anat.Xat.1D",
"Label": "warp.anat.Xat.1D",
"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:4a912de4-b861-4bd1-82bb-5147dcb9be43",
+ "GeneratedBy": "urn:tlrc-Djxy7vcJ",
"digest": {
"sha256": "800633fb5b4e9be64078bc181c4d5510ffb73fc5cccaf364c7fb6a294aa06728"
}
},
{
- "@id": "urn:b8ffcea9-b44b-4358-88db-1ac5e5ed7993",
+ "@id": "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
"Label": "sub-01_T1w_ns",
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@@ -366,16 +368,16 @@
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@@ -383,7 +385,7 @@
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@@ -391,7 +393,7 @@
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@@ -399,7 +401,7 @@
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@@ -407,7 +409,7 @@
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@@ -415,7 +417,7 @@
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@@ -423,7 +425,7 @@
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@@ -431,7 +433,7 @@
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@@ -439,97 +441,105 @@
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"AtLocation": "mat.r$run.vr.aff12.1D",
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- "GeneratedBy": "urn:34b6df30-bd5a-4398-9342-1874c1deb96d",
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"AtLocation": "rm.epi.nomask.r$run",
- "GeneratedBy": "urn:34b6df30-bd5a-4398-9342-1874c1deb96d",
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"AtLocation": "rm.epi.min.r$run",
- "GeneratedBy": "urn:34b6df30-bd5a-4398-9342-1874c1deb96d",
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- "GeneratedBy": "urn:34b6df30-bd5a-4398-9342-1874c1deb96d",
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{
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"Label": "mask_epi_extents",
"AtLocation": "mask_epi_extents",
- "GeneratedBy": "urn:34b6df30-bd5a-4398-9342-1874c1deb96d",
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"AtLocation": "pb02.$subj.r$run.volreg",
- "GeneratedBy": "urn:34b6df30-bd5a-4398-9342-1874c1deb96d",
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"AtLocation": "anat_final.$subj",
- "GeneratedBy": "urn:34b6df30-bd5a-4398-9342-1874c1deb96d",
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+ "@id": "bids::anat_w_skull_warped",
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"AtLocation": "anat_w_skull_warped",
- "GeneratedBy": "urn:34b6df30-bd5a-4398-9342-1874c1deb96d",
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@@ -537,7 +547,7 @@
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{
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@@ -545,7 +555,7 @@
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@@ -553,7 +563,7 @@
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{
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@@ -561,7 +571,7 @@
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@@ -569,7 +579,7 @@
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{
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@@ -577,7 +587,7 @@
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{
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"digest": {
@@ -585,7 +595,7 @@
}
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{
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@@ -593,7 +603,7 @@
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{
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"digest": {
@@ -601,7 +611,7 @@
}
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{
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"digest": {
@@ -609,61 +619,61 @@
}
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{
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"AtLocation": "rm.mask_r$run",
- "GeneratedBy": "urn:3cbb8f84-a9e2-44ca-8654-65448f05f932",
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"AtLocation": "full_mask.$subj",
- "GeneratedBy": "urn:3cbb8f84-a9e2-44ca-8654-65448f05f932",
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"AtLocation": "rm.resam.anat",
- "GeneratedBy": "urn:3cbb8f84-a9e2-44ca-8654-65448f05f932",
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"AtLocation": "mask_anat.$subj",
- "GeneratedBy": "urn:3cbb8f84-a9e2-44ca-8654-65448f05f932",
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"AtLocation": "./rm.resam.group",
- "GeneratedBy": "urn:3cbb8f84-a9e2-44ca-8654-65448f05f932",
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{
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+ "@id": "bids::mask_group",
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- "GeneratedBy": "urn:3cbb8f84-a9e2-44ca-8654-65448f05f932",
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@@ -671,7 +681,7 @@
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{
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@@ -679,7 +689,7 @@
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@@ -687,34 +697,34 @@
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{
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- "GeneratedBy": "urn:b59ccf17-52ef-44e6-8967-572a84fccdb9",
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- "GeneratedBy": "urn:b59ccf17-52ef-44e6-8967-572a84fccdb9",
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- "GeneratedBy": "urn:34b6df30-bd5a-4398-9342-1874c1deb96d",
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@@ -722,7 +732,7 @@
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{
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@@ -730,7 +740,7 @@
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{
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@@ -738,7 +748,7 @@
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{
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@@ -746,7 +756,7 @@
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@@ -754,7 +764,7 @@
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{
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@@ -762,7 +772,7 @@
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{
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+ "@id": "bids::errts.$%7Bsubj%7D+tlrc",
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"digest": {
@@ -770,7 +780,7 @@
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{
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@@ -778,7 +788,7 @@
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{
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+ "@id": "bids::rm.errts.unit+tlrc",
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"digest": {
@@ -786,7 +796,7 @@
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{
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"digest": {
@@ -794,7 +804,7 @@
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{
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+ "@id": "bids::X.nocensor.xmat.1D'[3]'",
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"digest": {
@@ -802,7 +812,7 @@
}
},
{
- "@id": "urn:1c76f216-0aa4-4f8e-85f7-bfbced813d7d",
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"digest": {
@@ -810,7 +820,7 @@
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{
- "@id": "urn:a1818c62-2095-4959-86e3-ffb15482055e",
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"AtLocation": "X.nocensor.xmat.1D\"[$reg_cols]\"",
"digest": {
@@ -818,133 +828,133 @@
}
},
{
- "@id": "urn:ad73a849-252a-4eab-a0ed-4e6f135564da",
+ "@id": "bids::motion_demean.1D",
"Label": "motion_demean.1D",
"AtLocation": "motion_demean.1D",
- "GeneratedBy": "urn:86bc592c-d2ec-4194-95e3-3ac6b1a98412",
+ "GeneratedBy": "urn:regress-uKPvbnOr",
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"sha256": "1de1e10c0120caa7b6cf441bd141a5a76716e458676ae56ce693039eecb79c85"
}
},
{
- "@id": "urn:c4839939-2e5f-41a7-acd2-fab9794c49cc",
+ "@id": "bids::motion_deriv.1D",
"Label": "motion_deriv.1D",
"AtLocation": "motion_deriv.1D",
- "GeneratedBy": "urn:86bc592c-d2ec-4194-95e3-3ac6b1a98412",
+ "GeneratedBy": "urn:regress-uKPvbnOr",
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"sha256": "47185bf319e91642ad6f2a396a43fc9f8db7b82f2a9aef326bfe4a955120038b"
}
},
{
- "@id": "urn:c9073dc8-0f92-4a58-87c6-462a9196c888",
+ "@id": "bids::all_runs.$subj",
"Label": "all_runs.$subj",
"AtLocation": "all_runs.$subj",
- "GeneratedBy": "urn:86bc592c-d2ec-4194-95e3-3ac6b1a98412",
+ "GeneratedBy": "urn:regress-uKPvbnOr",
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}
},
{
- "@id": "urn:678905c1-d3f9-4079-8e8a-ebeff7b289ba",
+ "@id": "bids::rm.signal.all",
"Label": "rm.signal.all",
"AtLocation": "rm.signal.all",
- "GeneratedBy": "urn:86bc592c-d2ec-4194-95e3-3ac6b1a98412",
+ "GeneratedBy": "urn:regress-uKPvbnOr",
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"sha256": "bda68a16c0afd5e55d4d7415c8c959e61a9aad7898dd456b0f3bb597363dde31"
}
},
{
- "@id": "urn:fef3aff5-1de5-4c25-8ff1-4d95a6ef5a30",
+ "@id": "bids::rm.noise.all",
"Label": "rm.noise.all",
"AtLocation": "rm.noise.all",
- "GeneratedBy": "urn:86bc592c-d2ec-4194-95e3-3ac6b1a98412",
+ "GeneratedBy": "urn:regress-uKPvbnOr",
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}
},
{
- "@id": "urn:5ff1801c-9116-43a9-aa4a-c72b55bfef4e",
+ "@id": "bids::TSNR.$subj",
"Label": "TSNR.$subj",
"AtLocation": "TSNR.$subj",
- "GeneratedBy": "urn:86bc592c-d2ec-4194-95e3-3ac6b1a98412",
+ "GeneratedBy": "urn:regress-uKPvbnOr",
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"sha256": "303f183145a1e295686c08335d3b70753777cf0fa0b3f9628cf8de5471359a00"
}
},
{
- "@id": "urn:f0025fe9-879f-4469-a137-261e544d5478",
+ "@id": "bids::rm.errts.unit",
"Label": "rm.errts.unit",
"AtLocation": "rm.errts.unit",
- "GeneratedBy": "urn:86bc592c-d2ec-4194-95e3-3ac6b1a98412",
+ "GeneratedBy": "urn:regress-uKPvbnOr",
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"sha256": "03b570ad773a00f51ab7e6cdedfebdeca45f5356de0c25f9e3be44d7bf2c7151"
}
},
{
- "@id": "urn:bc442431-361a-4ce5-971c-cf8eddac2c4c",
+ "@id": "urn:uuid:0231e881-7455-4a1c-84ae-5e8f5912264a",
"Label": "-",
"AtLocation": "-",
- "GeneratedBy": "urn:86bc592c-d2ec-4194-95e3-3ac6b1a98412",
+ "GeneratedBy": "urn:regress-uKPvbnOr",
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"sha256": "dac304c9f20899ca1ef5aa403e565345fd0ff4ed80c35f82007c9b03a68292b3"
}
},
{
- "@id": "urn:65685219-a9c7-427e-9264-79afd22a5c76",
+ "@id": "bids::rm.DP",
"Label": "rm.DP",
"AtLocation": "rm.DP",
- "GeneratedBy": "urn:86bc592c-d2ec-4194-95e3-3ac6b1a98412",
+ "GeneratedBy": "urn:regress-uKPvbnOr",
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"sha256": "06a0bfbc609c1a06ecf93c479a3288d2911c7f5f3e93cf49c5d26f721c2035ed"
}
},
{
- "@id": "urn:ca2dcba4-32ec-4f2a-9b1f-10f032c69a51",
+ "@id": "bids::corr_brain",
"Label": "corr_brain",
"AtLocation": "corr_brain",
- "GeneratedBy": "urn:86bc592c-d2ec-4194-95e3-3ac6b1a98412",
+ "GeneratedBy": "urn:regress-uKPvbnOr",
"digest": {
"sha256": "74e3aeae0da338b871ab5dc9e8859a4e81fcf1b3c0042cd22fe337eb7baf5eae"
}
},
{
- "@id": "urn:96298bd4-56d1-49ad-8c03-cecf40d46075",
+ "@id": "bids::ideal_tone_counting.1D",
"Label": "ideal_tone_counting.1D",
"AtLocation": "ideal_tone_counting.1D",
- "GeneratedBy": "urn:86bc592c-d2ec-4194-95e3-3ac6b1a98412",
+ "GeneratedBy": "urn:regress-uKPvbnOr",
"digest": {
"sha256": "9bb1cabac5ce7ca19dffa5cd6336a9bf82d362fea2ce9341978406e421b5333c"
}
},
{
- "@id": "urn:3caf99ff-86c7-4a3a-a51b-eead0a39284b",
+ "@id": "bids::ideal_probe.1D",
"Label": "ideal_probe.1D",
"AtLocation": "ideal_probe.1D",
- "GeneratedBy": "urn:86bc592c-d2ec-4194-95e3-3ac6b1a98412",
+ "GeneratedBy": "urn:regress-uKPvbnOr",
"digest": {
"sha256": "705d93afa8b6ded9f4f572db3f967b54e9906942669af51dd8287a9863bb4288"
}
},
{
- "@id": "urn:a9909b0a-06e7-42d5-ae5b-699ba62cce5c",
+ "@id": "bids::sum_ideal.1D",
"Label": "sum_ideal.1D",
"AtLocation": "sum_ideal.1D",
- "GeneratedBy": "urn:86bc592c-d2ec-4194-95e3-3ac6b1a98412",
+ "GeneratedBy": "urn:regress-uKPvbnOr",
"digest": {
"sha256": "b2dccadcd84b2d26ec9685c4d1846baf2f11b867f31c36a08748d1c85467b01a"
}
},
{
- "@id": "urn:3d40b104-d33a-4f3a-9458-8e07094dc092",
+ "@id": "bids::X.stim.xmat.1D",
"Label": "X.stim.xmat.1D",
"AtLocation": "X.stim.xmat.1D",
- "GeneratedBy": "urn:86bc592c-d2ec-4194-95e3-3ac6b1a98412",
+ "GeneratedBy": "urn:regress-uKPvbnOr",
"digest": {
"sha256": "7c61b2f4bbb9eb0cecb19f81faa3a79b94d547b7fb4087ed18e368619e0004e6"
}
},
{
- "@id": "urn:438c9f67-4c05-49df-bc1d-5321f4d5e6d4",
+ "@id": "bids::full_mask.$subj+tlrc",
"Label": "full_mask.$subj",
"AtLocation": "full_mask.$subj+tlrc",
"digest": {
@@ -952,34 +962,34 @@
}
},
{
- "@id": "urn:6dcdf35f-a3f4-40f7-900a-3e1d4515f85c",
+ "@id": "bids::blur.epits.1D",
"Label": "blur.epits.1D",
"AtLocation": "blur.epits.1D",
- "GeneratedBy": "urn:f92f1112-5e5e-475a-a057-1dffee538eca",
+ "GeneratedBy": "urn:bluresti-UQl2sHWq",
"digest": {
"sha256": "623e70a42214e56babc1f1dca156e0b11ba09865dbd6ca9549d54ca2fc601515"
}
},
{
- "@id": "urn:766c924e-2b0d-42fa-bb26-1f89e6182516",
+ "@id": "bids::blur.errts.1D",
"Label": "blur.errts.1D",
"AtLocation": "blur.errts.1D",
- "GeneratedBy": "urn:f92f1112-5e5e-475a-a057-1dffee538eca",
+ "GeneratedBy": "urn:bluresti-UQl2sHWq",
"digest": {
"sha256": "73969700079b5d3275536ac7eaf0e17571d7e74ec49553b6940f90d5718fc800"
}
},
{
- "@id": "urn:46008793-da4c-4675-95a2-9665da5c4eda",
+ "@id": "bids::ClustSim",
"Label": "ClustSim",
"AtLocation": "ClustSim",
- "GeneratedBy": "urn:f92f1112-5e5e-475a-a057-1dffee538eca",
+ "GeneratedBy": "urn:bluresti-UQl2sHWq",
"digest": {
"sha256": "2e0cdba2c91902ba12d742a39cb20df66cfd705ba8de767fbf68aae8eb65c6f0"
}
},
{
- "@id": "urn:5f936fa4-b3cf-47d1-99ed-f6ed17e7d2e9",
+ "@id": "bids::pb00.$subj.r*.tcat+orig.HEAD",
"Label": "pb00.$subj.r*.tcat",
"AtLocation": "pb00.$subj.r*.tcat+orig.HEAD",
"digest": {
@@ -987,10 +997,10 @@
}
},
{
- "@id": "urn:ea575ae5-8930-4141-a4c2-d8ef656487f6",
+ "@id": "bids::-exit0",
"Label": "-exit0",
"AtLocation": "-exit0",
- "GeneratedBy": "urn:380501ca-17d2-4ef6-b735-bdd2502c1fd6",
+ "GeneratedBy": "urn:autobloc-52StQ3NA",
"digest": {
"sha256": "871a4d3513ed2924cbb10c1c15a196eac4a46a05bdcc248e3bcdb23327b3ad90"
}
diff --git a/examples/from_parsers/afni/afni_default_proc_block.png b/examples/from_parsers/afni/afni_default_proc_block.png
index 99b179076..0cb5b7d6a 100644
Binary files a/examples/from_parsers/afni/afni_default_proc_block.png and b/examples/from_parsers/afni/afni_default_proc_block.png differ
diff --git a/examples/from_parsers/afni/afni_gam_proc.jsonld b/examples/from_parsers/afni/afni_gam_proc.jsonld
index 598cf30f7..ee176b6fd 100644
--- a/examples/from_parsers/afni/afni_gam_proc.jsonld
+++ b/examples/from_parsers/afni/afni_gam_proc.jsonld
@@ -4,567 +4,570 @@
"Records": {
"Software": [
{
- "@id": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:afni-f7u9iy8U",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
- "Version": "afni24"
+ "Version": "afni24",
+ "AltIdentifier": "RRID:SCR_005927"
}
],
"Activities": [
{
- "@id": "urn:8ac247a6-00f0-4da1-88e5-7e74e5df7066",
+ "@id": "urn:makedire-zf7V0epM",
"Label": "Make directory",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "mkdir $output_dir",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:62133b1c-e258-4578-8377-9c4c48a504b3",
+ "@id": "urn:makedire-UiQEc72f",
"Label": "Make directory",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "mkdir $output_dir/stimuli",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:a289d6a3-de2b-4f58-ae64-8f0d3eb75dc1",
+ "@id": "urn:cp-n0wB3JC9",
"Label": "cp",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "cp ./afni_gam/tone_counting_onset_times.txt $output_dir/stimuli",
"Parameters": {},
"Used": [
- "urn:966bda3f-ef3a-4c6b-96f3-37a8f63317ac"
+ "bids::afni_gam/tone_counting_onset_times.txt"
]
},
{
- "@id": "urn:926cfd79-5399-4ed5-a1ef-7ddac7372cb3",
+ "@id": "urn:3dcopy-kRqgajxm",
"Label": "3dcopy",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "3dcopy ./afni_gam/sub-01_T1w.nii.gz $output_dir/sub-01_T1w",
"Parameters": {},
"Used": [
- "urn:f2718969-5393-4474-810c-18a55930c2b3"
+ "bids::afni_gam/sub-01_T1w.nii.gz"
]
},
{
- "@id": "urn:d4855f22-1f95-4735-9a85-8c55d4f931b4",
+ "@id": "urn:3dtcat-9hBx7Xb5",
"Label": "3dTcat",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat ./afni_gam/sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Parameters": {},
"Used": [
- "urn:e49008ed-d256-4355-b47b-fc159cc53ed7"
+ "bids::afni_gam/sub-01_task-tonecounting_bold.nii.gz'[0..$]'"
]
},
{
- "@id": "urn:c81268eb-5e93-4ef2-a06f-12a37475e7f7",
+ "@id": "urn:3dtoutco-6h2RpeoD",
"Label": "3dToutcount",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D",
"Parameters": {},
"Used": [
- "urn:057aa3ca-32fa-4c88-98d3-5f6135ff173b"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:bb970877-b8e1-4deb-bcd4-3241dcacc59e",
+ "@id": "urn:cat-ec1ecOF8",
"Label": "cat",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "cat outcount.r*.1D > outcount_rall.1D",
"Parameters": {},
"Used": [
- "urn:f31acecb-0303-4585-a1a9-b58cce9cf77d"
+ "bids::outcount.r*.1D"
]
},
{
- "@id": "urn:91406eb5-1759-4dab-82d5-c0c43b5d80ef",
+ "@id": "urn:3dtshift-IbSPdLhN",
"Label": "3dTshift",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig",
"Parameters": {},
"Used": [
- "urn:057aa3ca-32fa-4c88-98d3-5f6135ff173b"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:d59e4156-cfd3-425b-aabf-92519931fc2c",
+ "@id": "urn:alignepi-7BZjwJ25",
"Label": "align_epi_anat.py",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off",
"Parameters": {},
"Used": [
- "urn:130be5b5-1d74-4f34-aa19-8883f9dc0198",
- "urn:fab5364a-1378-4e37-9a8b-cf22f60a9a30"
+ "bids::pb01.$subj.r01.tshift+orig",
+ "bids::sub-01_T1w+orig"
]
},
{
- "@id": "urn:2ddf06d7-bcb2-4949-b78b-7ebda1733463",
+ "@id": "urn:autotlrc-Y70c9vNS",
"Label": "@auto_tlrc",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss",
"Parameters": {},
"Used": [
- "urn:5b4c176f-8964-44e6-b0ca-9d734e1be7eb",
- "urn:a50a026c-f2ea-4900-81c3-2f3577e6a7c2"
+ "bids::TT_N27+tlrc",
+ "bids::sub-01_T1w_ns+orig"
]
},
{
- "@id": "urn:e413cb9e-66c0-45cb-a31f-541be143d96f",
+ "@id": "urn:catmatve-gKDe15pu",
"Label": "cat_matvec",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D",
"Parameters": {},
"Used": [
- "urn:1617de95-9492-49a4-997c-c3fff2ae8c6d"
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:4037cdbc-a9fa-42df-984c-8469028aa60a",
+ "@id": "urn:3dvolreg-7EILeENF",
"Label": "3dvolreg",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig",
"Parameters": {},
"Used": [
- "urn:e1f6cc09-c137-4859-894f-10d0a6bd0c23"
+ "bids::pb01.$subj.r$run.tshift+orig"
]
},
{
- "@id": "urn:afb7ccbc-ae02-4cf5-a4ad-e90da3838f67",
+ "@id": "urn:3dcalc-2zrP85y3",
"Label": "3dcalc",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1",
"Parameters": {},
"Used": [
- "urn:e1f6cc09-c137-4859-894f-10d0a6bd0c23"
+ "bids::pb01.$subj.r$run.tshift+orig"
]
},
{
- "@id": "urn:79061e66-aeab-4d4a-863d-f657c20101a1",
+ "@id": "urn:catmatve-RDcYdGjZ",
"Label": "cat_matvec",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D",
"Parameters": {},
"Used": [
- "urn:1617de95-9492-49a4-997c-c3fff2ae8c6d"
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:a9c2c6b0-9fb1-4dce-86b7-7718a9ef3d1a",
+ "@id": "urn:3dalline-DsMduKfA",
"Label": "3dAllineate",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run",
"Parameters": {},
"Used": [
- "urn:8a71a648-4d87-4e46-a43a-e9bca7ce84ba",
- "urn:9c28481d-da26-44f6-9946-0fb9b7a7e96f",
- "urn:e1f6cc09-c137-4859-894f-10d0a6bd0c23"
+ "bids::mat.r$run.warp.aff12.1D",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:97b6c82e-f1d3-48dc-82b4-17bfeb916d8b",
+ "@id": "urn:3dalline-kcJ790Fq",
"Label": "3dAllineate",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run",
"Parameters": {},
"Used": [
- "urn:83ae1c41-4e52-43b6-beef-857cab51b576",
- "urn:8a71a648-4d87-4e46-a43a-e9bca7ce84ba",
- "urn:9c28481d-da26-44f6-9946-0fb9b7a7e96f"
+ "bids::mat.r$run.warp.aff12.1D",
+ "bids::rm.epi.all1+orig",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:8a5097be-6b13-4048-a042-c2b8783f4d08",
+ "@id": "urn:3dtstat-GD8XVCMR",
"Label": "3dTstat",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc",
"Parameters": {},
"Used": [
- "urn:1a014967-de1c-46ed-a37f-26cb3f7eda52"
+ "bids::rm.epi.1.r$run+tlrc"
]
},
{
- "@id": "urn:ebf46ff4-7980-4938-a4bc-f6536d7e3282",
+ "@id": "urn:cat-mQD6kcqM",
"Label": "cat",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "cat dfile.r*.1D > dfile_rall.1D",
"Parameters": {},
"Used": [
- "urn:b749c781-f2ad-471d-a39c-effdffc69219"
+ "bids::dfile.r*.1D"
]
},
{
- "@id": "urn:6916c807-44ba-48eb-9a03-dfbf52c8a393",
+ "@id": "urn:3dcopy-kCVFiKEn",
"Label": "3dcopy",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents",
"Parameters": {},
"Used": [
- "urn:a9563344-2af3-4f9b-a158-b055df86882d"
+ "bids::rm.epi.min.r01+tlrc"
]
},
{
- "@id": "urn:dbbfca19-1a7b-4b70-ae99-015594ee8ce4",
+ "@id": "urn:3dcalc-nV98IIGh",
"Label": "3dcalc",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg",
"Parameters": {},
"Used": [
- "urn:aa2d4900-01b1-4586-94b8-bee17c62e5b8",
- "urn:da3000b5-650b-4cb2-8cbb-dc42cabb876e"
+ "bids::mask_epi_extents+tlrc",
+ "bids::rm.epi.nomask.r$run+tlrc"
]
},
{
- "@id": "urn:c97b4bb7-f8fa-4bc6-bcdf-8ab52723dc9e",
+ "@id": "urn:3dcopy-7imt6vzx",
"Label": "3dcopy",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj",
"Parameters": {},
"Used": [
- "urn:9c28481d-da26-44f6-9946-0fb9b7a7e96f"
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:1207013b-244d-4675-998f-ada93a74cded",
+ "@id": "urn:3dalline-TzJZcFHG",
"Label": "3dAllineate",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped",
"Parameters": {},
"Used": [
- "urn:c6bb8b00-5a11-4ad3-9079-e3e04b49cb2f"
+ "bids::anat_final.$subj+tlrc",
+ "bids::warp.anat.Xat.1D"
]
},
{
- "@id": "urn:d23d365d-bc81-4feb-aa92-49f60ef280ac",
+ "@id": "urn:3dmerge-31GahazW",
"Label": "3dmerge",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc",
"Parameters": {},
"Used": [
- "urn:3671fc62-2d49-4131-8bdf-c0c63ccef999",
- "urn:a8ddfdef-39e3-40e4-9746-bbe17c8576c2"
+ "bids::pb02.$subj.r$run.volreg+tlrc",
+ "bids::pb03.$subj.r$run.blur"
]
},
{
- "@id": "urn:f9850102-6111-4db5-9684-ff4deebda300",
+ "@id": "urn:3dautoma-RiQw0F5h",
"Label": "3dAutomask",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:15777a94-5d1a-439c-8527-3ba1b84a3995"
+ "bids::pb03.$subj.r$run.blur+tlrc"
]
},
{
- "@id": "urn:58593ee7-e92c-41c8-abd4-db8f69e4a693",
+ "@id": "urn:3dmaskto-zDFuqYZj",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:9334173e-be89-47f0-b122-4b20dc4548ea",
+ "@id": "urn:3dresamp-VLobe46F",
"Label": "3dresample",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat",
"Parameters": {},
"Used": [
- "urn:9c28481d-da26-44f6-9946-0fb9b7a7e96f",
- "urn:b8ddd52a-bbf4-4fc6-92fd-5dce1f764117"
+ "bids::full_mask.$subj+tlrc",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:1544c31e-843b-4eda-a65d-83f079e3454c",
+ "@id": "urn:3dmaskto-xRqeKVKk",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj",
"Parameters": {},
"Used": [
- "urn:cd8ee52e-85d2-4b0c-b985-30c2c54be1cd"
+ "bids::rm.resam.anat+tlrc"
]
},
{
- "@id": "urn:474f4339-61f5-4e4b-b95d-5ae31844cf5b",
+ "@id": "urn:3dabover-TKBoabul",
"Label": "3dABoverlap",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt",
"Parameters": {},
"Used": [
- "urn:085442e0-7613-43c0-be47-8b83e0e2604b",
- "urn:57907561-aabf-43fd-ab44-4d130188cf3e"
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee"
]
},
{
- "@id": "urn:ab757f74-c92c-4975-872c-4316678e0289",
+ "@id": "urn:3ddot-Hus14uyn",
"Label": "3ddot",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt",
"Parameters": {},
"Used": [
- "urn:085442e0-7613-43c0-be47-8b83e0e2604b",
- "urn:57907561-aabf-43fd-ab44-4d130188cf3e"
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee"
]
},
{
- "@id": "urn:b1d257f4-28f0-4e6e-b1d0-fa0dc15ca666",
+ "@id": "urn:3dresamp-R1fiidPv",
"Label": "3dresample",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc",
"Parameters": {},
"Used": [
- "urn:01fc591b-2bd8-4681-8a45-9ead959997ac",
- "urn:b8ddd52a-bbf4-4fc6-92fd-5dce1f764117"
+ "bids::/Users/u1591557/abin/TT_N27+tlrc",
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:7693af36-0c01-4257-9531-d5e8d89bd197",
+ "@id": "urn:3dmaskto-hTtHnRLQ",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group",
"Parameters": {},
"Used": [
- "urn:2ccd78dd-e38b-4537-a039-90c1a17501fb"
+ "bids::rm.resam.group+tlrc"
]
},
{
- "@id": "urn:1f817791-d0b3-4f52-b23f-4749f8999d41",
+ "@id": "urn:3dtstat-OetYnP1M",
"Label": "3dTstat",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:15777a94-5d1a-439c-8527-3ba1b84a3995"
+ "bids::pb03.$subj.r$run.blur+tlrc"
]
},
{
- "@id": "urn:880631f5-52f6-406a-9de7-403bffd538b7",
+ "@id": "urn:3dcalc-iKl15WK0",
"Label": "3dcalc",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale",
"Parameters": {},
"Used": [
- "urn:15777a94-5d1a-439c-8527-3ba1b84a3995",
- "urn:6707d5a3-8854-4f88-ab6c-0084ee707e1b",
- "urn:aa2d4900-01b1-4586-94b8-bee17c62e5b8"
+ "bids::mask_epi_extents+tlrc",
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::rm.mean_r$run+tlrc"
]
},
{
- "@id": "urn:6c55e71b-8928-46d6-9877-d304c2ba90b8",
+ "@id": "urn:1dtoolpy-UU0BxZHZ",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D",
"Parameters": {},
"Used": [
- "urn:69a3a04f-f0e7-428c-bf7f-98b6a0098ad3"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:35737c62-7629-4ffd-8d4e-5701ddd34404",
+ "@id": "urn:1dtoolpy-TyRwruqu",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D",
"Parameters": {},
"Used": [
- "urn:69a3a04f-f0e7-428c-bf7f-98b6a0098ad3"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:4fb3b843-49bb-41d9-95af-7ab01880f2fa",
+ "@id": "urn:1dtoolpy-HCa0bU14",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}",
"Parameters": {},
"Used": [
- "urn:69a3a04f-f0e7-428c-bf7f-98b6a0098ad3"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:194f9b1b-1cb5-4d04-a5b7-3322a5ae77e0",
+ "@id": "urn:3ddeconv-5AwXZgCN",
"Label": "3dDeconvolve",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 7 -stim_times 1 stimuli/tone_counting_onset_times.txt 'GAM' -stim_label 1 tone_counting_onset_times.txt -stim_file 2 motion_demean.1D'[0]' -stim_base 2 -stim_label 2 roll -stim_file 3 motion_demean.1D'[1]' -stim_base 3 -stim_label 3 pitch -stim_file 4 motion_demean.1D'[2]' -stim_base 4 -stim_label 4 yaw -stim_file 5 motion_demean.1D'[3]' -stim_base 5 -stim_label 5 dS -stim_file 6 motion_demean.1D'[4]' -stim_base 6 -stim_label 6 dL -stim_file 7 motion_demean.1D'[5]' -stim_base 7 -stim_label 7 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj",
"Parameters": {},
"Used": [
- "urn:2eb65be7-2c3d-451f-a186-14e31708f86e"
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD"
]
},
{
- "@id": "urn:c842ad68-03aa-4d56-a726-64bc81e2eb22",
+ "@id": "urn:1dtoolpy-nbOjPaaJ",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt",
"Parameters": {},
"Used": [
- "urn:15f66ca8-51cf-4e03-a671-0c6fb39383a9"
+ "bids::X.xmat.1D"
]
},
{
- "@id": "urn:e05b6219-dbc9-429f-9a68-34756ef5ca1c",
+ "@id": "urn:3dtcat-oM0YiFdz",
"Label": "3dTcat",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD",
"Parameters": {},
"Used": [
- "urn:2eb65be7-2c3d-451f-a186-14e31708f86e"
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD"
]
},
{
- "@id": "urn:1a32d6b1-17e6-41d4-a670-17fad8f133a0",
+ "@id": "urn:3dtstat-1QgQV99M",
"Label": "3dTstat",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:5bf8c031-4fac-437e-94a9-70bd54096121"
+ "bids::all_runs.$subj+tlrc%22[$ktrs]%22"
]
},
{
- "@id": "urn:09966e3e-1647-482c-a3cc-853889509946",
+ "@id": "urn:3dtstat-zOhAVK8U",
"Label": "3dTstat",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:f4e72b12-18f5-48bc-aeaf-1b74f56b1453"
+ "bids::errts.$%7Bsubj%7D+tlrc%22[$ktrs]%22"
]
},
{
- "@id": "urn:ebb3df15-79fe-45ab-b763-cf41c2520624",
+ "@id": "urn:3dcalc-tnX6Xq31",
"Label": "3dcalc",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj",
"Parameters": {},
"Used": [
- "urn:a5e6ae32-cb04-46f9-a999-7d0ebd8b8db9",
- "urn:ad46b9a2-0e4e-453c-b888-f4e79676cfeb",
- "urn:b8ddd52a-bbf4-4fc6-92fd-5dce1f764117"
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.noise.all+tlrc",
+ "bids::rm.signal.all+tlrc"
]
},
{
- "@id": "urn:bee9f96d-0344-4880-b428-3c0d4fe9f451",
+ "@id": "urn:3dtnorm-oxtrR3Pw",
"Label": "3dTnorm",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc",
"Parameters": {},
"Used": [
- "urn:92c3e4de-0ff4-4a84-bb19-096b59a10c02"
+ "bids::errts.$%7Bsubj%7D+tlrc"
]
},
{
- "@id": "urn:89ccbc96-0197-4eb7-b08c-980efea855eb",
+ "@id": "urn:3dmaskav-26CemRJA",
"Label": "3dmaskave",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D",
"Parameters": {},
- "Used": []
+ "Used": [
+ "bids::full_mask.$subj+tlrc"
+ ]
},
{
- "@id": "urn:6d333ab9-b325-4bde-b130-8685d6c388a2",
+ "@id": "urn:3dtstat-2DL2zRPf",
"Label": "3dTstat",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D",
"Parameters": {},
"Used": [
- "urn:53a5181e-d780-4ac6-af16-c100dbee7957"
+ "bids::out.gcor.1D"
]
},
{
- "@id": "urn:4a94eba4-13cf-43ef-bcf4-df58648e00e9",
+ "@id": "urn:3dcalc-LxtFiCX3",
"Label": "3dcalc",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP",
"Parameters": {},
"Used": [
- "urn:bb43a681-4381-4ce8-b43a-53df91bc4374",
- "urn:f4b9999c-6136-49d0-97a3-0d20890a86bc"
+ "bids::gmean.errts.unit.1D",
+ "bids::rm.errts.unit+tlrc"
]
},
{
- "@id": "urn:4dc13e11-7a79-4297-a361-531cb7311a66",
+ "@id": "urn:3dtstat-lgLdbXSA",
"Label": "3dTstat",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc",
"Parameters": {},
"Used": [
- "urn:eea02eb9-3c81-47ac-8fa1-4541570610fa"
+ "bids::rm.DP+tlrc"
]
},
{
- "@id": "urn:5a5ce852-41b3-42eb-8611-f778c35524b7",
+ "@id": "urn:1dcat-VkGX450W",
"Label": "1dcat",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting_onset_times.txt.1D",
"Parameters": {},
"Used": [
- "urn:e53e1630-eaf0-4075-9d40-b8dbdc32b896"
+ "bids::X.nocensor.xmat.1D'[3]'"
]
},
{
- "@id": "urn:38f6f4f9-5b85-4bb8-b056-0f3c0c71a69f",
+ "@id": "urn:3dtstat-cbVn67pE",
"Label": "3dTstat",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"",
"Parameters": {},
"Used": [
- "urn:5d2e648b-0728-4a90-9306-a6c1e1a8f7d8"
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:bd6744b9-2023-4e53-9ed3-e67bd58bfd97",
+ "@id": "urn:1dcat-awTQMceY",
"Label": "1dcat",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D",
"Parameters": {},
"Used": [
- "urn:5d2e648b-0728-4a90-9306-a6c1e1a8f7d8"
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:f564409f-84db-4594-ac89-518f2d4b8373",
+ "@id": "urn:3dfwhmx-Z8naRoVj",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D",
"Parameters": {},
"Used": [
- "urn:b8ddd52a-bbf4-4fc6-92fd-5dce1f764117"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:a365a7e3-6f69-48f8-aca7-ae5d99434345",
+ "@id": "urn:3dfwhmx-0fRbM5UT",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D",
"Parameters": {},
"Used": [
- "urn:b8ddd52a-bbf4-4fc6-92fd-5dce1f764117"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:e693c57c-65b6-445b-b9a2-bb2d67afd32b",
+ "@id": "urn:3dclusts-II6Bi7Zl",
"Label": "3dClustSim",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim",
"Parameters": {},
"Used": [
- "urn:b8ddd52a-bbf4-4fc6-92fd-5dce1f764117"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:af9b4299-4373-4423-8478-02481413a92c",
+ "@id": "urn:genepire-3ZC3FA44",
"Label": "gen_epi_review.py",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD",
"Parameters": {},
"Used": [
- "urn:bc712b9e-ebe7-442b-9cb0-524ae66cb09d"
+ "bids::pb00.$subj.r*.tcat+orig.HEAD"
]
},
{
- "@id": "urn:8967c63f-5fc7-44a6-a350-10e4d91420e5",
+ "@id": "urn:genssrev-EODYaufK",
"Label": "gen_ss_review_scripts.py",
- "AssociatedWith": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
+ "AssociatedWith": "urn:afni-f7u9iy8U",
"Command": "gen_ss_review_scripts.py -mot_limit 0.3 -exit0",
"Parameters": {
"-mot_limit": "0.3",
@@ -575,22 +578,22 @@
],
"Entities": [
{
- "@id": "urn:18311fc2-149b-4c8c-b4e7-10ca94048082",
+ "@id": "bids::$output_dir",
"Label": "$output_dir",
"AtLocation": "$output_dir",
- "GeneratedBy": "urn:8ac247a6-00f0-4da1-88e5-7e74e5df7066",
+ "GeneratedBy": "urn:makedire-zf7V0epM",
"digest": {
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}
},
{
- "@id": "urn:7c153386-680f-469c-9558-1ef58f5e9387",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:62133b1c-e258-4578-8377-9c4c48a504b3"
+ "GeneratedBy": "urn:makedire-UiQEc72f"
},
{
- "@id": "urn:966bda3f-ef3a-4c6b-96f3-37a8f63317ac",
+ "@id": "bids::afni_gam/tone_counting_onset_times.txt",
"Label": "tone_counting_onset_times.txt",
"AtLocation": "./afni_gam/tone_counting_onset_times.txt",
"digest": {
@@ -598,13 +601,13 @@
}
},
{
- "@id": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:a289d6a3-de2b-4f58-ae64-8f0d3eb75dc1"
+ "GeneratedBy": "urn:cp-n0wB3JC9"
},
{
- "@id": "urn:f2718969-5393-4474-810c-18a55930c2b3",
+ "@id": "bids::afni_gam/sub-01_T1w.nii.gz",
"Label": "sub-01_T1w.nii.gz",
"AtLocation": "./afni_gam/sub-01_T1w.nii.gz",
"digest": {
@@ -612,13 +615,13 @@
}
},
{
- "@id": "urn:9c8cfdcd-ec35-49e0-956d-6cf35f72bd8d",
+ "@id": "bids::$output_dir/sub-01_T1w",
"Label": "sub-01_T1w",
"AtLocation": "$output_dir/sub-01_T1w",
- "GeneratedBy": "urn:926cfd79-5399-4ed5-a1ef-7ddac7372cb3"
+ "GeneratedBy": "urn:3dcopy-kRqgajxm"
},
{
- "@id": "urn:e49008ed-d256-4355-b47b-fc159cc53ed7",
+ "@id": "bids::afni_gam/sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Label": "sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "./afni_gam/sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"digest": {
@@ -626,13 +629,13 @@
}
},
{
- "@id": "urn:7a6ac72f-175e-48b5-82a7-24552b43801e",
+ "@id": "bids::$output_dir/pb00.$subj.r01.tcat",
"Label": "pb00.$subj.r01.tcat",
"AtLocation": "$output_dir/pb00.$subj.r01.tcat",
- "GeneratedBy": "urn:d4855f22-1f95-4735-9a85-8c55d4f931b4"
+ "GeneratedBy": "urn:3dtcat-9hBx7Xb5"
},
{
- "@id": "urn:057aa3ca-32fa-4c88-98d3-5f6135ff173b",
+ "@id": "bids::pb00.$subj.r$run.tcat+orig",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -640,16 +643,16 @@
}
},
{
- "@id": "urn:11c746a8-eb09-416f-b8ea-c33e1df14da6",
+ "@id": "bids::outcount.r$run.1D",
"Label": "outcount.r$run.1D",
"AtLocation": "outcount.r$run.1D",
- "GeneratedBy": "urn:c81268eb-5e93-4ef2-a06f-12a37475e7f7",
+ "GeneratedBy": "urn:3dtoutco-6h2RpeoD",
"digest": {
"sha256": "63d9f539e5470badc625d557109f68bc4eecbb02ca2667483739d52f95e5d0dd"
}
},
{
- "@id": "urn:f31acecb-0303-4585-a1a9-b58cce9cf77d",
+ "@id": "bids::outcount.r*.1D",
"Label": "outcount.r*.1D",
"AtLocation": "outcount.r*.1D",
"digest": {
@@ -657,25 +660,25 @@
}
},
{
- "@id": "urn:d5b3e31f-3f7d-476d-a1c9-a7d3d4e9e991",
+ "@id": "bids::outcount_rall.1D",
"Label": "outcount_rall.1D",
"AtLocation": "outcount_rall.1D",
- "GeneratedBy": "urn:bb970877-b8e1-4deb-bcd4-3241dcacc59e",
+ "GeneratedBy": "urn:cat-ec1ecOF8",
"digest": {
"sha256": "cb887fd5e4d5e9acb3a24820d0f7a62ed38a5ffb0fdedd373440ac0219fb186a"
}
},
{
- "@id": "urn:a20b66f5-dc52-4a8a-ab60-eab714ac4963",
+ "@id": "bids::pb01.$subj.r$run.tshift",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift",
- "GeneratedBy": "urn:91406eb5-1759-4dab-82d5-c0c43b5d80ef",
+ "GeneratedBy": "urn:3dtshift-IbSPdLhN",
"digest": {
"sha256": "c6bf01cea8d2eac1d7a866f80b865c6e7d4b4e012dbb63d480ac9a8551162d72"
}
},
{
- "@id": "urn:130be5b5-1d74-4f34-aa19-8883f9dc0198",
+ "@id": "bids::sub-01_T1w+orig",
"Label": "sub-01_T1w",
"AtLocation": "sub-01_T1w+orig",
"digest": {
@@ -683,7 +686,7 @@
}
},
{
- "@id": "urn:fab5364a-1378-4e37-9a8b-cf22f60a9a30",
+ "@id": "bids::pb01.$subj.r01.tshift+orig",
"Label": "pb01.$subj.r01.tshift",
"AtLocation": "pb01.$subj.r01.tshift+orig",
"digest": {
@@ -691,16 +694,16 @@
}
},
{
- "@id": "urn:fbc4b24a-d16d-4e16-b839-a4b3f2de8748",
+ "@id": "bids::_al_junk",
"Label": "_al_junk",
"AtLocation": "_al_junk",
- "GeneratedBy": "urn:d59e4156-cfd3-425b-aabf-92519931fc2c",
+ "GeneratedBy": "urn:alignepi-7BZjwJ25",
"digest": {
"sha256": "bd785a075a4c6446e1e54de9e628913f7f1c814e86b69a9fbfe933209e6d37b5"
}
},
{
- "@id": "urn:a50a026c-f2ea-4900-81c3-2f3577e6a7c2",
+ "@id": "bids::TT_N27+tlrc",
"Label": "TT_N27",
"AtLocation": "TT_N27+tlrc",
"digest": {
@@ -708,7 +711,7 @@
}
},
{
- "@id": "urn:5b4c176f-8964-44e6-b0ca-9d734e1be7eb",
+ "@id": "bids::sub-01_T1w_ns+orig",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+orig",
"digest": {
@@ -716,7 +719,7 @@
}
},
{
- "@id": "urn:1617de95-9492-49a4-997c-c3fff2ae8c6d",
+ "@id": "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc::WARP_DATA",
"digest": {
@@ -724,16 +727,16 @@
}
},
{
- "@id": "urn:c6bb8b00-5a11-4ad3-9079-e3e04b49cb2f",
+ "@id": "bids::warp.anat.Xat.1D",
"Label": "warp.anat.Xat.1D",
"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:e413cb9e-66c0-45cb-a31f-541be143d96f",
+ "GeneratedBy": "urn:catmatve-gKDe15pu",
"digest": {
"sha256": "800633fb5b4e9be64078bc181c4d5510ffb73fc5cccaf364c7fb6a294aa06728"
}
},
{
- "@id": "urn:e1f6cc09-c137-4859-894f-10d0a6bd0c23",
+ "@id": "bids::pb01.$subj.r$run.tshift+orig",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift+orig",
"digest": {
@@ -741,34 +744,34 @@
}
},
{
- "@id": "urn:f2c84bf5-9702-4567-8403-cfa1b8cffc1e",
+ "@id": "bids::mat.r$run.vr.aff12.1D",
"Label": "mat.r$run.vr.aff12.1D",
"AtLocation": "mat.r$run.vr.aff12.1D",
- "GeneratedBy": "urn:4037cdbc-a9fa-42df-984c-8469028aa60a",
+ "GeneratedBy": "urn:3dvolreg-7EILeENF",
"digest": {
"sha256": "2e6e6c2ce8089cfa3c6e11dc72fca0cc8497f7a55faae2ced402de4867466c91"
}
},
{
- "@id": "urn:686a8225-b31f-4025-9b31-c2c64bb0c114",
+ "@id": "bids::rm.epi.all1",
"Label": "rm.epi.all1",
"AtLocation": "rm.epi.all1",
- "GeneratedBy": "urn:afb7ccbc-ae02-4cf5-a4ad-e90da3838f67",
+ "GeneratedBy": "urn:3dcalc-2zrP85y3",
"digest": {
"sha256": "1023e3c16cecdbdc73ea456bcf33c2e5bb4f1e07094b73d29022d651e5fa3f85"
}
},
{
- "@id": "urn:8a71a648-4d87-4e46-a43a-e9bca7ce84ba",
+ "@id": "bids::mat.r$run.warp.aff12.1D",
"Label": "mat.r$run.warp.aff12.1D",
"AtLocation": "mat.r$run.warp.aff12.1D",
- "GeneratedBy": "urn:79061e66-aeab-4d4a-863d-f657c20101a1",
+ "GeneratedBy": "urn:catmatve-RDcYdGjZ",
"digest": {
"sha256": "7c536b6f582a067c718f9e5ea2566cb535c73b43b4e15116c4c46045734d6eee"
}
},
{
- "@id": "urn:9c28481d-da26-44f6-9946-0fb9b7a7e96f",
+ "@id": "bids::sub-01_T1w_ns+tlrc",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc",
"digest": {
@@ -776,16 +779,16 @@
}
},
{
- "@id": "urn:081fa336-6cc1-4eb4-8b76-659180dbea4b",
+ "@id": "bids::rm.epi.nomask.r$run",
"Label": "rm.epi.nomask.r$run",
"AtLocation": "rm.epi.nomask.r$run",
- "GeneratedBy": "urn:a9c2c6b0-9fb1-4dce-86b7-7718a9ef3d1a",
+ "GeneratedBy": "urn:3dalline-DsMduKfA",
"digest": {
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}
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{
- "@id": "urn:83ae1c41-4e52-43b6-beef-857cab51b576",
+ "@id": "bids::rm.epi.all1+orig",
"Label": "rm.epi.all1",
"AtLocation": "rm.epi.all1+orig",
"digest": {
@@ -793,16 +796,16 @@
}
},
{
- "@id": "urn:b5a834c1-6209-4d61-82c6-3409448659ea",
+ "@id": "bids::rm.epi.1.r$run",
"Label": "rm.epi.1.r$run",
"AtLocation": "rm.epi.1.r$run",
- "GeneratedBy": "urn:97b6c82e-f1d3-48dc-82b4-17bfeb916d8b",
+ "GeneratedBy": "urn:3dalline-kcJ790Fq",
"digest": {
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}
},
{
- "@id": "urn:1a014967-de1c-46ed-a37f-26cb3f7eda52",
+ "@id": "bids::rm.epi.1.r$run+tlrc",
"Label": "rm.epi.1.r$run",
"AtLocation": "rm.epi.1.r$run+tlrc",
"digest": {
@@ -810,16 +813,16 @@
}
},
{
- "@id": "urn:bde49ce6-af3e-4616-8f87-272181752a26",
+ "@id": "bids::rm.epi.min.r$run",
"Label": "rm.epi.min.r$run",
"AtLocation": "rm.epi.min.r$run",
- "GeneratedBy": "urn:8a5097be-6b13-4048-a042-c2b8783f4d08",
+ "GeneratedBy": "urn:3dtstat-GD8XVCMR",
"digest": {
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{
- "@id": "urn:b749c781-f2ad-471d-a39c-effdffc69219",
+ "@id": "bids::dfile.r*.1D",
"Label": "dfile.r*.1D",
"AtLocation": "dfile.r*.1D",
"digest": {
@@ -827,16 +830,16 @@
}
},
{
- "@id": "urn:69a3a04f-f0e7-428c-bf7f-98b6a0098ad3",
+ "@id": "bids::dfile_rall.1D",
"Label": "dfile_rall.1D",
"AtLocation": "dfile_rall.1D",
- "GeneratedBy": "urn:ebf46ff4-7980-4938-a4bc-f6536d7e3282",
+ "GeneratedBy": "urn:cat-mQD6kcqM",
"digest": {
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{
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+ "@id": "bids::rm.epi.min.r01+tlrc",
"Label": "rm.epi.min.r01",
"AtLocation": "rm.epi.min.r01+tlrc",
"digest": {
@@ -844,16 +847,16 @@
}
},
{
- "@id": "urn:4bb24dcb-7e84-4293-af56-cf0afe4d1ca9",
+ "@id": "bids::mask_epi_extents",
"Label": "mask_epi_extents",
"AtLocation": "mask_epi_extents",
- "GeneratedBy": "urn:6916c807-44ba-48eb-9a03-dfbf52c8a393",
+ "GeneratedBy": "urn:3dcopy-kCVFiKEn",
"digest": {
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{
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+ "@id": "bids::rm.epi.nomask.r$run+tlrc",
"Label": "rm.epi.nomask.r$run",
"AtLocation": "rm.epi.nomask.r$run+tlrc",
"digest": {
@@ -861,7 +864,7 @@
}
},
{
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+ "@id": "bids::mask_epi_extents+tlrc",
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"AtLocation": "mask_epi_extents+tlrc",
"digest": {
@@ -869,34 +872,42 @@
}
},
{
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"AtLocation": "pb02.$subj.r$run.volreg",
- "GeneratedBy": "urn:dbbfca19-1a7b-4b70-ae99-015594ee8ce4",
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@@ -904,7 +915,7 @@
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@@ -912,7 +923,7 @@
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@@ -920,25 +931,25 @@
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@@ -946,16 +957,16 @@
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@@ -963,16 +974,16 @@
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@@ -980,7 +991,7 @@
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@@ -988,7 +999,7 @@
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@@ -996,16 +1007,16 @@
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@@ -1013,25 +1024,25 @@
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@@ -1039,34 +1050,34 @@
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@@ -1074,25 +1085,25 @@
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@@ -1100,16 +1111,16 @@
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@@ -1117,16 +1128,16 @@
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@@ -1134,7 +1145,7 @@
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@@ -1142,16 +1153,16 @@
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@@ -1159,25 +1170,25 @@
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@@ -1185,16 +1196,16 @@
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@@ -1202,16 +1213,16 @@
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@@ -1219,16 +1230,16 @@
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@@ -1236,16 +1247,16 @@
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@@ -1253,52 +1264,52 @@
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"AtLocation": "ClustSim",
- "GeneratedBy": "urn:e693c57c-65b6-445b-b9a2-bb2d67afd32b",
+ "GeneratedBy": "urn:3dclusts-II6Bi7Zl",
"digest": {
"sha256": "2e0cdba2c91902ba12d742a39cb20df66cfd705ba8de767fbf68aae8eb65c6f0"
}
},
{
- "@id": "urn:bc712b9e-ebe7-442b-9cb0-524ae66cb09d",
+ "@id": "bids::pb00.$subj.r*.tcat+orig.HEAD",
"Label": "pb00.$subj.r*.tcat",
"AtLocation": "pb00.$subj.r*.tcat+orig.HEAD",
"digest": {
@@ -1306,10 +1317,10 @@
}
},
{
- "@id": "urn:f0664c49-ddd6-4d24-a5ba-c6bbf6b11662",
+ "@id": "bids::-exit0",
"Label": "-exit0",
"AtLocation": "-exit0",
- "GeneratedBy": "urn:8967c63f-5fc7-44a6-a350-10e4d91420e5",
+ "GeneratedBy": "urn:genssrev-EODYaufK",
"digest": {
"sha256": "871a4d3513ed2924cbb10c1c15a196eac4a46a05bdcc248e3bcdb23327b3ad90"
}
diff --git a/examples/from_parsers/afni/afni_gam_proc.png b/examples/from_parsers/afni/afni_gam_proc.png
index d8499ab18..e277d5e7f 100644
Binary files a/examples/from_parsers/afni/afni_gam_proc.png and b/examples/from_parsers/afni/afni_gam_proc.png differ
diff --git a/examples/from_parsers/afni/afni_gam_proc_block.jsonld b/examples/from_parsers/afni/afni_gam_proc_block.jsonld
index 3f48eecb1..e30c9cb2a 100644
--- a/examples/from_parsers/afni/afni_gam_proc_block.jsonld
+++ b/examples/from_parsers/afni/afni_gam_proc_block.jsonld
@@ -4,185 +4,187 @@
"Records": {
"Software": [
{
- "@id": "urn:0baf18c4-bdb8-4a8e-a7f5-eb209c19659e",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:afni-WGdKEOYU",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
- "Version": "afni24"
+ "Version": "afni24",
+ "AltIdentifier": "RRID:SCR_005927"
}
],
"Activities": [
{
- "@id": "urn:ef2fb089-5fca-41c9-8153-e4ea3c94cbe6",
+ "@id": "urn:autobloc-yawH2nHi",
"Label": "auto block: setup",
- "AssociatedWith": "urn:0baf18c4-bdb8-4a8e-a7f5-eb209c19659e",
+ "AssociatedWith": "urn:afni-WGdKEOYU",
"Command": "mkdir $output_dir; mkdir $output_dir/stimuli; cp ./afni_gam/tone_counting_onset_times.txt $output_dir/stimuli; 3dcopy ./afni_gam/sub-01_T1w.nii.gz $output_dir/sub-01_T1w; ",
"Used": [
- "urn:5d71ef67-fdc3-4c22-b0ce-a46353f96da6",
- "urn:2b4f94e0-5fc5-4ffe-bef1-0aac47d21a99"
+ "bids::afni_gam/tone_counting_onset_times.txt",
+ "bids::afni_gam/sub-01_T1w.nii.gz"
]
},
{
- "@id": "urn:996f1cd6-3d7c-4d4f-80dd-bcb84552882e",
+ "@id": "urn:autobloc-3S8o18SD",
"Label": "auto block: tcat",
- "AssociatedWith": "urn:0baf18c4-bdb8-4a8e-a7f5-eb209c19659e",
+ "AssociatedWith": "urn:afni-WGdKEOYU",
"Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat ./afni_gam/sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ",
"Used": [
- "urn:6ff19661-8154-4797-b030-ee8a39539ab9"
+ "bids::afni_gam/sub-01_task-tonecounting_bold.nii.gz'[0..$]'"
]
},
{
- "@id": "urn:acf8913a-9478-43b6-9eb7-6dcc45e2a69c",
+ "@id": "urn:autobloc-nSqVpUzm",
"Label": "auto block: outcount",
- "AssociatedWith": "urn:0baf18c4-bdb8-4a8e-a7f5-eb209c19659e",
+ "AssociatedWith": "urn:afni-WGdKEOYU",
"Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ",
"Used": [
- "urn:c46767c5-eee1-46c5-be47-43f187434027",
- "urn:e2161cb4-2cf0-4eea-b9fd-88b0157f0df4"
+ "bids::pb00.$subj.r$run.tcat+orig",
+ "bids::outcount.r*.1D"
]
},
{
- "@id": "urn:49c9198c-4a9b-41b5-9f05-19ea027991b4",
+ "@id": "urn:tshift-kA1RR45z",
"Label": "tshift",
- "AssociatedWith": "urn:0baf18c4-bdb8-4a8e-a7f5-eb209c19659e",
+ "AssociatedWith": "urn:afni-WGdKEOYU",
"Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ",
"Used": [
- "urn:c46767c5-eee1-46c5-be47-43f187434027"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:10560f83-0a91-456e-9358-48a8a5ea215a",
+ "@id": "urn:align-aiaahkOe",
"Label": "align",
- "AssociatedWith": "urn:0baf18c4-bdb8-4a8e-a7f5-eb209c19659e",
+ "AssociatedWith": "urn:afni-WGdKEOYU",
"Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ",
"Used": [
- "urn:c5248d48-74a5-470d-8bcb-ad95174cda17",
- "urn:f9d9798b-3574-4575-9644-32356a2670e4"
+ "bids::pb01.$subj.r01.tshift+orig",
+ "bids::sub-01_T1w+orig"
]
},
{
- "@id": "urn:2d488bb1-949e-4c1a-b097-1303f780e022",
+ "@id": "urn:tlrc-PPEYvXwo",
"Label": "tlrc",
- "AssociatedWith": "urn:0baf18c4-bdb8-4a8e-a7f5-eb209c19659e",
+ "AssociatedWith": "urn:afni-WGdKEOYU",
"Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ",
"Used": [
- "urn:4fec4485-79c7-453b-9e8e-2109477a7006",
- "urn:e3b9829e-8528-4df2-ad9e-83ece0e34f80",
- "urn:852711dd-38a1-484b-afd1-8cb94648ec83"
+ "bids::TT_N27+tlrc",
+ "bids::sub-01_T1w_ns+orig",
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:c2f72589-1f04-4e3e-b32a-d89946bd5ced",
+ "@id": "urn:volreg-INMo0BDF",
"Label": "volreg",
- "AssociatedWith": "urn:0baf18c4-bdb8-4a8e-a7f5-eb209c19659e",
+ "AssociatedWith": "urn:afni-WGdKEOYU",
"Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig; 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1; cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D; 3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run; 3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run; 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc; cat dfile.r*.1D > dfile_rall.1D; 3dcopy rm.epi.min.r01+tlrc mask_epi_extents; 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg; 3dcopy sub-01_T1w_ns+tlrc anat_final.$subj; 3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped; ",
"Used": [
- "urn:37c03f2d-8a70-4275-af3d-8741c84377e7",
- "urn:37c03f2d-8a70-4275-af3d-8741c84377e7",
- "urn:852711dd-38a1-484b-afd1-8cb94648ec83",
- "urn:37c03f2d-8a70-4275-af3d-8741c84377e7",
- "urn:7113ba83-fbcd-46a9-a4a8-fa6e7707d0ac",
- "urn:48c367db-2751-4b3a-bb8d-ebc2b5bf75a6",
- "urn:7113ba83-fbcd-46a9-a4a8-fa6e7707d0ac",
- "urn:b3221acf-e8f3-4857-b126-4685ff6d89e8",
- "urn:d8be2762-fa93-4e54-8cee-c1cf4627ab75",
- "urn:61ad2da1-fa96-453d-8ea2-ffdaf4e76f3f",
- "urn:14f92534-636d-49c9-9e96-ca067ef99a0b",
- "urn:60479ac6-9e5e-4a5c-8257-cb26169c528f",
- "urn:7113ba83-fbcd-46a9-a4a8-fa6e7707d0ac",
- "urn:57e7bf09-1c5f-491e-9910-1019217f0492"
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.epi.all1+orig",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.epi.1.r$run+tlrc",
+ "bids::dfile.r*.1D",
+ "bids::rm.epi.min.r01+tlrc",
+ "bids::mask_epi_extents+tlrc",
+ "bids::rm.epi.nomask.r$run+tlrc",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::anat_final.$subj+tlrc",
+ "bids::warp.anat.Xat.1D"
]
},
{
- "@id": "urn:f39c080a-20e3-4515-a8e0-7550561ca24b",
+ "@id": "urn:blur-XtAAvg9l",
"Label": "blur",
- "AssociatedWith": "urn:0baf18c4-bdb8-4a8e-a7f5-eb209c19659e",
+ "AssociatedWith": "urn:afni-WGdKEOYU",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc; ",
"Used": [
- "urn:0c1606a0-a39e-4f39-bbf7-dee0968d0aa2",
- "urn:da7a47f5-c7b8-4af8-b049-e14b0fede0d4"
+ "bids::pb02.$subj.r$run.volreg+tlrc",
+ "bids::pb03.$subj.r$run.blur"
]
},
{
- "@id": "urn:2b9046a4-2675-47b0-b2f6-fbfebe991c68",
+ "@id": "urn:mask-ZYjLayXi",
"Label": "mask",
- "AssociatedWith": "urn:0baf18c4-bdb8-4a8e-a7f5-eb209c19659e",
+ "AssociatedWith": "urn:afni-WGdKEOYU",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc; 3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj; 3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj; 3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt; 3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt; 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group; ",
"Used": [
- "urn:f065ba49-0061-4710-9e72-51bedf075cff",
- "urn:5312e31a-60d3-4749-af9e-23ed6e42382f",
- "urn:7113ba83-fbcd-46a9-a4a8-fa6e7707d0ac",
- "urn:4eb45450-e358-46a7-86ee-cfdb9902415e",
- "urn:58a1acaf-fb60-40ba-9f05-b1c92504a557",
- "urn:f97e9638-f9aa-4f35-8225-62aeaa38350d",
- "urn:58a1acaf-fb60-40ba-9f05-b1c92504a557",
- "urn:f97e9638-f9aa-4f35-8225-62aeaa38350d",
- "urn:2ec74de8-9ad4-49f3-8e6b-a2fd4c979565",
- "urn:5312e31a-60d3-4749-af9e-23ed6e42382f",
- "urn:88fa4f58-2669-4fbd-8716-253871594873"
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.resam.anat+tlrc",
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee",
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee",
+ "bids::/Users/u1591557/abin/TT_N27+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.resam.group+tlrc"
]
},
{
- "@id": "urn:25d73731-5632-459e-8971-ccf6f4acf1c3",
+ "@id": "urn:scale-nNPoyA13",
"Label": "scale",
- "AssociatedWith": "urn:0baf18c4-bdb8-4a8e-a7f5-eb209c19659e",
+ "AssociatedWith": "urn:afni-WGdKEOYU",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc; 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale; ",
"Used": [
- "urn:f065ba49-0061-4710-9e72-51bedf075cff",
- "urn:14f92534-636d-49c9-9e96-ca067ef99a0b",
- "urn:28f3ad86-7bbc-4bad-935d-7d4416682ba1",
- "urn:f065ba49-0061-4710-9e72-51bedf075cff"
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::mask_epi_extents+tlrc",
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::rm.mean_r$run+tlrc"
]
},
{
- "@id": "urn:c8a9dde6-7e34-4dfc-993a-35bac4d8693c",
+ "@id": "urn:regress-g4vzalJ0",
"Label": "regress",
- "AssociatedWith": "urn:0baf18c4-bdb8-4a8e-a7f5-eb209c19659e",
+ "AssociatedWith": "urn:afni-WGdKEOYU",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}; 3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 7 -stim_times 1 stimuli/tone_counting_onset_times.txt 'GAM' -stim_label 1 tone_counting_onset_times.txt -stim_file 2 motion_demean.1D'[0]' -stim_base 2 -stim_label 2 roll -stim_file 3 motion_demean.1D'[1]' -stim_base 3 -stim_label 3 pitch -stim_file 4 motion_demean.1D'[2]' -stim_base 4 -stim_label 4 yaw -stim_file 5 motion_demean.1D'[3]' -stim_base 5 -stim_label 5 dS -stim_file 6 motion_demean.1D'[4]' -stim_base 6 -stim_label 6 dL -stim_file 7 motion_demean.1D'[5]' -stim_base 7 -stim_label 7 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj; 1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt; 3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD; 3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"; 3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"; 3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj; 3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc; 3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D; 3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D; 3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP; 3dTstat -sum -prefix corr_brain rm.DP+tlrc; 1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting_onset_times.txt.1D; 3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"; 1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D; ",
"Used": [
- "urn:fcde3b82-23d2-47a4-8cf1-6e6487be366a",
- "urn:fcde3b82-23d2-47a4-8cf1-6e6487be366a",
- "urn:fcde3b82-23d2-47a4-8cf1-6e6487be366a",
- "urn:17d2cc88-4bae-4444-9530-b8c84f76341b",
- "urn:17d2cc88-4bae-4444-9530-b8c84f76341b",
- "urn:92942894-91d4-46da-a851-212428e5ffd6",
- "urn:82715994-f108-4d17-ba20-8b5e1fe14ac3",
- "urn:5312e31a-60d3-4749-af9e-23ed6e42382f",
- "urn:aec7fb9b-2ee8-4f2d-b523-9da2972acaab",
- "urn:beaf7a4a-26f6-4baf-a898-33fed1de6dd1",
- "urn:0daa00f1-fd07-4481-a724-16ce22dd13cf",
- "urn:b4269c4f-f3a9-4fde-ba7c-9e73f98efa77",
- "urn:dcbb3e88-d6dd-4ce7-81f0-f836944dfb88",
- "urn:ed09bfc0-4e0f-4033-bdc5-2697ab125380",
- "urn:3ee13e32-1c59-4bee-b8d6-3486ed62edbb",
- "urn:327caea3-5cef-4821-a4fe-f2306d78ad61",
- "urn:327caea3-5cef-4821-a4fe-f2306d78ad61"
+ "bids::dfile_rall.1D",
+ "bids::dfile_rall.1D",
+ "bids::dfile_rall.1D",
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD",
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD",
+ "bids::all_runs.$subj+tlrc%22[$ktrs]%22",
+ "bids::errts.$%7Bsubj%7D+tlrc%22[$ktrs]%22",
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.noise.all+tlrc",
+ "bids::rm.signal.all+tlrc",
+ "bids::errts.$%7Bsubj%7D+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::out.gcor.1D",
+ "bids::rm.errts.unit+tlrc",
+ "bids::rm.DP+tlrc",
+ "bids::X.nocensor.xmat.1D'[3]'",
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22",
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:ed07977b-6030-4daa-a75e-26c91008b808",
+ "@id": "urn:bluresti-C7yt9SsZ",
"Label": "blur estimation",
- "AssociatedWith": "urn:0baf18c4-bdb8-4a8e-a7f5-eb209c19659e",
+ "AssociatedWith": "urn:afni-WGdKEOYU",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D; 3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D; 3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim; ",
"Used": [
- "urn:5312e31a-60d3-4749-af9e-23ed6e42382f",
- "urn:5312e31a-60d3-4749-af9e-23ed6e42382f",
- "urn:5312e31a-60d3-4749-af9e-23ed6e42382f"
+ "bids::full_mask.$subj+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:0df00aab-8630-4a0a-87d4-d948ff20b516",
+ "@id": "urn:autobloc-dj10kUao",
"Label": "auto block: generate review scripts",
- "AssociatedWith": "urn:0baf18c4-bdb8-4a8e-a7f5-eb209c19659e",
+ "AssociatedWith": "urn:afni-WGdKEOYU",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD; gen_ss_review_scripts.py -mot_limit 0.3 -exit0; ",
"Used": [
- "urn:2ccdf1c9-e316-48ef-a874-202db6a99cb0"
+ "bids::pb00.$subj.r*.tcat+orig.HEAD"
]
}
],
"Entities": [
{
- "@id": "urn:5d71ef67-fdc3-4c22-b0ce-a46353f96da6",
+ "@id": "bids::afni_gam/tone_counting_onset_times.txt",
"Label": "tone_counting_onset_times.txt",
"AtLocation": "./afni_gam/tone_counting_onset_times.txt",
"digest": {
@@ -190,7 +192,7 @@
}
},
{
- "@id": "urn:2b4f94e0-5fc5-4ffe-bef1-0aac47d21a99",
+ "@id": "bids::afni_gam/sub-01_T1w.nii.gz",
"Label": "sub-01_T1w.nii.gz",
"AtLocation": "./afni_gam/sub-01_T1w.nii.gz",
"digest": {
@@ -198,34 +200,34 @@
}
},
{
- "@id": "urn:220e246a-5616-474f-b2a6-2ad927e35ec0",
+ "@id": "bids::$output_dir",
"Label": "$output_dir",
"AtLocation": "$output_dir",
- "GeneratedBy": "urn:ef2fb089-5fca-41c9-8153-e4ea3c94cbe6",
+ "GeneratedBy": "urn:autobloc-yawH2nHi",
"digest": {
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}
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{
- "@id": "urn:b4cb0bba-46e0-4c70-b0ed-fc17fcc0c5d5",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:ef2fb089-5fca-41c9-8153-e4ea3c94cbe6"
+ "GeneratedBy": "urn:autobloc-yawH2nHi"
},
{
- "@id": "urn:71935ebf-a6ab-4500-ad8b-7f5e8da5e05e",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:ef2fb089-5fca-41c9-8153-e4ea3c94cbe6"
+ "GeneratedBy": "urn:autobloc-yawH2nHi"
},
{
- "@id": "urn:fe638e60-c25e-4ea2-9402-d0a17266edce",
+ "@id": "bids::$output_dir/sub-01_T1w",
"Label": "sub-01_T1w",
"AtLocation": "$output_dir/sub-01_T1w",
- "GeneratedBy": "urn:ef2fb089-5fca-41c9-8153-e4ea3c94cbe6"
+ "GeneratedBy": "urn:autobloc-yawH2nHi"
},
{
- "@id": "urn:6ff19661-8154-4797-b030-ee8a39539ab9",
+ "@id": "bids::afni_gam/sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Label": "sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "./afni_gam/sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"digest": {
@@ -233,13 +235,13 @@
}
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{
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+ "@id": "bids::$output_dir/pb00.$subj.r01.tcat",
"Label": "pb00.$subj.r01.tcat",
"AtLocation": "$output_dir/pb00.$subj.r01.tcat",
- "GeneratedBy": "urn:996f1cd6-3d7c-4d4f-80dd-bcb84552882e"
+ "GeneratedBy": "urn:autobloc-3S8o18SD"
},
{
- "@id": "urn:c46767c5-eee1-46c5-be47-43f187434027",
+ "@id": "bids::pb00.$subj.r$run.tcat+orig",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -247,7 +249,7 @@
}
},
{
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"digest": {
@@ -255,25 +257,25 @@
}
},
{
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+ "@id": "bids::outcount.r$run.1D",
"Label": "outcount.r$run.1D",
"AtLocation": "outcount.r$run.1D",
- "GeneratedBy": "urn:acf8913a-9478-43b6-9eb7-6dcc45e2a69c",
+ "GeneratedBy": "urn:autobloc-nSqVpUzm",
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{
- "@id": "urn:112723b4-9501-4fe9-aa4b-fa63a6c56252",
+ "@id": "bids::outcount_rall.1D",
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"AtLocation": "outcount_rall.1D",
- "GeneratedBy": "urn:acf8913a-9478-43b6-9eb7-6dcc45e2a69c",
+ "GeneratedBy": "urn:autobloc-nSqVpUzm",
"digest": {
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}
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{
- "@id": "urn:c46767c5-eee1-46c5-be47-43f187434027",
+ "@id": "bids::pb00.$subj.r$run.tcat+orig",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -281,16 +283,16 @@
}
},
{
- "@id": "urn:8ae3884c-450f-43e5-b055-4b370616b43d",
+ "@id": "bids::pb01.$subj.r$run.tshift",
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"AtLocation": "pb01.$subj.r$run.tshift",
- "GeneratedBy": "urn:49c9198c-4a9b-41b5-9f05-19ea027991b4",
+ "GeneratedBy": "urn:tshift-kA1RR45z",
"digest": {
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{
- "@id": "urn:f9d9798b-3574-4575-9644-32356a2670e4",
+ "@id": "bids::sub-01_T1w+orig",
"Label": "sub-01_T1w",
"AtLocation": "sub-01_T1w+orig",
"digest": {
@@ -298,7 +300,7 @@
}
},
{
- "@id": "urn:c5248d48-74a5-470d-8bcb-ad95174cda17",
+ "@id": "bids::pb01.$subj.r01.tshift+orig",
"Label": "pb01.$subj.r01.tshift",
"AtLocation": "pb01.$subj.r01.tshift+orig",
"digest": {
@@ -306,16 +308,16 @@
}
},
{
- "@id": "urn:f39dd174-9880-4dbd-93b8-049bcd504001",
+ "@id": "bids::_al_junk",
"Label": "_al_junk",
"AtLocation": "_al_junk",
- "GeneratedBy": "urn:10560f83-0a91-456e-9358-48a8a5ea215a",
+ "GeneratedBy": "urn:align-aiaahkOe",
"digest": {
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}
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{
- "@id": "urn:4fec4485-79c7-453b-9e8e-2109477a7006",
+ "@id": "bids::TT_N27+tlrc",
"Label": "TT_N27",
"AtLocation": "TT_N27+tlrc",
"digest": {
@@ -323,7 +325,7 @@
}
},
{
- "@id": "urn:e3b9829e-8528-4df2-ad9e-83ece0e34f80",
+ "@id": "bids::sub-01_T1w_ns+orig",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+orig",
"digest": {
@@ -331,7 +333,7 @@
}
},
{
- "@id": "urn:852711dd-38a1-484b-afd1-8cb94648ec83",
+ "@id": "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc::WARP_DATA",
"digest": {
@@ -339,16 +341,16 @@
}
},
{
- "@id": "urn:57e7bf09-1c5f-491e-9910-1019217f0492",
+ "@id": "bids::warp.anat.Xat.1D",
"Label": "warp.anat.Xat.1D",
"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:2d488bb1-949e-4c1a-b097-1303f780e022",
+ "GeneratedBy": "urn:tlrc-PPEYvXwo",
"digest": {
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}
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{
- "@id": "urn:852711dd-38a1-484b-afd1-8cb94648ec83",
+ "@id": "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc::WARP_DATA",
"digest": {
@@ -356,16 +358,16 @@
}
},
{
- "@id": "urn:57e7bf09-1c5f-491e-9910-1019217f0492",
+ "@id": "bids::warp.anat.Xat.1D",
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"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:2d488bb1-949e-4c1a-b097-1303f780e022",
+ "GeneratedBy": "urn:tlrc-PPEYvXwo",
"digest": {
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}
},
{
- "@id": "urn:37c03f2d-8a70-4275-af3d-8741c84377e7",
+ "@id": "bids::pb01.$subj.r$run.tshift+orig",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift+orig",
"digest": {
@@ -373,7 +375,7 @@
}
},
{
- "@id": "urn:7113ba83-fbcd-46a9-a4a8-fa6e7707d0ac",
+ "@id": "bids::sub-01_T1w_ns+tlrc",
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"AtLocation": "sub-01_T1w_ns+tlrc",
"digest": {
@@ -381,7 +383,7 @@
}
},
{
- "@id": "urn:48c367db-2751-4b3a-bb8d-ebc2b5bf75a6",
+ "@id": "bids::rm.epi.all1+orig",
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"digest": {
@@ -389,7 +391,7 @@
}
},
{
- "@id": "urn:b3221acf-e8f3-4857-b126-4685ff6d89e8",
+ "@id": "bids::rm.epi.1.r$run+tlrc",
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"AtLocation": "rm.epi.1.r$run+tlrc",
"digest": {
@@ -397,7 +399,7 @@
}
},
{
- "@id": "urn:d8be2762-fa93-4e54-8cee-c1cf4627ab75",
+ "@id": "bids::dfile.r*.1D",
"Label": "dfile.r*.1D",
"AtLocation": "dfile.r*.1D",
"digest": {
@@ -405,7 +407,7 @@
}
},
{
- "@id": "urn:61ad2da1-fa96-453d-8ea2-ffdaf4e76f3f",
+ "@id": "bids::rm.epi.min.r01+tlrc",
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"digest": {
@@ -413,7 +415,7 @@
}
},
{
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+ "@id": "bids::rm.epi.nomask.r$run+tlrc",
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"AtLocation": "rm.epi.nomask.r$run+tlrc",
"digest": {
@@ -421,7 +423,7 @@
}
},
{
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+ "@id": "bids::mask_epi_extents+tlrc",
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"digest": {
@@ -429,97 +431,105 @@
}
},
{
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+ "@id": "bids::anat_final.$subj+tlrc",
+ "Label": "anat_final.$subj",
+ "AtLocation": "anat_final.$subj+tlrc",
+ "digest": {
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+ {
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"Label": "mat.r$run.vr.aff12.1D",
"AtLocation": "mat.r$run.vr.aff12.1D",
- "GeneratedBy": "urn:c2f72589-1f04-4e3e-b32a-d89946bd5ced",
+ "GeneratedBy": "urn:volreg-INMo0BDF",
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{
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"AtLocation": "rm.epi.all1",
- "GeneratedBy": "urn:c2f72589-1f04-4e3e-b32a-d89946bd5ced",
+ "GeneratedBy": "urn:volreg-INMo0BDF",
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{
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+ "@id": "bids::rm.epi.nomask.r$run",
"Label": "rm.epi.nomask.r$run",
"AtLocation": "rm.epi.nomask.r$run",
- "GeneratedBy": "urn:c2f72589-1f04-4e3e-b32a-d89946bd5ced",
+ "GeneratedBy": "urn:volreg-INMo0BDF",
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{
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+ "@id": "bids::rm.epi.1.r$run",
"Label": "rm.epi.1.r$run",
"AtLocation": "rm.epi.1.r$run",
- "GeneratedBy": "urn:c2f72589-1f04-4e3e-b32a-d89946bd5ced",
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{
- "@id": "urn:84bb4292-c4fb-4630-9b9e-4d2f4ad4e630",
+ "@id": "bids::rm.epi.min.r$run",
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"AtLocation": "rm.epi.min.r$run",
- "GeneratedBy": "urn:c2f72589-1f04-4e3e-b32a-d89946bd5ced",
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{
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+ "@id": "bids::dfile_rall.1D",
"Label": "dfile_rall.1D",
"AtLocation": "dfile_rall.1D",
- "GeneratedBy": "urn:c2f72589-1f04-4e3e-b32a-d89946bd5ced",
+ "GeneratedBy": "urn:volreg-INMo0BDF",
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{
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+ "@id": "bids::mask_epi_extents",
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"AtLocation": "mask_epi_extents",
- "GeneratedBy": "urn:c2f72589-1f04-4e3e-b32a-d89946bd5ced",
+ "GeneratedBy": "urn:volreg-INMo0BDF",
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{
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"AtLocation": "pb02.$subj.r$run.volreg",
- "GeneratedBy": "urn:c2f72589-1f04-4e3e-b32a-d89946bd5ced",
+ "GeneratedBy": "urn:volreg-INMo0BDF",
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}
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{
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+ "@id": "bids::anat_final.$subj",
"Label": "anat_final.$subj",
"AtLocation": "anat_final.$subj",
- "GeneratedBy": "urn:c2f72589-1f04-4e3e-b32a-d89946bd5ced",
+ "GeneratedBy": "urn:volreg-INMo0BDF",
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}
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{
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+ "@id": "bids::anat_w_skull_warped",
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"AtLocation": "anat_w_skull_warped",
- "GeneratedBy": "urn:c2f72589-1f04-4e3e-b32a-d89946bd5ced",
+ "GeneratedBy": "urn:volreg-INMo0BDF",
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@@ -527,7 +537,7 @@
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{
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@@ -535,7 +545,7 @@
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{
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@@ -543,7 +553,7 @@
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{
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@@ -551,7 +561,7 @@
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@@ -559,7 +569,7 @@
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{
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@@ -567,7 +577,7 @@
}
},
{
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"digest": {
@@ -575,7 +585,7 @@
}
},
{
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@@ -583,7 +593,7 @@
}
},
{
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"AtLocation": "/Users/u1591557/abin/TT_N27+tlrc",
"digest": {
@@ -591,7 +601,7 @@
}
},
{
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+ "@id": "bids::rm.resam.group+tlrc",
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"digest": {
@@ -599,61 +609,61 @@
}
},
{
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diff --git a/examples/from_parsers/afni/afni_gam_proc_block.png b/examples/from_parsers/afni/afni_gam_proc_block.png
index f1a6a80c4..5ad3c3e78 100644
Binary files a/examples/from_parsers/afni/afni_gam_proc_block.png and b/examples/from_parsers/afni/afni_gam_proc_block.png differ
diff --git a/examples/from_parsers/afni/afni_hrf_gammadiff_proc.jsonld b/examples/from_parsers/afni/afni_hrf_gammadiff_proc.jsonld
index 2760ff877..fc8b76e1f 100644
--- a/examples/from_parsers/afni/afni_hrf_gammadiff_proc.jsonld
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- "urn:45579f06-fc67-4a72-a435-4a2bde6046c2"
+ "bids::/Users/cmaumet/Projects/Data_sharing/dev/nidmresults-examples/afni_voxelwise_p0001/subject_results/group.DS0011/subj.sub_001/sub_001.results/stimuli/tone_counting_onset_times.txt",
+ "bids::/Users/cmaumet/Projects/Data_sharing/dev/nidmresults-examples/afni_voxelwise_p0001/subject_results/group.DS0011/subj.sub_001/sub_001.results/stimuli/tone_counting_probe_duration.txt"
]
},
{
- "@id": "urn:bf51fb88-d326-4f30-be43-ab454615eef4",
+ "@id": "urn:3dcopy-j7QzAy9Y",
"Label": "3dcopy",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "3dcopy /Users/cmaumet/Projects/Data_sharing/dev/nidmresults-examples/raw/ds011/sub-01/anat/sub-01_T1w.nii.gz $output_dir/sub-01_T1w",
"Parameters": {},
"Used": [
- "urn:d1e447a7-bec3-421c-b7c3-9138d92c7206"
+ "bids::/Users/cmaumet/Projects/Data_sharing/dev/nidmresults-examples/raw/ds011/sub-01/anat/sub-01_T1w.nii.gz"
]
},
{
- "@id": "urn:b6722269-67c1-45e2-a55d-94e6e075c7f4",
+ "@id": "urn:3dtcat-dI1c6m9j",
"Label": "3dTcat",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat /Users/cmaumet/Projects/Data_sharing/dev/nidmresults-examples/raw/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Parameters": {},
"Used": [
- "urn:33f25266-483a-4f84-b431-94d1e059dbfa"
+ "bids::/Users/cmaumet/Projects/Data_sharing/dev/nidmresults-examples/raw/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'[0..$]'"
]
},
{
- "@id": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
+ "@id": "urn:3dtoutco-wsZI1sDP",
"Label": "3dToutcount",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D",
"Parameters": {},
"Used": [
- "urn:1f888d36-8dc1-4dd9-aed3-6307c376c266"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:fd1d4aff-2275-4cf2-a575-8ee7b01253b0",
+ "@id": "urn:cat-u7xX4giX",
"Label": "cat",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "cat outcount.r*.1D > outcount_rall.1D",
"Parameters": {},
"Used": [
- "urn:a46ad4e6-5621-4686-b06f-2f4c85f6fded"
+ "bids::outcount.r*.1D"
]
},
{
- "@id": "urn:e4838222-2b8c-4e52-9bcb-14121cde4681",
+ "@id": "urn:3dtshift-sItZf4Nw",
"Label": "3dTshift",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig",
"Parameters": {},
"Used": [
- "urn:1f888d36-8dc1-4dd9-aed3-6307c376c266"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:abe0ec4f-41d6-4388-83b3-816399fb430b",
+ "@id": "urn:alignepi-oXmvtYx9",
"Label": "align_epi_anat.py",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off",
"Parameters": {},
"Used": [
- "urn:3888ab93-e11b-43ed-a1f4-4829a093becf",
- "urn:6d9c0313-572b-46d4-acdc-537652e3b978"
+ "bids::pb01.$subj.r01.tshift+orig",
+ "bids::sub-01_T1w+orig"
]
},
{
- "@id": "urn:ae83add3-6da7-4eae-8dfe-79cea4c4d1ac",
+ "@id": "urn:autotlrc-Aq2WvqW4",
"Label": "@auto_tlrc",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss",
"Parameters": {},
"Used": [
- "urn:98a3c2dc-d375-4d4b-b976-391124a62240",
- "urn:b627d50b-31e2-462e-b4f6-a5e381e2a660"
+ "bids::TT_N27+tlrc",
+ "bids::sub-01_T1w_ns+orig"
]
},
{
- "@id": "urn:3cd9afa2-db8f-4e97-8362-708061f8f699",
+ "@id": "urn:catmatve-J2zFwWGS",
"Label": "cat_matvec",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D",
"Parameters": {},
"Used": [
- "urn:cd61fdbd-13e5-4d2a-a477-0490ac58a3e6"
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:63a082a5-9059-43ac-834b-1a3d36baad81",
+ "@id": "urn:3dvolreg-Cq6T5XNy",
"Label": "3dvolreg",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig",
"Parameters": {},
"Used": [
- "urn:ef7cd13f-2235-415b-bd96-d61aa27414a2"
+ "bids::pb01.$subj.r$run.tshift+orig"
]
},
{
- "@id": "urn:38bb386d-c8e8-4b21-ba22-678b7a5e04c3",
+ "@id": "urn:3dcalc-0Ja1pte4",
"Label": "3dcalc",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1",
"Parameters": {},
"Used": [
- "urn:ef7cd13f-2235-415b-bd96-d61aa27414a2"
+ "bids::pb01.$subj.r$run.tshift+orig"
]
},
{
- "@id": "urn:37437965-1cad-4a6c-b415-8573d8824906",
+ "@id": "urn:catmatve-SKhupqPf",
"Label": "cat_matvec",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D",
"Parameters": {},
"Used": [
- "urn:cd61fdbd-13e5-4d2a-a477-0490ac58a3e6"
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:59c02573-9cbb-4549-8392-40ca73f87032",
+ "@id": "urn:3dalline-LTjxwict",
"Label": "3dAllineate",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run",
"Parameters": {},
"Used": [
- "urn:2ecd0a9e-1a8d-4673-9477-d000fa050f71",
- "urn:b5fb0d63-fa1e-4ec0-9133-db27e5aebc66",
- "urn:ef7cd13f-2235-415b-bd96-d61aa27414a2"
+ "bids::mat.r$run.warp.aff12.1D",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:e6ac63ff-c9dc-4262-a728-c238e58fe52a",
+ "@id": "urn:3dalline-aadbI5yi",
"Label": "3dAllineate",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run",
"Parameters": {},
"Used": [
- "urn:2ecd0a9e-1a8d-4673-9477-d000fa050f71",
- "urn:6a0124c1-72b2-49ce-9672-d4fbcca25c05",
- "urn:b5fb0d63-fa1e-4ec0-9133-db27e5aebc66"
+ "bids::mat.r$run.warp.aff12.1D",
+ "bids::rm.epi.all1+orig",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:eb442016-d304-41a3-bc43-10b5afeb249c",
+ "@id": "urn:3dtstat-y5G8BFbB",
"Label": "3dTstat",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc",
"Parameters": {},
"Used": [
- "urn:65996a2a-c60d-4c82-a7e9-1d7931c8a96c"
+ "bids::rm.epi.1.r$run+tlrc"
]
},
{
- "@id": "urn:09ccab5e-c297-47cc-840d-dcb4a219870b",
+ "@id": "urn:cat-253bV9ng",
"Label": "cat",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "cat dfile.r*.1D > dfile_rall.1D",
"Parameters": {},
"Used": [
- "urn:79a192b9-7d24-4e19-a5f7-1f2e64eae12d"
+ "bids::dfile.r*.1D"
]
},
{
- "@id": "urn:e03b05f2-b598-43fb-ba90-7bbfe1cd0208",
+ "@id": "urn:3dcopy-XEa7vJeI",
"Label": "3dcopy",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents",
"Parameters": {},
"Used": [
- "urn:33d5974c-41b2-41e1-b5e4-2f2a63eb1f54"
+ "bids::rm.epi.min.r01+tlrc"
]
},
{
- "@id": "urn:caa87586-13ee-4b3b-81b8-2e25b51c127c",
+ "@id": "urn:3dcalc-1YvbY0PC",
"Label": "3dcalc",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg",
"Parameters": {},
"Used": [
- "urn:c8ad3c2e-e845-4477-970f-bc294a486166",
- "urn:d90b8219-e948-4937-93da-b06c6674d1ee"
+ "bids::mask_epi_extents+tlrc",
+ "bids::rm.epi.nomask.r$run+tlrc"
]
},
{
- "@id": "urn:cf1cc1cc-9dc5-4b44-8bb2-dac4fb80d8f6",
+ "@id": "urn:3dcopy-dCftIe4a",
"Label": "3dcopy",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj",
"Parameters": {},
"Used": [
- "urn:2ecd0a9e-1a8d-4673-9477-d000fa050f71"
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:232aa214-57d4-4533-bcb4-59ec9c7b9d91",
+ "@id": "urn:3dalline-UosLclnS",
"Label": "3dAllineate",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped",
"Parameters": {},
"Used": [
- "urn:cd713e3c-37f1-4250-99e4-76f14e82c809"
+ "bids::anat_final.$subj+tlrc",
+ "bids::warp.anat.Xat.1D"
]
},
{
- "@id": "urn:81c04b1a-a3ec-4d42-b1f6-42b18c514646",
+ "@id": "urn:3dmerge-Ne0kAscL",
"Label": "3dmerge",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc",
"Parameters": {},
"Used": [
- "urn:85587900-6bdf-405e-bf4e-462e65816619",
- "urn:ad109349-69fe-4a60-b465-4d80062a78f7"
+ "bids::pb02.$subj.r$run.volreg+tlrc",
+ "bids::pb03.$subj.r$run.blur"
]
},
{
- "@id": "urn:6a032884-a9c4-43cd-a82b-1fac1bb4e69d",
+ "@id": "urn:3dautoma-s2OEFl98",
"Label": "3dAutomask",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:de610101-9dcf-45d2-8497-300a87b7fab3"
+ "bids::pb03.$subj.r$run.blur+tlrc"
]
},
{
- "@id": "urn:09594336-1e9c-446b-b3be-b49612843b38",
+ "@id": "urn:3dmaskto-iHTEgBWH",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:10dca6cc-020e-4ffe-949a-2c2e6fb21676",
+ "@id": "urn:3dresamp-pocDgAWQ",
"Label": "3dresample",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat",
"Parameters": {},
"Used": [
- "urn:2ecd0a9e-1a8d-4673-9477-d000fa050f71",
- "urn:ccbfde72-5a96-4917-8207-ce3636ecd805"
+ "bids::full_mask.$subj+tlrc",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:69bd8371-4d91-4695-8a53-d23d8bb89fbb",
+ "@id": "urn:3dmaskto-vqzd0AtF",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj",
"Parameters": {},
"Used": [
- "urn:62df8828-cf33-4091-8518-365ab8ca3ab6"
+ "bids::rm.resam.anat+tlrc"
]
},
{
- "@id": "urn:23b28468-d90f-44eb-8840-5d8d7352eb13",
+ "@id": "urn:3dabover-1xpPMyYj",
"Label": "3dABoverlap",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt",
"Parameters": {},
"Used": [
- "urn:a4a63ed1-9f8f-4ec9-aeb1-694ffee15022",
- "urn:f324d88e-8045-4f3c-a171-892fdf42d03f"
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee"
]
},
{
- "@id": "urn:75c052c3-ec3a-429d-8e8a-0f96d49e1947",
+ "@id": "urn:3ddot-vG3Ho8HD",
"Label": "3ddot",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt",
"Parameters": {},
"Used": [
- "urn:a4a63ed1-9f8f-4ec9-aeb1-694ffee15022",
- "urn:f324d88e-8045-4f3c-a171-892fdf42d03f"
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee"
]
},
{
- "@id": "urn:1359d5fa-6bbf-4b9c-90fe-d70df32b0c40",
+ "@id": "urn:3dresamp-ZykKjp5v",
"Label": "3dresample",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/cmaumet/Softs/external/AFNI/macosx_10.7_Intel_64/TT_N27+tlrc",
"Parameters": {},
"Used": [
- "urn:ccbfde72-5a96-4917-8207-ce3636ecd805",
- "urn:d6832605-5fa6-4561-a827-ed86a4904dc5"
+ "bids::/Users/cmaumet/Softs/external/AFNI/macosx_10.7_Intel_64/TT_N27+tlrc",
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:5bf68f22-01ae-4964-a4f6-61566ca7444a",
+ "@id": "urn:3dmaskto-zk5klqdp",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group",
"Parameters": {},
"Used": [
- "urn:708f863a-df71-4a1d-94b8-0fb25aa20102"
+ "bids::rm.resam.group+tlrc"
]
},
{
- "@id": "urn:e5e4090a-a4ea-4043-b74f-f7256d572210",
+ "@id": "urn:3dtstat-wkDlzccF",
"Label": "3dTstat",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:de610101-9dcf-45d2-8497-300a87b7fab3"
+ "bids::pb03.$subj.r$run.blur+tlrc"
]
},
{
- "@id": "urn:aac3fd58-c3b6-494d-b664-6601b5ab0704",
+ "@id": "urn:3dcalc-ND3i7gG2",
"Label": "3dcalc",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale",
"Parameters": {},
"Used": [
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- "urn:d90b8219-e948-4937-93da-b06c6674d1ee",
- "urn:de610101-9dcf-45d2-8497-300a87b7fab3"
+ "bids::mask_epi_extents+tlrc",
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::rm.mean_r$run+tlrc"
]
},
{
- "@id": "urn:8e9dd447-40ed-4518-b363-7b3ec7685fae",
+ "@id": "urn:1dtoolpy-jmVZrg5v",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D",
"Parameters": {},
"Used": [
- "urn:09db061b-af1a-4075-8483-02a9dae5a07f"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:79016ba0-b32f-4f71-b679-fd2caaa2e63d",
+ "@id": "urn:1dtoolpy-WpZBMKSn",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D",
"Parameters": {},
"Used": [
- "urn:09db061b-af1a-4075-8483-02a9dae5a07f"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:079d7cac-4058-4041-9cf2-90593a76d661",
+ "@id": "urn:1dtoolpy-qyqyePOj",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}",
"Parameters": {},
"Used": [
- "urn:09db061b-af1a-4075-8483-02a9dae5a07f"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:c92087a6-3795-4d7f-bf8d-e88741c51954",
+ "@id": "urn:3ddeconv-lGWPUoyd",
"Label": "3dDeconvolve",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'SPMG1(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj",
"Parameters": {},
"Used": [
- "urn:9b4cae5d-4de4-4e98-ad24-dc42a0b9e38c"
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD"
]
},
{
- "@id": "urn:02bf0272-90eb-449e-b7c2-12a1c3be169e",
+ "@id": "urn:1dtoolpy-7JKuHRGb",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt",
"Parameters": {},
"Used": [
- "urn:a991adb4-ce07-49d7-8b9e-f2cd479bb698"
+ "bids::X.xmat.1D"
]
},
{
- "@id": "urn:6f4cf849-a7eb-4c81-970f-47a667c23b32",
+ "@id": "urn:3dtcat-VE6isJJF",
"Label": "3dTcat",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD",
"Parameters": {},
"Used": [
- "urn:9b4cae5d-4de4-4e98-ad24-dc42a0b9e38c"
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD"
]
},
{
- "@id": "urn:23a8c607-74ff-4ab1-998e-4cc2c2d228aa",
+ "@id": "urn:3dtstat-j6wPnIPn",
"Label": "3dTstat",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:8686801c-6354-4d39-80f7-52a85f1e1b00"
+ "bids::all_runs.$subj+tlrc%22[$ktrs]%22"
]
},
{
- "@id": "urn:718d8d0d-3d99-4491-a744-63bba1e72fa3",
+ "@id": "urn:3dtstat-sL2ktdxz",
"Label": "3dTstat",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:f28f2fa6-6cb8-4300-9866-8d4918e9b493"
+ "bids::errts.$%7Bsubj%7D+tlrc%22[$ktrs]%22"
]
},
{
- "@id": "urn:5eb19834-e313-4f3e-9e36-ada7e9e336ce",
+ "@id": "urn:3dcalc-Mt6kd9m5",
"Label": "3dcalc",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj",
"Parameters": {},
"Used": [
- "urn:5d074665-77df-4364-9e45-0fc22694215c",
- "urn:6add6bab-95e0-411c-be61-24f213edbb8c",
- "urn:ccbfde72-5a96-4917-8207-ce3636ecd805"
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.noise.all+tlrc",
+ "bids::rm.signal.all+tlrc"
]
},
{
- "@id": "urn:824606da-683f-4db1-8310-2850ded25d2f",
+ "@id": "urn:3dtnorm-5j01dczD",
"Label": "3dTnorm",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc",
"Parameters": {},
"Used": [
- "urn:7d46adc6-f120-4f44-8c70-ad3b8eaa5890"
+ "bids::errts.$%7Bsubj%7D+tlrc"
]
},
{
- "@id": "urn:f0a4f640-ad91-4683-ab30-e64c753264b1",
+ "@id": "urn:3dmaskav-oAcYVWNX",
"Label": "3dmaskave",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D",
"Parameters": {},
- "Used": []
+ "Used": [
+ "bids::full_mask.$subj+tlrc"
+ ]
},
{
- "@id": "urn:e90963c7-4df4-4e92-90a6-11df69e7316b",
+ "@id": "urn:3dtstat-aobd0oPt",
"Label": "3dTstat",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D",
"Parameters": {},
"Used": [
- "urn:c7532fdd-ac39-43ff-acdd-62f316b3f815"
+ "bids::out.gcor.1D"
]
},
{
- "@id": "urn:ab15cd3f-1b9d-4006-9c10-7c7816794d53",
+ "@id": "urn:3dcalc-RnanHX9O",
"Label": "3dcalc",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP",
"Parameters": {},
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- "urn:7889534a-66ae-4929-a22a-f26301659043",
- "urn:98d2956c-0306-4d9c-98a1-8d3d8cce396d"
+ "bids::gmean.errts.unit.1D",
+ "bids::rm.errts.unit+tlrc"
]
},
{
- "@id": "urn:e917b63e-a583-43d1-b0a5-4b96417917d5",
+ "@id": "urn:3dtstat-qIVnovdP",
"Label": "3dTstat",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc",
"Parameters": {},
"Used": [
- "urn:4bd66238-a389-4bff-9a22-dfff5c122f77"
+ "bids::rm.DP+tlrc"
]
},
{
- "@id": "urn:703a45c1-fcbe-4d35-adda-d89aca9c8e21",
+ "@id": "urn:1dcat-YMqDTdmD",
"Label": "1dcat",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D",
"Parameters": {},
"Used": [
- "urn:f81c36df-64ce-49ff-b928-c7ddf0b4c8c3"
+ "bids::X.nocensor.xmat.1D'[3]'"
]
},
{
- "@id": "urn:125ed038-94b2-44ff-b08a-6b20a34563d1",
+ "@id": "urn:1dcat-wxWuGyPa",
"Label": "1dcat",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D",
"Parameters": {},
"Used": [
- "urn:7f65789c-9a04-408a-b158-bb43c2962ac1"
+ "bids::X.nocensor.xmat.1D'[4]'"
]
},
{
- "@id": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "@id": "urn:3dtstat-g09qekV2",
"Label": "3dTstat",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"",
"Parameters": {},
"Used": [
- "urn:e2361583-12d5-4b48-87ee-8480606b9e53"
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:4082dae8-2701-4657-b4b2-bffea6e63154",
+ "@id": "urn:1dcat-rVexAwDh",
"Label": "1dcat",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D",
"Parameters": {},
"Used": [
- "urn:e2361583-12d5-4b48-87ee-8480606b9e53"
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:ba3dd657-906b-41cf-a5f5-83133c309ce7",
+ "@id": "urn:3dfwhmx-HbowdNMj",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D",
"Parameters": {},
"Used": [
- "urn:ccbfde72-5a96-4917-8207-ce3636ecd805"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:b78facde-a697-4422-ae67-e24ff6504011",
+ "@id": "urn:3dfwhmx-AgcWE97u",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D",
"Parameters": {},
"Used": [
- "urn:ccbfde72-5a96-4917-8207-ce3636ecd805"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:e9119f46-4f9f-4cbd-8fb9-12dd2ad9409c",
+ "@id": "urn:3dclusts-xWsyKiqb",
"Label": "3dClustSim",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim",
"Parameters": {},
"Used": [
- "urn:ccbfde72-5a96-4917-8207-ce3636ecd805"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:e1f9ff86-4ee6-48df-8546-1158ea752adb",
+ "@id": "urn:genepire-JDKTjSo7",
"Label": "gen_epi_review.py",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD",
"Parameters": {},
"Used": [
- "urn:a0096f78-1a37-4831-9297-028f78e5f5bb"
+ "bids::pb00.$subj.r*.tcat+orig.HEAD"
]
},
{
- "@id": "urn:53178dbd-3483-4bbf-8398-98782bf53c73",
+ "@id": "urn:genssrev-bLXWWzXw",
"Label": "gen_ss_review_scripts.py",
- "AssociatedWith": "urn:e9bde71d-f34d-46ad-bc01-2b70f5087e08",
+ "AssociatedWith": "urn:afni-LuUPJG0l",
"Command": "gen_ss_review_scripts.py -mot_limit 0.3 -exit0",
"Parameters": {
"-mot_limit": "0.3",
@@ -586,22 +589,22 @@
],
"Entities": [
{
- "@id": "urn:634b8ef5-df07-4afc-8509-66a3973abbeb",
+ "@id": "bids::$output_dir",
"Label": "$output_dir",
"AtLocation": "$output_dir",
- "GeneratedBy": "urn:3abf1821-674f-43d7-bf35-eea0528ecc38",
+ "GeneratedBy": "urn:makedire-cRfuDYOz",
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"sha256": "9fa4c635e6533ddf2fed54295920052818d948c3ffe97bc753bd7336b453f8cb"
}
},
{
- "@id": "urn:105801bb-7b35-42d6-9ff2-4966a82149c5",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:083e7a48-1f1e-4a25-8049-d4b80641baae"
+ "GeneratedBy": "urn:makedire-EJ8DYuNJ"
},
{
- "@id": "urn:1ae8f36b-01cf-4052-ac85-d10dc0aa6524",
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"Label": "tone_counting_onset_times.txt",
"AtLocation": "/Users/cmaumet/Projects/Data_sharing/dev/nidmresults-examples/afni_voxelwise_p0001/subject_results/group.DS0011/subj.sub_001/sub_001.results/stimuli/tone_counting_onset_times.txt",
"digest": {
@@ -609,7 +612,7 @@
}
},
{
- "@id": "urn:45579f06-fc67-4a72-a435-4a2bde6046c2",
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"Label": "tone_counting_probe_duration.txt",
"AtLocation": "/Users/cmaumet/Projects/Data_sharing/dev/nidmresults-examples/afni_voxelwise_p0001/subject_results/group.DS0011/subj.sub_001/sub_001.results/stimuli/tone_counting_probe_duration.txt",
"digest": {
@@ -617,13 +620,13 @@
}
},
{
- "@id": "urn:d6be4df1-d211-401a-8876-ee0cf6e05ac3",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:dc28ed67-83ae-483a-9eeb-de245979553a"
+ "GeneratedBy": "urn:cp-z68XKlh0"
},
{
- "@id": "urn:d1e447a7-bec3-421c-b7c3-9138d92c7206",
+ "@id": "bids::/Users/cmaumet/Projects/Data_sharing/dev/nidmresults-examples/raw/ds011/sub-01/anat/sub-01_T1w.nii.gz",
"Label": "sub-01_T1w.nii.gz",
"AtLocation": "/Users/cmaumet/Projects/Data_sharing/dev/nidmresults-examples/raw/ds011/sub-01/anat/sub-01_T1w.nii.gz",
"digest": {
@@ -631,13 +634,13 @@
}
},
{
- "@id": "urn:b740cb2c-c571-42cb-92e6-030da5016c8f",
+ "@id": "bids::$output_dir/sub-01_T1w",
"Label": "sub-01_T1w",
"AtLocation": "$output_dir/sub-01_T1w",
- "GeneratedBy": "urn:bf51fb88-d326-4f30-be43-ab454615eef4"
+ "GeneratedBy": "urn:3dcopy-j7QzAy9Y"
},
{
- "@id": "urn:33f25266-483a-4f84-b431-94d1e059dbfa",
+ "@id": "bids::/Users/cmaumet/Projects/Data_sharing/dev/nidmresults-examples/raw/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Label": "sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "/Users/cmaumet/Projects/Data_sharing/dev/nidmresults-examples/raw/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"digest": {
@@ -645,13 +648,13 @@
}
},
{
- "@id": "urn:ae25f772-385e-4722-90fd-3d6bca543569",
+ "@id": "bids::$output_dir/pb00.$subj.r01.tcat",
"Label": "pb00.$subj.r01.tcat",
"AtLocation": "$output_dir/pb00.$subj.r01.tcat",
- "GeneratedBy": "urn:b6722269-67c1-45e2-a55d-94e6e075c7f4"
+ "GeneratedBy": "urn:3dtcat-dI1c6m9j"
},
{
- "@id": "urn:1f888d36-8dc1-4dd9-aed3-6307c376c266",
+ "@id": "bids::pb00.$subj.r$run.tcat+orig",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -659,16 +662,16 @@
}
},
{
- "@id": "urn:2a713eec-eb1a-4ace-9328-7e0d28524daa",
+ "@id": "bids::outcount.r$run.1D",
"Label": "outcount.r$run.1D",
"AtLocation": "outcount.r$run.1D",
- "GeneratedBy": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
+ "GeneratedBy": "urn:3dtoutco-wsZI1sDP",
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}
},
{
- "@id": "urn:a46ad4e6-5621-4686-b06f-2f4c85f6fded",
+ "@id": "bids::outcount.r*.1D",
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@@ -676,25 +679,25 @@
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@@ -702,7 +705,7 @@
}
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{
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@@ -710,16 +713,16 @@
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@@ -727,7 +730,7 @@
}
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@@ -735,7 +738,7 @@
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@@ -743,16 +746,16 @@
}
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{
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@@ -760,34 +763,34 @@
}
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- "GeneratedBy": "urn:63a082a5-9059-43ac-834b-1a3d36baad81",
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{
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"AtLocation": "rm.epi.all1",
- "GeneratedBy": "urn:38bb386d-c8e8-4b21-ba22-678b7a5e04c3",
+ "GeneratedBy": "urn:3dcalc-0Ja1pte4",
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{
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"AtLocation": "mat.r$run.warp.aff12.1D",
- "GeneratedBy": "urn:37437965-1cad-4a6c-b415-8573d8824906",
+ "GeneratedBy": "urn:catmatve-SKhupqPf",
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@@ -795,16 +798,16 @@
}
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{
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- "GeneratedBy": "urn:59c02573-9cbb-4549-8392-40ca73f87032",
+ "GeneratedBy": "urn:3dalline-LTjxwict",
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@@ -812,16 +815,16 @@
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@@ -829,16 +832,16 @@
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@@ -846,16 +849,16 @@
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{
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@@ -863,16 +866,16 @@
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{
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@@ -880,7 +883,7 @@
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{
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@@ -888,34 +891,42 @@
}
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"AtLocation": "pb02.$subj.r$run.volreg",
- "GeneratedBy": "urn:caa87586-13ee-4b3b-81b8-2e25b51c127c",
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{
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@@ -923,7 +934,7 @@
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@@ -931,7 +942,7 @@
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@@ -939,25 +950,25 @@
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@@ -965,16 +976,16 @@
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{
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@@ -982,16 +993,16 @@
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@@ -999,7 +1010,7 @@
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{
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@@ -1007,7 +1018,7 @@
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{
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@@ -1015,16 +1026,16 @@
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- "GeneratedBy": "urn:1359d5fa-6bbf-4b9c-90fe-d70df32b0c40",
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@@ -1032,25 +1043,25 @@
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{
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@@ -1058,34 +1069,34 @@
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{
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{
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{
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@@ -1093,25 +1104,25 @@
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{
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+ "@id": "bids::X.xmat.1D",
"Label": "X.xmat.1D",
"AtLocation": "X.xmat.1D",
- "GeneratedBy": "urn:c92087a6-3795-4d7f-bf8d-e88741c51954",
+ "GeneratedBy": "urn:3ddeconv-lGWPUoyd",
"digest": {
"sha256": "cdbd4f4edf6fa02a9d7fcf9a3e593893438e9279c9523fbb6993630a83ad5162"
}
},
{
- "@id": "urn:78569eec-8f25-476a-af06-a67ddfefd121",
+ "@id": "bids::all_runs.$subj",
"Label": "all_runs.$subj",
"AtLocation": "all_runs.$subj",
- "GeneratedBy": "urn:6f4cf849-a7eb-4c81-970f-47a667c23b32",
+ "GeneratedBy": "urn:3dtcat-VE6isJJF",
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"sha256": "bcf27fc2e339e751d0ea9bba931674c21fd9d434ff411330f4df55f872a8cc7e"
}
},
{
- "@id": "urn:8686801c-6354-4d39-80f7-52a85f1e1b00",
+ "@id": "bids::all_runs.$subj+tlrc%22[$ktrs]%22",
"Label": "all_runs.$subj",
"AtLocation": "all_runs.$subj+tlrc\"[$ktrs]\"",
"digest": {
@@ -1119,16 +1130,16 @@
}
},
{
- "@id": "urn:378d2b0f-09ba-4f38-b77d-549ea7a15246",
+ "@id": "bids::rm.signal.all",
"Label": "rm.signal.all",
"AtLocation": "rm.signal.all",
- "GeneratedBy": "urn:23a8c607-74ff-4ab1-998e-4cc2c2d228aa",
+ "GeneratedBy": "urn:3dtstat-j6wPnIPn",
"digest": {
"sha256": "bda68a16c0afd5e55d4d7415c8c959e61a9aad7898dd456b0f3bb597363dde31"
}
},
{
- "@id": "urn:f28f2fa6-6cb8-4300-9866-8d4918e9b493",
+ "@id": "bids::errts.$%7Bsubj%7D+tlrc%22[$ktrs]%22",
"Label": "errts.${subj}",
"AtLocation": "errts.${subj}+tlrc\"[$ktrs]\"",
"digest": {
@@ -1136,16 +1147,16 @@
}
},
{
- "@id": "urn:1732aee3-f835-45d5-9d6c-7b9bdbce72a5",
+ "@id": "bids::rm.noise.all",
"Label": "rm.noise.all",
"AtLocation": "rm.noise.all",
- "GeneratedBy": "urn:718d8d0d-3d99-4491-a744-63bba1e72fa3",
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"digest": {
"sha256": "431314eb75d086ce08373b3a374427969e89414c4a2d607e449c1f6485c547af"
}
},
{
- "@id": "urn:6add6bab-95e0-411c-be61-24f213edbb8c",
+ "@id": "bids::rm.signal.all+tlrc",
"Label": "rm.signal.all",
"AtLocation": "rm.signal.all+tlrc",
"digest": {
@@ -1153,7 +1164,7 @@
}
},
{
- "@id": "urn:5d074665-77df-4364-9e45-0fc22694215c",
+ "@id": "bids::rm.noise.all+tlrc",
"Label": "rm.noise.all",
"AtLocation": "rm.noise.all+tlrc",
"digest": {
@@ -1161,16 +1172,16 @@
}
},
{
- "@id": "urn:9f91de42-958b-4994-a2a1-cd5df69db358",
+ "@id": "bids::TSNR.$subj",
"Label": "TSNR.$subj",
"AtLocation": "TSNR.$subj",
- "GeneratedBy": "urn:5eb19834-e313-4f3e-9e36-ada7e9e336ce",
+ "GeneratedBy": "urn:3dcalc-Mt6kd9m5",
"digest": {
"sha256": "303f183145a1e295686c08335d3b70753777cf0fa0b3f9628cf8de5471359a00"
}
},
{
- "@id": "urn:7d46adc6-f120-4f44-8c70-ad3b8eaa5890",
+ "@id": "bids::errts.$%7Bsubj%7D+tlrc",
"Label": "errts.${subj}",
"AtLocation": "errts.${subj}+tlrc",
"digest": {
@@ -1178,25 +1189,25 @@
}
},
{
- "@id": "urn:b454e49b-12d9-4aff-94c3-3fd59398132c",
+ "@id": "bids::rm.errts.unit",
"Label": "rm.errts.unit",
"AtLocation": "rm.errts.unit",
- "GeneratedBy": "urn:824606da-683f-4db1-8310-2850ded25d2f",
+ "GeneratedBy": "urn:3dtnorm-5j01dczD",
"digest": {
"sha256": "03b570ad773a00f51ab7e6cdedfebdeca45f5356de0c25f9e3be44d7bf2c7151"
}
},
{
- "@id": "urn:98d2956c-0306-4d9c-98a1-8d3d8cce396d",
+ "@id": "bids::gmean.errts.unit.1D",
"Label": "gmean.errts.unit.1D",
"AtLocation": "gmean.errts.unit.1D",
- "GeneratedBy": "urn:f0a4f640-ad91-4683-ab30-e64c753264b1",
+ "GeneratedBy": "urn:3dmaskav-oAcYVWNX",
"digest": {
"sha256": "a35a66cce2e2d487762823c197ca1edc450a9887f46f125826b69c5021662f95"
}
},
{
- "@id": "urn:c7532fdd-ac39-43ff-acdd-62f316b3f815",
+ "@id": "bids::out.gcor.1D",
"Label": "out.gcor.1D",
"AtLocation": "out.gcor.1D",
"digest": {
@@ -1204,16 +1215,16 @@
}
},
{
- "@id": "urn:a30e7f05-30c9-4a93-831f-178beca06da5",
+ "@id": "urn:uuid:3f57ec61-e1a1-43d0-8fb9-75d582643f56",
"Label": "-",
"AtLocation": "-",
- "GeneratedBy": "urn:e90963c7-4df4-4e92-90a6-11df69e7316b",
+ "GeneratedBy": "urn:3dtstat-aobd0oPt",
"digest": {
"sha256": "dac304c9f20899ca1ef5aa403e565345fd0ff4ed80c35f82007c9b03a68292b3"
}
},
{
- "@id": "urn:7889534a-66ae-4929-a22a-f26301659043",
+ "@id": "bids::rm.errts.unit+tlrc",
"Label": "rm.errts.unit",
"AtLocation": "rm.errts.unit+tlrc",
"digest": {
@@ -1221,16 +1232,16 @@
}
},
{
- "@id": "urn:57e13588-8328-49bb-b343-c3fd2ba12c4e",
+ "@id": "bids::rm.DP",
"Label": "rm.DP",
"AtLocation": "rm.DP",
- "GeneratedBy": "urn:ab15cd3f-1b9d-4006-9c10-7c7816794d53",
+ "GeneratedBy": "urn:3dcalc-RnanHX9O",
"digest": {
"sha256": "06a0bfbc609c1a06ecf93c479a3288d2911c7f5f3e93cf49c5d26f721c2035ed"
}
},
{
- "@id": "urn:4bd66238-a389-4bff-9a22-dfff5c122f77",
+ "@id": "bids::rm.DP+tlrc",
"Label": "rm.DP",
"AtLocation": "rm.DP+tlrc",
"digest": {
@@ -1238,16 +1249,16 @@
}
},
{
- "@id": "urn:96abea8f-96a7-4c19-9aec-d37b19881a27",
+ "@id": "bids::corr_brain",
"Label": "corr_brain",
"AtLocation": "corr_brain",
- "GeneratedBy": "urn:e917b63e-a583-43d1-b0a5-4b96417917d5",
+ "GeneratedBy": "urn:3dtstat-qIVnovdP",
"digest": {
"sha256": "74e3aeae0da338b871ab5dc9e8859a4e81fcf1b3c0042cd22fe337eb7baf5eae"
}
},
{
- "@id": "urn:f81c36df-64ce-49ff-b928-c7ddf0b4c8c3",
+ "@id": "bids::X.nocensor.xmat.1D'[3]'",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D'[3]'",
"digest": {
@@ -1255,16 +1266,16 @@
}
},
{
- "@id": "urn:44af0e0a-f673-4ba5-881b-84df514ff7f1",
+ "@id": "bids::ideal_tone_counting.1D",
"Label": "ideal_tone_counting.1D",
"AtLocation": "ideal_tone_counting.1D",
- "GeneratedBy": "urn:703a45c1-fcbe-4d35-adda-d89aca9c8e21",
+ "GeneratedBy": "urn:1dcat-YMqDTdmD",
"digest": {
"sha256": "9bb1cabac5ce7ca19dffa5cd6336a9bf82d362fea2ce9341978406e421b5333c"
}
},
{
- "@id": "urn:7f65789c-9a04-408a-b158-bb43c2962ac1",
+ "@id": "bids::X.nocensor.xmat.1D'[4]'",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D'[4]'",
"digest": {
@@ -1272,16 +1283,16 @@
}
},
{
- "@id": "urn:45354d21-9918-4d74-ab12-ab46e2456b13",
+ "@id": "bids::ideal_probe.1D",
"Label": "ideal_probe.1D",
"AtLocation": "ideal_probe.1D",
- "GeneratedBy": "urn:125ed038-94b2-44ff-b08a-6b20a34563d1",
+ "GeneratedBy": "urn:1dcat-wxWuGyPa",
"digest": {
"sha256": "705d93afa8b6ded9f4f572db3f967b54e9906942669af51dd8287a9863bb4288"
}
},
{
- "@id": "urn:e2361583-12d5-4b48-87ee-8480606b9e53",
+ "@id": "bids::X.nocensor.xmat.1D%22[$reg_cols]%22",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D\"[$reg_cols]\"",
"digest": {
@@ -1289,52 +1300,52 @@
}
},
{
- "@id": "urn:ee75043c-c987-4b82-a8bd-a4ddd3561414",
+ "@id": "bids::sum_ideal.1D",
"Label": "sum_ideal.1D",
"AtLocation": "sum_ideal.1D",
- "GeneratedBy": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "GeneratedBy": "urn:3dtstat-g09qekV2",
"digest": {
"sha256": "b2dccadcd84b2d26ec9685c4d1846baf2f11b867f31c36a08748d1c85467b01a"
}
},
{
- "@id": "urn:0c8c8fbb-e360-4d28-b747-c286b78bef9a",
+ "@id": "bids::X.stim.xmat.1D",
"Label": "X.stim.xmat.1D",
"AtLocation": "X.stim.xmat.1D",
- "GeneratedBy": "urn:4082dae8-2701-4657-b4b2-bffea6e63154",
+ "GeneratedBy": "urn:1dcat-rVexAwDh",
"digest": {
"sha256": "7c61b2f4bbb9eb0cecb19f81faa3a79b94d547b7fb4087ed18e368619e0004e6"
}
},
{
- "@id": "urn:d644d81d-ded2-4c68-8bea-533046815e23",
+ "@id": "bids::blur.epits.1D",
"Label": "blur.epits.1D",
"AtLocation": "blur.epits.1D",
- "GeneratedBy": "urn:ba3dd657-906b-41cf-a5f5-83133c309ce7",
+ "GeneratedBy": "urn:3dfwhmx-HbowdNMj",
"digest": {
"sha256": "623e70a42214e56babc1f1dca156e0b11ba09865dbd6ca9549d54ca2fc601515"
}
},
{
- "@id": "urn:6b8a71c3-0cda-469b-aafd-ac593f5cc414",
+ "@id": "bids::blur.errts.1D",
"Label": "blur.errts.1D",
"AtLocation": "blur.errts.1D",
- "GeneratedBy": "urn:b78facde-a697-4422-ae67-e24ff6504011",
+ "GeneratedBy": "urn:3dfwhmx-AgcWE97u",
"digest": {
"sha256": "73969700079b5d3275536ac7eaf0e17571d7e74ec49553b6940f90d5718fc800"
}
},
{
- "@id": "urn:2cb9bdac-3da5-4505-a8d5-4858a059c59d",
+ "@id": "bids::ClustSim",
"Label": "ClustSim",
"AtLocation": "ClustSim",
- "GeneratedBy": "urn:e9119f46-4f9f-4cbd-8fb9-12dd2ad9409c",
+ "GeneratedBy": "urn:3dclusts-xWsyKiqb",
"digest": {
"sha256": "2e0cdba2c91902ba12d742a39cb20df66cfd705ba8de767fbf68aae8eb65c6f0"
}
},
{
- "@id": "urn:a0096f78-1a37-4831-9297-028f78e5f5bb",
+ "@id": "bids::pb00.$subj.r*.tcat+orig.HEAD",
"Label": "pb00.$subj.r*.tcat",
"AtLocation": "pb00.$subj.r*.tcat+orig.HEAD",
"digest": {
@@ -1342,10 +1353,10 @@
}
},
{
- "@id": "urn:eb7102a3-b371-47c7-84a7-6f3f9fc24fa6",
+ "@id": "bids::-exit0",
"Label": "-exit0",
"AtLocation": "-exit0",
- "GeneratedBy": "urn:53178dbd-3483-4bbf-8398-98782bf53c73",
+ "GeneratedBy": "urn:genssrev-bLXWWzXw",
"digest": {
"sha256": "871a4d3513ed2924cbb10c1c15a196eac4a46a05bdcc248e3bcdb23327b3ad90"
}
diff --git a/examples/from_parsers/afni/afni_hrf_gammadiff_proc.png b/examples/from_parsers/afni/afni_hrf_gammadiff_proc.png
index 2307c5e17..8c75b8903 100644
Binary files a/examples/from_parsers/afni/afni_hrf_gammadiff_proc.png and b/examples/from_parsers/afni/afni_hrf_gammadiff_proc.png differ
diff --git a/examples/from_parsers/afni/afni_hrf_gammadiff_proc_block.jsonld b/examples/from_parsers/afni/afni_hrf_gammadiff_proc_block.jsonld
index 548dfc2bb..f9025140a 100644
--- a/examples/from_parsers/afni/afni_hrf_gammadiff_proc_block.jsonld
+++ b/examples/from_parsers/afni/afni_hrf_gammadiff_proc_block.jsonld
@@ -4,187 +4,189 @@
"Records": {
"Software": [
{
- "@id": "urn:96e62f9d-b1bc-4d08-8a56-80c4267c1dde",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:afni-ams3QlzR",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
- "Version": "afni24"
+ "Version": "afni24",
+ "AltIdentifier": "RRID:SCR_005927"
}
],
"Activities": [
{
- "@id": "urn:1f4c0713-f660-426f-90a7-8a053bb099f6",
+ "@id": "urn:autobloc-5KgJTiu3",
"Label": "auto block: setup",
- "AssociatedWith": "urn:96e62f9d-b1bc-4d08-8a56-80c4267c1dde",
+ "AssociatedWith": "urn:afni-ams3QlzR",
"Command": "mkdir $output_dir; mkdir $output_dir/stimuli; cp /Users/cmaumet/Projects/Data_sharing/dev/nidmresults-examples/afni_voxelwise_p0001/subject_results/group.DS0011/subj.sub_001/sub_001.results/stimuli/tone_counting_onset_times.txt /Users/cmaumet/Projects/Data_sharing/dev/nidmresults-examples/afni_voxelwise_p0001/subject_results/group.DS0011/subj.sub_001/sub_001.results/stimuli/tone_counting_probe_duration.txt $output_dir/stimuli; 3dcopy /Users/cmaumet/Projects/Data_sharing/dev/nidmresults-examples/raw/ds011/sub-01/anat/sub-01_T1w.nii.gz $output_dir/sub-01_T1w; ",
"Used": [
- "urn:1297dbd7-23fe-4261-a4b7-62ac5775ae55",
- "urn:b9a5473a-60c6-4714-958c-a8d3e58fab95",
- "urn:2a0f2321-a75e-4613-b39e-0462b3551323"
+ "bids::/Users/cmaumet/Projects/Data_sharing/dev/nidmresults-examples/afni_voxelwise_p0001/subject_results/group.DS0011/subj.sub_001/sub_001.results/stimuli/tone_counting_onset_times.txt",
+ "bids::/Users/cmaumet/Projects/Data_sharing/dev/nidmresults-examples/afni_voxelwise_p0001/subject_results/group.DS0011/subj.sub_001/sub_001.results/stimuli/tone_counting_probe_duration.txt",
+ "bids::/Users/cmaumet/Projects/Data_sharing/dev/nidmresults-examples/raw/ds011/sub-01/anat/sub-01_T1w.nii.gz"
]
},
{
- "@id": "urn:5b5798a2-a216-41fb-8cb0-ef650c5c95fe",
+ "@id": "urn:autobloc-VH75Af2k",
"Label": "auto block: tcat",
- "AssociatedWith": "urn:96e62f9d-b1bc-4d08-8a56-80c4267c1dde",
+ "AssociatedWith": "urn:afni-ams3QlzR",
"Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat /Users/cmaumet/Projects/Data_sharing/dev/nidmresults-examples/raw/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ",
"Used": [
- "urn:9fd8ffd2-1776-4af3-a24c-acdeaff9cf12"
+ "bids::/Users/cmaumet/Projects/Data_sharing/dev/nidmresults-examples/raw/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'[0..$]'"
]
},
{
- "@id": "urn:5532669b-e4be-439f-ad6c-7eaec203e36d",
+ "@id": "urn:autobloc-Dev6mf7h",
"Label": "auto block: outcount",
- "AssociatedWith": "urn:96e62f9d-b1bc-4d08-8a56-80c4267c1dde",
+ "AssociatedWith": "urn:afni-ams3QlzR",
"Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ",
"Used": [
- "urn:6134bd82-c6ba-4031-a0f6-1da02585d5eb",
- "urn:89fee5f0-1524-467f-8e87-4af5ee8abd9f"
+ "bids::pb00.$subj.r$run.tcat+orig",
+ "bids::outcount.r*.1D"
]
},
{
- "@id": "urn:4601a4cd-a630-418f-beb8-4815818cd73a",
+ "@id": "urn:tshift-7nObZinu",
"Label": "tshift",
- "AssociatedWith": "urn:96e62f9d-b1bc-4d08-8a56-80c4267c1dde",
+ "AssociatedWith": "urn:afni-ams3QlzR",
"Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ",
"Used": [
- "urn:6134bd82-c6ba-4031-a0f6-1da02585d5eb"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:aec43d8a-1acf-483e-839f-a6b9d0413d1e",
+ "@id": "urn:align-8x9H6ddn",
"Label": "align",
- "AssociatedWith": "urn:96e62f9d-b1bc-4d08-8a56-80c4267c1dde",
+ "AssociatedWith": "urn:afni-ams3QlzR",
"Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ",
"Used": [
- "urn:ac338e03-8c6a-4d36-a540-1e90fe86db13",
- "urn:e0b55535-1ed2-485c-afc5-1a0f64f8d8fe"
+ "bids::pb01.$subj.r01.tshift+orig",
+ "bids::sub-01_T1w+orig"
]
},
{
- "@id": "urn:3bee4548-3d99-4d3b-8ecf-fe9fe26023a6",
+ "@id": "urn:tlrc-YlBDOp0O",
"Label": "tlrc",
- "AssociatedWith": "urn:96e62f9d-b1bc-4d08-8a56-80c4267c1dde",
+ "AssociatedWith": "urn:afni-ams3QlzR",
"Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ",
"Used": [
- "urn:2a2831db-7ec1-4ea8-9870-d9e7a2776e5b",
- "urn:815262c7-f8be-4a52-a3f7-b7110b0a1f1a",
- "urn:83b1c647-25a9-4c03-897b-14beedad3f17"
+ "bids::TT_N27+tlrc",
+ "bids::sub-01_T1w_ns+orig",
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:c8bd47b3-a87e-4881-adc1-63175661aaa7",
+ "@id": "urn:volreg-kb7kw99N",
"Label": "volreg",
- "AssociatedWith": "urn:96e62f9d-b1bc-4d08-8a56-80c4267c1dde",
+ "AssociatedWith": "urn:afni-ams3QlzR",
"Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig; 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1; cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D; 3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run; 3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run; 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc; cat dfile.r*.1D > dfile_rall.1D; 3dcopy rm.epi.min.r01+tlrc mask_epi_extents; 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg; 3dcopy sub-01_T1w_ns+tlrc anat_final.$subj; 3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped; ",
"Used": [
- "urn:055baac7-d18b-486b-8f9e-4cf47f891f28",
- "urn:055baac7-d18b-486b-8f9e-4cf47f891f28",
- "urn:83b1c647-25a9-4c03-897b-14beedad3f17",
- "urn:055baac7-d18b-486b-8f9e-4cf47f891f28",
- "urn:db9ba97e-dc78-4984-ba0a-f5e433a02af3",
- "urn:0add8a2e-685b-4ffb-b51c-33fe56d30fa7",
- "urn:db9ba97e-dc78-4984-ba0a-f5e433a02af3",
- "urn:d8674169-2dfa-45af-ae52-683c72874335",
- "urn:235e03ab-4e6d-43fa-947c-18213c5b8159",
- "urn:590ba71a-c6d9-434e-a343-6f856119883b",
- "urn:719afeb9-a1ed-4c0c-9b64-4b8d6aa33a9d",
- "urn:9afa03eb-c567-4dc5-be4b-5e5535fc712c",
- "urn:db9ba97e-dc78-4984-ba0a-f5e433a02af3",
- "urn:3b79334f-2482-4ea7-94d4-6e6090623211"
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.epi.all1+orig",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.epi.1.r$run+tlrc",
+ "bids::dfile.r*.1D",
+ "bids::rm.epi.min.r01+tlrc",
+ "bids::mask_epi_extents+tlrc",
+ "bids::rm.epi.nomask.r$run+tlrc",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::anat_final.$subj+tlrc",
+ "bids::warp.anat.Xat.1D"
]
},
{
- "@id": "urn:c3f11886-2058-47ab-9ea0-93a32da106d8",
+ "@id": "urn:blur-g3K2TO8T",
"Label": "blur",
- "AssociatedWith": "urn:96e62f9d-b1bc-4d08-8a56-80c4267c1dde",
+ "AssociatedWith": "urn:afni-ams3QlzR",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc; ",
"Used": [
- "urn:70dbec60-b908-498d-826f-65d7633bb261",
- "urn:b834a4fc-bc36-42fa-a712-3100e7dbcb90"
+ "bids::pb02.$subj.r$run.volreg+tlrc",
+ "bids::pb03.$subj.r$run.blur"
]
},
{
- "@id": "urn:68d31ef2-236f-48f3-a4db-d45f22bfcc43",
+ "@id": "urn:mask-PfjxTDnW",
"Label": "mask",
- "AssociatedWith": "urn:96e62f9d-b1bc-4d08-8a56-80c4267c1dde",
+ "AssociatedWith": "urn:afni-ams3QlzR",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc; 3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj; 3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj; 3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt; 3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt; 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/cmaumet/Softs/external/AFNI/macosx_10.7_Intel_64/TT_N27+tlrc; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group; ",
"Used": [
- "urn:ba2ddac7-ea39-45cc-b261-8e86907e891d",
- "urn:77b2e673-f6c4-4126-a0b2-14df6011123c",
- "urn:db9ba97e-dc78-4984-ba0a-f5e433a02af3",
- "urn:a5ae59a2-c246-483d-8555-2d6f0ad1dc75",
- "urn:0d0e2d05-f309-4b04-a2a5-f10351b10b2c",
- "urn:1a7df79f-5d60-474a-b28f-8b9b822bcc19",
- "urn:0d0e2d05-f309-4b04-a2a5-f10351b10b2c",
- "urn:1a7df79f-5d60-474a-b28f-8b9b822bcc19",
- "urn:77b2e673-f6c4-4126-a0b2-14df6011123c",
- "urn:7f0c003b-cd9b-46bd-a0cb-e23e674efa0c",
- "urn:6d8aa8f6-be8d-4b10-ba9e-5b431404b51c"
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.resam.anat+tlrc",
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee",
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee",
+ "bids::/Users/cmaumet/Softs/external/AFNI/macosx_10.7_Intel_64/TT_N27+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.resam.group+tlrc"
]
},
{
- "@id": "urn:8b2c4ce3-6f47-46bc-b31b-3380285a85df",
+ "@id": "urn:scale-W7kJCRkA",
"Label": "scale",
- "AssociatedWith": "urn:96e62f9d-b1bc-4d08-8a56-80c4267c1dde",
+ "AssociatedWith": "urn:afni-ams3QlzR",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc; 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale; ",
"Used": [
- "urn:ba2ddac7-ea39-45cc-b261-8e86907e891d",
- "urn:48853dc0-415a-4073-abdc-bc78808e64ef",
- "urn:719afeb9-a1ed-4c0c-9b64-4b8d6aa33a9d",
- "urn:ba2ddac7-ea39-45cc-b261-8e86907e891d"
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::mask_epi_extents+tlrc",
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::rm.mean_r$run+tlrc"
]
},
{
- "@id": "urn:4a346665-2f68-41f7-ad09-0c4d8f65ca4f",
+ "@id": "urn:regress-ieJMqRzA",
"Label": "regress",
- "AssociatedWith": "urn:96e62f9d-b1bc-4d08-8a56-80c4267c1dde",
+ "AssociatedWith": "urn:afni-ams3QlzR",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}; 3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'SPMG1(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj; 1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt; 3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD; 3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"; 3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"; 3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj; 3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc; 3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D; 3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D; 3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP; 3dTstat -sum -prefix corr_brain rm.DP+tlrc; 1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D; 1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D; 3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"; 1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D; ",
"Used": [
- "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
- "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
- "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
- "urn:b9764b4c-90f2-4ca6-8158-ea28ee9fff68",
- "urn:b9764b4c-90f2-4ca6-8158-ea28ee9fff68",
- "urn:158b1d1a-cfcc-4545-903e-ecc0c0c1554c",
- "urn:d962259d-c7e2-4732-9f0b-c56983f6dc36",
- "urn:01193415-1f3f-43c8-8274-9c3c29cca603",
- "urn:4fd3e945-daaa-4e92-91ab-7e2849037ffa",
- "urn:77b2e673-f6c4-4126-a0b2-14df6011123c",
- "urn:16efefb5-f541-4233-82d6-1e9fe0e35bce",
- "urn:0ea02055-d0c6-4707-80d3-61cdeb1cb36c",
- "urn:a91c074f-a725-4f84-aa83-73630b62aadf",
- "urn:d1d82229-9f97-4cbc-bec1-e900fc856882",
- "urn:cfbdc37d-4f9f-4297-b2ed-b01ff2a85ed0",
- "urn:dc32a6ba-52b8-4331-8c20-c103684d9607",
- "urn:d61ba711-53ab-409c-b0f7-ca672b380ffe",
- "urn:d61ba711-53ab-409c-b0f7-ca672b380ffe"
+ "bids::dfile_rall.1D",
+ "bids::dfile_rall.1D",
+ "bids::dfile_rall.1D",
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD",
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD",
+ "bids::all_runs.$subj+tlrc%22[$ktrs]%22",
+ "bids::errts.$%7Bsubj%7D+tlrc%22[$ktrs]%22",
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.noise.all+tlrc",
+ "bids::rm.signal.all+tlrc",
+ "bids::errts.$%7Bsubj%7D+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::out.gcor.1D",
+ "bids::rm.errts.unit+tlrc",
+ "bids::rm.DP+tlrc",
+ "bids::X.nocensor.xmat.1D'[3]'",
+ "bids::X.nocensor.xmat.1D'[4]'",
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22",
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:e23fad7b-8ec6-4e75-ad8d-dc6ac8a84649",
+ "@id": "urn:bluresti-25XSZU9P",
"Label": "blur estimation",
- "AssociatedWith": "urn:96e62f9d-b1bc-4d08-8a56-80c4267c1dde",
+ "AssociatedWith": "urn:afni-ams3QlzR",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D; 3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D; 3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim; ",
"Used": [
- "urn:77b2e673-f6c4-4126-a0b2-14df6011123c",
- "urn:77b2e673-f6c4-4126-a0b2-14df6011123c",
- "urn:77b2e673-f6c4-4126-a0b2-14df6011123c"
+ "bids::full_mask.$subj+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:31d0fef0-41a4-4f4c-b800-6e08386d1bfd",
+ "@id": "urn:autobloc-mzC0nGoF",
"Label": "auto block: generate review scripts",
- "AssociatedWith": "urn:96e62f9d-b1bc-4d08-8a56-80c4267c1dde",
+ "AssociatedWith": "urn:afni-ams3QlzR",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD; gen_ss_review_scripts.py -mot_limit 0.3 -exit0; ",
"Used": [
- "urn:7ca09081-d282-4ecd-95b6-9c293a08f0c1"
+ "bids::pb00.$subj.r*.tcat+orig.HEAD"
]
}
],
"Entities": [
{
- "@id": "urn:1297dbd7-23fe-4261-a4b7-62ac5775ae55",
+ "@id": "bids::/Users/cmaumet/Projects/Data_sharing/dev/nidmresults-examples/afni_voxelwise_p0001/subject_results/group.DS0011/subj.sub_001/sub_001.results/stimuli/tone_counting_onset_times.txt",
"Label": "tone_counting_onset_times.txt",
"AtLocation": "/Users/cmaumet/Projects/Data_sharing/dev/nidmresults-examples/afni_voxelwise_p0001/subject_results/group.DS0011/subj.sub_001/sub_001.results/stimuli/tone_counting_onset_times.txt",
"digest": {
@@ -192,7 +194,7 @@
}
},
{
- "@id": "urn:b9a5473a-60c6-4714-958c-a8d3e58fab95",
+ "@id": "bids::/Users/cmaumet/Projects/Data_sharing/dev/nidmresults-examples/afni_voxelwise_p0001/subject_results/group.DS0011/subj.sub_001/sub_001.results/stimuli/tone_counting_probe_duration.txt",
"Label": "tone_counting_probe_duration.txt",
"AtLocation": "/Users/cmaumet/Projects/Data_sharing/dev/nidmresults-examples/afni_voxelwise_p0001/subject_results/group.DS0011/subj.sub_001/sub_001.results/stimuli/tone_counting_probe_duration.txt",
"digest": {
@@ -200,7 +202,7 @@
}
},
{
- "@id": "urn:2a0f2321-a75e-4613-b39e-0462b3551323",
+ "@id": "bids::/Users/cmaumet/Projects/Data_sharing/dev/nidmresults-examples/raw/ds011/sub-01/anat/sub-01_T1w.nii.gz",
"Label": "sub-01_T1w.nii.gz",
"AtLocation": "/Users/cmaumet/Projects/Data_sharing/dev/nidmresults-examples/raw/ds011/sub-01/anat/sub-01_T1w.nii.gz",
"digest": {
@@ -208,34 +210,34 @@
}
},
{
- "@id": "urn:506374dd-d23d-493d-bfaf-7750736efb06",
+ "@id": "bids::$output_dir",
"Label": "$output_dir",
"AtLocation": "$output_dir",
- "GeneratedBy": "urn:1f4c0713-f660-426f-90a7-8a053bb099f6",
+ "GeneratedBy": "urn:autobloc-5KgJTiu3",
"digest": {
"sha256": "9fa4c635e6533ddf2fed54295920052818d948c3ffe97bc753bd7336b453f8cb"
}
},
{
- "@id": "urn:31972545-5912-43dc-ad05-41b1982cf51e",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:1f4c0713-f660-426f-90a7-8a053bb099f6"
+ "GeneratedBy": "urn:autobloc-5KgJTiu3"
},
{
- "@id": "urn:6e926570-0c7d-4610-98ac-8cbb9779eceb",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:1f4c0713-f660-426f-90a7-8a053bb099f6"
+ "GeneratedBy": "urn:autobloc-5KgJTiu3"
},
{
- "@id": "urn:c84c5016-2179-4942-915f-6b8d41c9e35d",
+ "@id": "bids::$output_dir/sub-01_T1w",
"Label": "sub-01_T1w",
"AtLocation": "$output_dir/sub-01_T1w",
- "GeneratedBy": "urn:1f4c0713-f660-426f-90a7-8a053bb099f6"
+ "GeneratedBy": "urn:autobloc-5KgJTiu3"
},
{
- "@id": "urn:9fd8ffd2-1776-4af3-a24c-acdeaff9cf12",
+ "@id": "bids::/Users/cmaumet/Projects/Data_sharing/dev/nidmresults-examples/raw/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Label": "sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "/Users/cmaumet/Projects/Data_sharing/dev/nidmresults-examples/raw/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"digest": {
@@ -243,13 +245,13 @@
}
},
{
- "@id": "urn:b355b136-80b5-4fb9-a493-1c28a29700b2",
+ "@id": "bids::$output_dir/pb00.$subj.r01.tcat",
"Label": "pb00.$subj.r01.tcat",
"AtLocation": "$output_dir/pb00.$subj.r01.tcat",
- "GeneratedBy": "urn:5b5798a2-a216-41fb-8cb0-ef650c5c95fe"
+ "GeneratedBy": "urn:autobloc-VH75Af2k"
},
{
- "@id": "urn:6134bd82-c6ba-4031-a0f6-1da02585d5eb",
+ "@id": "bids::pb00.$subj.r$run.tcat+orig",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -257,7 +259,7 @@
}
},
{
- "@id": "urn:89fee5f0-1524-467f-8e87-4af5ee8abd9f",
+ "@id": "bids::outcount.r*.1D",
"Label": "outcount.r*.1D",
"AtLocation": "outcount.r*.1D",
"digest": {
@@ -265,25 +267,25 @@
}
},
{
- "@id": "urn:69027950-f2cb-40ce-9227-567626ceeece",
+ "@id": "bids::outcount.r$run.1D",
"Label": "outcount.r$run.1D",
"AtLocation": "outcount.r$run.1D",
- "GeneratedBy": "urn:5532669b-e4be-439f-ad6c-7eaec203e36d",
+ "GeneratedBy": "urn:autobloc-Dev6mf7h",
"digest": {
"sha256": "63d9f539e5470badc625d557109f68bc4eecbb02ca2667483739d52f95e5d0dd"
}
},
{
- "@id": "urn:e3c381f4-cc66-424c-9d66-89012fc3da27",
+ "@id": "bids::outcount_rall.1D",
"Label": "outcount_rall.1D",
"AtLocation": "outcount_rall.1D",
- "GeneratedBy": "urn:5532669b-e4be-439f-ad6c-7eaec203e36d",
+ "GeneratedBy": "urn:autobloc-Dev6mf7h",
"digest": {
"sha256": "cb887fd5e4d5e9acb3a24820d0f7a62ed38a5ffb0fdedd373440ac0219fb186a"
}
},
{
- "@id": "urn:6134bd82-c6ba-4031-a0f6-1da02585d5eb",
+ "@id": "bids::pb00.$subj.r$run.tcat+orig",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -291,16 +293,16 @@
}
},
{
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+ "@id": "bids::pb01.$subj.r$run.tshift",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift",
- "GeneratedBy": "urn:4601a4cd-a630-418f-beb8-4815818cd73a",
+ "GeneratedBy": "urn:tshift-7nObZinu",
"digest": {
"sha256": "c6bf01cea8d2eac1d7a866f80b865c6e7d4b4e012dbb63d480ac9a8551162d72"
}
},
{
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+ "@id": "bids::sub-01_T1w+orig",
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"AtLocation": "sub-01_T1w+orig",
"digest": {
@@ -308,7 +310,7 @@
}
},
{
- "@id": "urn:e0b55535-1ed2-485c-afc5-1a0f64f8d8fe",
+ "@id": "bids::pb01.$subj.r01.tshift+orig",
"Label": "pb01.$subj.r01.tshift",
"AtLocation": "pb01.$subj.r01.tshift+orig",
"digest": {
@@ -316,16 +318,16 @@
}
},
{
- "@id": "urn:4942dc4f-78e8-4afe-90ea-4fed7af53baa",
+ "@id": "bids::_al_junk",
"Label": "_al_junk",
"AtLocation": "_al_junk",
- "GeneratedBy": "urn:aec43d8a-1acf-483e-839f-a6b9d0413d1e",
+ "GeneratedBy": "urn:align-8x9H6ddn",
"digest": {
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}
},
{
- "@id": "urn:2a2831db-7ec1-4ea8-9870-d9e7a2776e5b",
+ "@id": "bids::TT_N27+tlrc",
"Label": "TT_N27",
"AtLocation": "TT_N27+tlrc",
"digest": {
@@ -333,7 +335,7 @@
}
},
{
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+ "@id": "bids::sub-01_T1w_ns+orig",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+orig",
"digest": {
@@ -341,7 +343,7 @@
}
},
{
- "@id": "urn:83b1c647-25a9-4c03-897b-14beedad3f17",
+ "@id": "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc::WARP_DATA",
"digest": {
@@ -349,16 +351,16 @@
}
},
{
- "@id": "urn:3b79334f-2482-4ea7-94d4-6e6090623211",
+ "@id": "bids::warp.anat.Xat.1D",
"Label": "warp.anat.Xat.1D",
"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:3bee4548-3d99-4d3b-8ecf-fe9fe26023a6",
+ "GeneratedBy": "urn:tlrc-YlBDOp0O",
"digest": {
"sha256": "800633fb5b4e9be64078bc181c4d5510ffb73fc5cccaf364c7fb6a294aa06728"
}
},
{
- "@id": "urn:83b1c647-25a9-4c03-897b-14beedad3f17",
+ "@id": "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc::WARP_DATA",
"digest": {
@@ -366,16 +368,16 @@
}
},
{
- "@id": "urn:3b79334f-2482-4ea7-94d4-6e6090623211",
+ "@id": "bids::warp.anat.Xat.1D",
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"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:3bee4548-3d99-4d3b-8ecf-fe9fe26023a6",
+ "GeneratedBy": "urn:tlrc-YlBDOp0O",
"digest": {
"sha256": "800633fb5b4e9be64078bc181c4d5510ffb73fc5cccaf364c7fb6a294aa06728"
}
},
{
- "@id": "urn:055baac7-d18b-486b-8f9e-4cf47f891f28",
+ "@id": "bids::pb01.$subj.r$run.tshift+orig",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift+orig",
"digest": {
@@ -383,7 +385,7 @@
}
},
{
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+ "@id": "bids::sub-01_T1w_ns+tlrc",
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"digest": {
@@ -391,7 +393,7 @@
}
},
{
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+ "@id": "bids::rm.epi.all1+orig",
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"digest": {
@@ -399,7 +401,7 @@
}
},
{
- "@id": "urn:d8674169-2dfa-45af-ae52-683c72874335",
+ "@id": "bids::rm.epi.1.r$run+tlrc",
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"AtLocation": "rm.epi.1.r$run+tlrc",
"digest": {
@@ -407,7 +409,7 @@
}
},
{
- "@id": "urn:235e03ab-4e6d-43fa-947c-18213c5b8159",
+ "@id": "bids::dfile.r*.1D",
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"AtLocation": "dfile.r*.1D",
"digest": {
@@ -415,7 +417,7 @@
}
},
{
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+ "@id": "bids::rm.epi.min.r01+tlrc",
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"digest": {
@@ -423,7 +425,7 @@
}
},
{
- "@id": "urn:9afa03eb-c567-4dc5-be4b-5e5535fc712c",
+ "@id": "bids::rm.epi.nomask.r$run+tlrc",
"Label": "rm.epi.nomask.r$run",
"AtLocation": "rm.epi.nomask.r$run+tlrc",
"digest": {
@@ -431,7 +433,7 @@
}
},
{
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+ "@id": "bids::mask_epi_extents+tlrc",
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"AtLocation": "mask_epi_extents+tlrc",
"digest": {
@@ -439,97 +441,105 @@
}
},
{
- "@id": "urn:f7d52db8-8d49-4e3f-8fcc-4b0b01aec0f6",
+ "@id": "bids::anat_final.$subj+tlrc",
+ "Label": "anat_final.$subj",
+ "AtLocation": "anat_final.$subj+tlrc",
+ "digest": {
+ "sha256": "94eb1853614cc085b22772c011f119f6a0ad7ec06cba2850587762e7f1a6eae6"
+ }
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+ {
+ "@id": "bids::mat.r$run.vr.aff12.1D",
"Label": "mat.r$run.vr.aff12.1D",
"AtLocation": "mat.r$run.vr.aff12.1D",
- "GeneratedBy": "urn:c8bd47b3-a87e-4881-adc1-63175661aaa7",
+ "GeneratedBy": "urn:volreg-kb7kw99N",
"digest": {
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}
},
{
- "@id": "urn:4879466b-3b4a-48aa-8a01-b92df00778fe",
+ "@id": "bids::rm.epi.all1",
"Label": "rm.epi.all1",
"AtLocation": "rm.epi.all1",
- "GeneratedBy": "urn:c8bd47b3-a87e-4881-adc1-63175661aaa7",
+ "GeneratedBy": "urn:volreg-kb7kw99N",
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{
- "@id": "urn:4affc0e0-f2f6-410c-98cd-dda7019b68ed",
+ "@id": "bids::rm.epi.nomask.r$run",
"Label": "rm.epi.nomask.r$run",
"AtLocation": "rm.epi.nomask.r$run",
- "GeneratedBy": "urn:c8bd47b3-a87e-4881-adc1-63175661aaa7",
+ "GeneratedBy": "urn:volreg-kb7kw99N",
"digest": {
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{
- "@id": "urn:f0961f03-78cc-43e3-b7c3-fda09a73d42c",
+ "@id": "bids::rm.epi.1.r$run",
"Label": "rm.epi.1.r$run",
"AtLocation": "rm.epi.1.r$run",
- "GeneratedBy": "urn:c8bd47b3-a87e-4881-adc1-63175661aaa7",
+ "GeneratedBy": "urn:volreg-kb7kw99N",
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}
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{
- "@id": "urn:472415a7-8fa4-47d7-90a9-d77af101c59b",
+ "@id": "bids::rm.epi.min.r$run",
"Label": "rm.epi.min.r$run",
"AtLocation": "rm.epi.min.r$run",
- "GeneratedBy": "urn:c8bd47b3-a87e-4881-adc1-63175661aaa7",
+ "GeneratedBy": "urn:volreg-kb7kw99N",
"digest": {
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{
- "@id": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
+ "@id": "bids::dfile_rall.1D",
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"AtLocation": "dfile_rall.1D",
- "GeneratedBy": "urn:c8bd47b3-a87e-4881-adc1-63175661aaa7",
+ "GeneratedBy": "urn:volreg-kb7kw99N",
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}
},
{
- "@id": "urn:f8be5416-8122-419c-b982-29067b5dc5ea",
+ "@id": "bids::mask_epi_extents",
"Label": "mask_epi_extents",
"AtLocation": "mask_epi_extents",
- "GeneratedBy": "urn:c8bd47b3-a87e-4881-adc1-63175661aaa7",
+ "GeneratedBy": "urn:volreg-kb7kw99N",
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}
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{
- "@id": "urn:8bd97ac6-43b4-427f-8481-3297908a83ef",
+ "@id": "bids::pb02.$subj.r$run.volreg",
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"AtLocation": "pb02.$subj.r$run.volreg",
- "GeneratedBy": "urn:c8bd47b3-a87e-4881-adc1-63175661aaa7",
+ "GeneratedBy": "urn:volreg-kb7kw99N",
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}
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{
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+ "@id": "bids::anat_final.$subj",
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"AtLocation": "anat_final.$subj",
- "GeneratedBy": "urn:c8bd47b3-a87e-4881-adc1-63175661aaa7",
+ "GeneratedBy": "urn:volreg-kb7kw99N",
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{
- "@id": "urn:fa97c292-3cc3-49ca-bfd1-3d2096c6eeee",
+ "@id": "bids::anat_w_skull_warped",
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"AtLocation": "anat_w_skull_warped",
- "GeneratedBy": "urn:c8bd47b3-a87e-4881-adc1-63175661aaa7",
+ "GeneratedBy": "urn:volreg-kb7kw99N",
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{
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+ "@id": "bids::pb03.$subj.r$run.blur",
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"AtLocation": "pb03.$subj.r$run.blur",
"digest": {
@@ -537,7 +547,7 @@
}
},
{
- "@id": "urn:70dbec60-b908-498d-826f-65d7633bb261",
+ "@id": "bids::pb02.$subj.r$run.volreg+tlrc",
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"AtLocation": "pb02.$subj.r$run.volreg+tlrc",
"digest": {
@@ -545,7 +555,7 @@
}
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{
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+ "@id": "bids::sub-01_T1w_ns+tlrc",
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"digest": {
@@ -553,7 +563,7 @@
}
},
{
- "@id": "urn:ba2ddac7-ea39-45cc-b261-8e86907e891d",
+ "@id": "bids::pb03.$subj.r$run.blur+tlrc",
"Label": "pb03.$subj.r$run.blur",
"AtLocation": "pb03.$subj.r$run.blur+tlrc",
"digest": {
@@ -561,7 +571,7 @@
}
},
{
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+ "@id": "bids::full_mask.$subj+tlrc",
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"digest": {
@@ -569,7 +579,7 @@
}
},
{
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+ "@id": "bids::rm.resam.anat+tlrc",
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"digest": {
@@ -577,7 +587,7 @@
}
},
{
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+ "@id": "bids::mask_anat.$subj+tlrc",
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"AtLocation": "mask_anat.$subj+tlrc",
"digest": {
@@ -585,7 +595,7 @@
}
},
{
- "@id": "urn:1a7df79f-5d60-474a-b28f-8b9b822bcc19",
+ "@id": "bids::tee",
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"digest": {
@@ -593,7 +603,7 @@
}
},
{
- "@id": "urn:7f0c003b-cd9b-46bd-a0cb-e23e674efa0c",
+ "@id": "bids::/Users/cmaumet/Softs/external/AFNI/macosx_10.7_Intel_64/TT_N27+tlrc",
"Label": "TT_N27",
"AtLocation": "/Users/cmaumet/Softs/external/AFNI/macosx_10.7_Intel_64/TT_N27+tlrc",
"digest": {
@@ -601,7 +611,7 @@
}
},
{
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+ "@id": "bids::rm.resam.group+tlrc",
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"digest": {
@@ -609,61 +619,61 @@
}
},
{
- "@id": "urn:fec24f26-05bc-46b1-a308-e387bad0083c",
+ "@id": "bids::rm.mask_r$run",
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"AtLocation": "rm.mask_r$run",
- "GeneratedBy": "urn:68d31ef2-236f-48f3-a4db-d45f22bfcc43",
+ "GeneratedBy": "urn:mask-PfjxTDnW",
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}
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{
- "@id": "urn:345fc00b-87bb-4394-992d-88b581c53a1e",
+ "@id": "bids::full_mask.$subj",
"Label": "full_mask.$subj",
"AtLocation": "full_mask.$subj",
- "GeneratedBy": "urn:68d31ef2-236f-48f3-a4db-d45f22bfcc43",
+ "GeneratedBy": "urn:mask-PfjxTDnW",
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}
},
{
- "@id": "urn:da7c4a76-1cc5-4b5a-9b7a-aeee1f25a262",
+ "@id": "bids::rm.resam.anat",
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"AtLocation": "rm.resam.anat",
- "GeneratedBy": "urn:68d31ef2-236f-48f3-a4db-d45f22bfcc43",
+ "GeneratedBy": "urn:mask-PfjxTDnW",
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}
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{
- "@id": "urn:dac866b4-d456-4117-8d49-7ed57506aee0",
+ "@id": "bids::mask_anat.$subj",
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"AtLocation": "mask_anat.$subj",
- "GeneratedBy": "urn:68d31ef2-236f-48f3-a4db-d45f22bfcc43",
+ "GeneratedBy": "urn:mask-PfjxTDnW",
"digest": {
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},
{
- "@id": "urn:bc402a7d-a8df-41e0-bf0f-30a4f6f4eb5d",
+ "@id": "bids::rm.resam.group",
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"AtLocation": "./rm.resam.group",
- "GeneratedBy": "urn:68d31ef2-236f-48f3-a4db-d45f22bfcc43",
+ "GeneratedBy": "urn:mask-PfjxTDnW",
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},
{
- "@id": "urn:c71d2b44-1418-4682-a878-d1c3043c2ce7",
+ "@id": "bids::mask_group",
"Label": "mask_group",
"AtLocation": "mask_group",
- "GeneratedBy": "urn:68d31ef2-236f-48f3-a4db-d45f22bfcc43",
+ "GeneratedBy": "urn:mask-PfjxTDnW",
"digest": {
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{
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+ "@id": "bids::mask_epi_extents+tlrc",
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"digest": {
@@ -671,7 +681,7 @@
}
},
{
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+ "@id": "bids::pb03.$subj.r$run.blur+tlrc",
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"digest": {
@@ -679,7 +689,7 @@
}
},
{
- "@id": "urn:48853dc0-415a-4073-abdc-bc78808e64ef",
+ "@id": "bids::rm.mean_r$run+tlrc",
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"digest": {
@@ -687,34 +697,34 @@
}
},
{
- "@id": "urn:7284b9e7-6c6e-4be4-a460-4c982404ecf9",
+ "@id": "bids::rm.mean_r$run",
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"AtLocation": "rm.mean_r$run",
- "GeneratedBy": "urn:8b2c4ce3-6f47-46bc-b31b-3380285a85df",
+ "GeneratedBy": "urn:scale-W7kJCRkA",
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{
- "@id": "urn:6d405d1a-7fbd-4849-a1ee-23f4303f3b1f",
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"AtLocation": "pb04.$subj.r$run.scale",
- "GeneratedBy": "urn:8b2c4ce3-6f47-46bc-b31b-3380285a85df",
+ "GeneratedBy": "urn:scale-W7kJCRkA",
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{
- "@id": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
+ "@id": "bids::dfile_rall.1D",
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"AtLocation": "dfile_rall.1D",
- "GeneratedBy": "urn:c8bd47b3-a87e-4881-adc1-63175661aaa7",
+ "GeneratedBy": "urn:volreg-kb7kw99N",
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{
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@@ -722,7 +732,7 @@
}
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@@ -730,7 +740,7 @@
}
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@@ -738,7 +748,7 @@
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@@ -746,7 +756,7 @@
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@@ -754,7 +764,7 @@
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@@ -762,7 +772,7 @@
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@@ -770,7 +780,7 @@
}
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{
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@@ -778,7 +788,7 @@
}
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{
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@@ -786,7 +796,7 @@
}
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{
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@@ -794,7 +804,7 @@
}
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{
- "@id": "urn:cfbdc37d-4f9f-4297-b2ed-b01ff2a85ed0",
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@@ -802,7 +812,7 @@
}
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{
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"digest": {
@@ -810,7 +820,7 @@
}
},
{
- "@id": "urn:d61ba711-53ab-409c-b0f7-ca672b380ffe",
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"digest": {
@@ -818,133 +828,133 @@
}
},
{
- "@id": "urn:791e3f41-1d41-4379-8c6f-783af998fdfc",
+ "@id": "bids::motion_demean.1D",
"Label": "motion_demean.1D",
"AtLocation": "motion_demean.1D",
- "GeneratedBy": "urn:4a346665-2f68-41f7-ad09-0c4d8f65ca4f",
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"sha256": "1de1e10c0120caa7b6cf441bd141a5a76716e458676ae56ce693039eecb79c85"
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{
- "@id": "urn:8771ca6d-79d5-46c0-a9f8-018a97f037d0",
+ "@id": "bids::motion_deriv.1D",
"Label": "motion_deriv.1D",
"AtLocation": "motion_deriv.1D",
- "GeneratedBy": "urn:4a346665-2f68-41f7-ad09-0c4d8f65ca4f",
+ "GeneratedBy": "urn:regress-ieJMqRzA",
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"sha256": "47185bf319e91642ad6f2a396a43fc9f8db7b82f2a9aef326bfe4a955120038b"
}
},
{
- "@id": "urn:4aeef158-d26c-4a7d-9ecd-51c007325113",
+ "@id": "bids::all_runs.$subj",
"Label": "all_runs.$subj",
"AtLocation": "all_runs.$subj",
- "GeneratedBy": "urn:4a346665-2f68-41f7-ad09-0c4d8f65ca4f",
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}
},
{
- "@id": "urn:3fb67843-9a96-48ae-b535-b18a05d6de44",
+ "@id": "bids::rm.signal.all",
"Label": "rm.signal.all",
"AtLocation": "rm.signal.all",
- "GeneratedBy": "urn:4a346665-2f68-41f7-ad09-0c4d8f65ca4f",
+ "GeneratedBy": "urn:regress-ieJMqRzA",
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}
},
{
- "@id": "urn:a604e485-33c0-49ce-8657-1649b10f2247",
+ "@id": "bids::rm.noise.all",
"Label": "rm.noise.all",
"AtLocation": "rm.noise.all",
- "GeneratedBy": "urn:4a346665-2f68-41f7-ad09-0c4d8f65ca4f",
+ "GeneratedBy": "urn:regress-ieJMqRzA",
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"sha256": "431314eb75d086ce08373b3a374427969e89414c4a2d607e449c1f6485c547af"
}
},
{
- "@id": "urn:3b721c25-1fab-41a2-a931-79bbaf958ba1",
+ "@id": "bids::TSNR.$subj",
"Label": "TSNR.$subj",
"AtLocation": "TSNR.$subj",
- "GeneratedBy": "urn:4a346665-2f68-41f7-ad09-0c4d8f65ca4f",
+ "GeneratedBy": "urn:regress-ieJMqRzA",
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"sha256": "303f183145a1e295686c08335d3b70753777cf0fa0b3f9628cf8de5471359a00"
}
},
{
- "@id": "urn:9080e1ed-e597-485c-b563-6642ff91b475",
+ "@id": "bids::rm.errts.unit",
"Label": "rm.errts.unit",
"AtLocation": "rm.errts.unit",
- "GeneratedBy": "urn:4a346665-2f68-41f7-ad09-0c4d8f65ca4f",
+ "GeneratedBy": "urn:regress-ieJMqRzA",
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"sha256": "03b570ad773a00f51ab7e6cdedfebdeca45f5356de0c25f9e3be44d7bf2c7151"
}
},
{
- "@id": "urn:5256b601-32fe-4e3a-89da-4c22e8865939",
+ "@id": "urn:uuid:521a1422-bf72-4868-a196-36ea32e32333",
"Label": "-",
"AtLocation": "-",
- "GeneratedBy": "urn:4a346665-2f68-41f7-ad09-0c4d8f65ca4f",
+ "GeneratedBy": "urn:regress-ieJMqRzA",
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}
},
{
- "@id": "urn:a2aaea60-1d90-4ef3-926f-fec383eccbe1",
+ "@id": "bids::rm.DP",
"Label": "rm.DP",
"AtLocation": "rm.DP",
- "GeneratedBy": "urn:4a346665-2f68-41f7-ad09-0c4d8f65ca4f",
+ "GeneratedBy": "urn:regress-ieJMqRzA",
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"sha256": "06a0bfbc609c1a06ecf93c479a3288d2911c7f5f3e93cf49c5d26f721c2035ed"
}
},
{
- "@id": "urn:98f15577-ff6b-46bc-9bf2-acb04558545b",
+ "@id": "bids::corr_brain",
"Label": "corr_brain",
"AtLocation": "corr_brain",
- "GeneratedBy": "urn:4a346665-2f68-41f7-ad09-0c4d8f65ca4f",
+ "GeneratedBy": "urn:regress-ieJMqRzA",
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"sha256": "74e3aeae0da338b871ab5dc9e8859a4e81fcf1b3c0042cd22fe337eb7baf5eae"
}
},
{
- "@id": "urn:4c5b85fe-32e6-4d2c-b34c-8a2fc87aec51",
+ "@id": "bids::ideal_tone_counting.1D",
"Label": "ideal_tone_counting.1D",
"AtLocation": "ideal_tone_counting.1D",
- "GeneratedBy": "urn:4a346665-2f68-41f7-ad09-0c4d8f65ca4f",
+ "GeneratedBy": "urn:regress-ieJMqRzA",
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"sha256": "9bb1cabac5ce7ca19dffa5cd6336a9bf82d362fea2ce9341978406e421b5333c"
}
},
{
- "@id": "urn:0e12140c-f0fa-4b1c-afdc-6b4072852687",
+ "@id": "bids::ideal_probe.1D",
"Label": "ideal_probe.1D",
"AtLocation": "ideal_probe.1D",
- "GeneratedBy": "urn:4a346665-2f68-41f7-ad09-0c4d8f65ca4f",
+ "GeneratedBy": "urn:regress-ieJMqRzA",
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"sha256": "705d93afa8b6ded9f4f572db3f967b54e9906942669af51dd8287a9863bb4288"
}
},
{
- "@id": "urn:1ff46c81-17ab-417c-898c-5c967b8b6b74",
+ "@id": "bids::sum_ideal.1D",
"Label": "sum_ideal.1D",
"AtLocation": "sum_ideal.1D",
- "GeneratedBy": "urn:4a346665-2f68-41f7-ad09-0c4d8f65ca4f",
+ "GeneratedBy": "urn:regress-ieJMqRzA",
"digest": {
"sha256": "b2dccadcd84b2d26ec9685c4d1846baf2f11b867f31c36a08748d1c85467b01a"
}
},
{
- "@id": "urn:bab102ed-4797-4fa1-84b8-fa18fe447a52",
+ "@id": "bids::X.stim.xmat.1D",
"Label": "X.stim.xmat.1D",
"AtLocation": "X.stim.xmat.1D",
- "GeneratedBy": "urn:4a346665-2f68-41f7-ad09-0c4d8f65ca4f",
+ "GeneratedBy": "urn:regress-ieJMqRzA",
"digest": {
"sha256": "7c61b2f4bbb9eb0cecb19f81faa3a79b94d547b7fb4087ed18e368619e0004e6"
}
},
{
- "@id": "urn:77b2e673-f6c4-4126-a0b2-14df6011123c",
+ "@id": "bids::full_mask.$subj+tlrc",
"Label": "full_mask.$subj",
"AtLocation": "full_mask.$subj+tlrc",
"digest": {
@@ -952,34 +962,34 @@
}
},
{
- "@id": "urn:78794883-5fae-4bcb-95e2-79995ba6442e",
+ "@id": "bids::blur.epits.1D",
"Label": "blur.epits.1D",
"AtLocation": "blur.epits.1D",
- "GeneratedBy": "urn:e23fad7b-8ec6-4e75-ad8d-dc6ac8a84649",
+ "GeneratedBy": "urn:bluresti-25XSZU9P",
"digest": {
"sha256": "623e70a42214e56babc1f1dca156e0b11ba09865dbd6ca9549d54ca2fc601515"
}
},
{
- "@id": "urn:e83d851c-9631-44c8-8c4f-5ffd4bb94feb",
+ "@id": "bids::blur.errts.1D",
"Label": "blur.errts.1D",
"AtLocation": "blur.errts.1D",
- "GeneratedBy": "urn:e23fad7b-8ec6-4e75-ad8d-dc6ac8a84649",
+ "GeneratedBy": "urn:bluresti-25XSZU9P",
"digest": {
"sha256": "73969700079b5d3275536ac7eaf0e17571d7e74ec49553b6940f90d5718fc800"
}
},
{
- "@id": "urn:4a81a54c-f691-4024-8f90-299b7e38f7fc",
+ "@id": "bids::ClustSim",
"Label": "ClustSim",
"AtLocation": "ClustSim",
- "GeneratedBy": "urn:e23fad7b-8ec6-4e75-ad8d-dc6ac8a84649",
+ "GeneratedBy": "urn:bluresti-25XSZU9P",
"digest": {
"sha256": "2e0cdba2c91902ba12d742a39cb20df66cfd705ba8de767fbf68aae8eb65c6f0"
}
},
{
- "@id": "urn:7ca09081-d282-4ecd-95b6-9c293a08f0c1",
+ "@id": "bids::pb00.$subj.r*.tcat+orig.HEAD",
"Label": "pb00.$subj.r*.tcat",
"AtLocation": "pb00.$subj.r*.tcat+orig.HEAD",
"digest": {
@@ -987,10 +997,10 @@
}
},
{
- "@id": "urn:da2f36c8-f656-4f6e-a4a8-8f2618a20752",
+ "@id": "bids::-exit0",
"Label": "-exit0",
"AtLocation": "-exit0",
- "GeneratedBy": "urn:31d0fef0-41a4-4f4c-b800-6e08386d1bfd",
+ "GeneratedBy": "urn:autobloc-mzC0nGoF",
"digest": {
"sha256": "871a4d3513ed2924cbb10c1c15a196eac4a46a05bdcc248e3bcdb23327b3ad90"
}
diff --git a/examples/from_parsers/afni/afni_hrf_gammadiff_proc_block.png b/examples/from_parsers/afni/afni_hrf_gammadiff_proc_block.png
index b3fc37b9b..c651030d8 100644
Binary files a/examples/from_parsers/afni/afni_hrf_gammadiff_proc_block.png and b/examples/from_parsers/afni/afni_hrf_gammadiff_proc_block.png differ
diff --git a/examples/from_parsers/afni/afni_hrf_tent_proc.jsonld b/examples/from_parsers/afni/afni_hrf_tent_proc.jsonld
index 1bc008550..ecd6e548d 100644
--- a/examples/from_parsers/afni/afni_hrf_tent_proc.jsonld
+++ b/examples/from_parsers/afni/afni_hrf_tent_proc.jsonld
@@ -4,407 +4,408 @@
"Records": {
"Software": [
{
- "@id": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:afni-KInB335j",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
- "Version": "afni24"
+ "Version": "afni24",
+ "AltIdentifier": "RRID:SCR_005927"
}
],
"Activities": [
{
- "@id": "urn:5d66c68e-3383-423b-a9a7-bc6dd08e0d21",
+ "@id": "urn:makedire-rMBB43ru",
"Label": "Make directory",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "mkdir $output_dir",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:208eefab-d051-4765-bff4-67f1743005b2",
+ "@id": "urn:makedire-pCcQt8Hm",
"Label": "Make directory",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "mkdir $output_dir/stimuli",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:9b52e42b-e126-46e8-8f25-8f5aaaa31b85",
+ "@id": "urn:cp-4seTsodx",
"Label": "cp",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "cp ./afni_tent_basis_function/tone_counting_onset_times.txt ./afni_tent_basis_function/tone_counting_probe_onsets.txt $output_dir/stimuli",
"Parameters": {},
"Used": [
- "urn:7c5a9367-dab4-4e86-97df-749978bfe8cb",
- "urn:fa2f1c7b-7751-4b85-b51c-c0c7ff606a4e"
+ "bids::afni_tent_basis_function/tone_counting_onset_times.txt",
+ "bids::afni_tent_basis_function/tone_counting_probe_onsets.txt"
]
},
{
- "@id": "urn:5bbc1c18-26eb-4371-a51f-6060dc8d9342",
+ "@id": "urn:3dcopy-YpRyxDa0",
"Label": "3dcopy",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "3dcopy ./afni_tent_basis_function/sub-01_T1w.nii.gz $output_dir/sub-01_T1w",
"Parameters": {},
"Used": [
- "urn:792ea18a-543c-4720-bb39-266ed3d5a6f2"
+ "bids::afni_tent_basis_function/sub-01_T1w.nii.gz"
]
},
{
- "@id": "urn:08254780-9d70-4efc-8615-576ba6205e13",
+ "@id": "urn:3dtcat-FRtKXMIi",
"Label": "3dTcat",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat ./afni_tent_basis_function/sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Parameters": {},
"Used": [
- "urn:2e21b4e4-5935-4855-8b93-dd5e88819342"
+ "bids::afni_tent_basis_function/sub-01_task-tonecounting_bold.nii.gz'[0..$]'"
]
},
{
- "@id": "urn:497d8112-4d30-4d69-8445-f21e9299b37d",
+ "@id": "urn:3dtoutco-9zsBBDsR",
"Label": "3dToutcount",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D",
"Parameters": {},
"Used": [
- "urn:8c4fb7bc-b852-4995-9c0d-f57f3bc4ff9d"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:33ed22a7-1c99-4461-8c48-648b04cd652a",
+ "@id": "urn:cat-kqzAufE3",
"Label": "cat",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "cat outcount.r*.1D > outcount_rall.1D",
"Parameters": {},
"Used": [
- "urn:a11d9f65-21e9-4639-956e-2670338fb5a4"
+ "bids::outcount.r*.1D"
]
},
{
- "@id": "urn:e1684662-ca16-489b-91c8-d1c156f0d690",
+ "@id": "urn:3dtshift-6OSZ30P3",
"Label": "3dTshift",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig",
"Parameters": {},
"Used": [
- "urn:8c4fb7bc-b852-4995-9c0d-f57f3bc4ff9d"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:c4a68c32-0925-45db-89b7-3831e4e76e01",
+ "@id": "urn:alignepi-TEeGO0Xs",
"Label": "align_epi_anat.py",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off",
"Parameters": {},
"Used": [
- "urn:ac8b5b17-4954-4507-b9ff-cc76b89ef95b",
- "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9"
+ "bids::pb01.$subj.r01.tshift+orig",
+ "bids::sub-01_T1w+orig"
]
},
{
- "@id": "urn:e1d15475-ff8f-4283-85cf-e17fe947c022",
+ "@id": "urn:autotlrc-nYCl29ey",
"Label": "@auto_tlrc",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss",
"Parameters": {},
"Used": [
- "urn:a78d4805-0251-477e-af6b-e6c89ff27f3b",
- "urn:aa1738e1-fffa-413c-b8ed-5027efbeb699"
+ "bids::TT_N27+tlrc",
+ "bids::sub-01_T1w_ns+orig"
]
},
{
- "@id": "urn:0cb803af-3a44-41a2-8c2c-049d588667e8",
+ "@id": "urn:catmatve-DttU0PXp",
"Label": "cat_matvec",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D",
"Parameters": {},
"Used": [
- "urn:e06a687b-df2b-48e6-8c5f-a2c14a0b1980"
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:04ed6b15-acd8-4153-bd79-745075ff58fb",
+ "@id": "urn:3dvolreg-Zl1YHCQi",
"Label": "3dvolreg",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig",
"Parameters": {},
"Used": [
- "urn:b51223eb-e691-4d0b-9b2b-21688c76b1f1"
+ "bids::pb01.$subj.r$run.tshift+orig"
]
},
{
- "@id": "urn:5a0983f2-8f5b-4f8c-a9b9-1dd457e1bcea",
+ "@id": "urn:3dcalc-RS2awq0W",
"Label": "3dcalc",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1",
"Parameters": {},
"Used": [
- "urn:b51223eb-e691-4d0b-9b2b-21688c76b1f1"
+ "bids::pb01.$subj.r$run.tshift+orig"
]
},
{
- "@id": "urn:7583d6d9-67d6-4bbc-a100-f16a38448de8",
+ "@id": "urn:catmatve-d1oJD0qG",
"Label": "cat_matvec",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D",
"Parameters": {},
"Used": [
- "urn:e06a687b-df2b-48e6-8c5f-a2c14a0b1980"
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:09658342-b347-432e-a0ca-39ead0b8b6bb",
+ "@id": "urn:3dalline-TDVcAxMn",
"Label": "3dAllineate",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run",
"Parameters": {},
"Used": [
- "urn:5c04b2ac-9263-4f7e-84b9-e4b1c26db771",
- "urn:695559a1-9da1-4abf-8ffd-18797ec1ce59",
- "urn:b51223eb-e691-4d0b-9b2b-21688c76b1f1"
+ "bids::mat.r$run.warp.aff12.1D",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:e7c2b1da-9d10-4647-b4dc-5b76e1756e66",
+ "@id": "urn:3dalline-zUGfDpz1",
"Label": "3dAllineate",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run",
"Parameters": {},
"Used": [
- "urn:5c04b2ac-9263-4f7e-84b9-e4b1c26db771",
- "urn:5c7b80bb-a52c-4191-8763-48cd3ae1992f",
- "urn:695559a1-9da1-4abf-8ffd-18797ec1ce59"
+ "bids::mat.r$run.warp.aff12.1D",
+ "bids::rm.epi.all1+orig",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:486eea1d-5943-405c-b940-d322acff9ee4",
+ "@id": "urn:3dtstat-PDDSvUoK",
"Label": "3dTstat",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc",
"Parameters": {},
"Used": [
- "urn:bd75912f-9996-4e47-a434-dce8b0d6fc39"
+ "bids::rm.epi.1.r$run+tlrc"
]
},
{
- "@id": "urn:47f2e70e-0f03-42ae-baee-8eb44818c65b",
+ "@id": "urn:cat-V4HmPyNP",
"Label": "cat",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "cat dfile.r*.1D > dfile_rall.1D",
"Parameters": {},
"Used": [
- "urn:16753022-6cf4-41c0-8d10-bba03c02c719"
+ "bids::dfile.r*.1D"
]
},
{
- "@id": "urn:4d02f3d2-4dc9-48d7-9335-a65829cbaf4e",
+ "@id": "urn:3dcopy-a49D5QLO",
"Label": "3dcopy",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents",
"Parameters": {},
"Used": [
- "urn:196d4e36-94b4-4ed6-bccd-fa569b52c996"
+ "bids::rm.epi.min.r01+tlrc"
]
},
{
- "@id": "urn:86e2b612-99e2-477b-b627-e50595fb6deb",
+ "@id": "urn:3dcalc-UrcTwseN",
"Label": "3dcalc",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg",
"Parameters": {},
"Used": [
- "urn:37683ca5-1963-41df-b40c-cd03888b8d3f",
- "urn:5ec5b225-a716-4c41-97e5-9e46f4542350"
+ "bids::mask_epi_extents+tlrc",
+ "bids::rm.epi.nomask.r$run+tlrc"
]
},
{
- "@id": "urn:64f1e5cf-a973-4928-a6c1-7de24f6ec447",
+ "@id": "urn:3dcopy-qsNxunE4",
"Label": "3dcopy",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj",
"Parameters": {},
"Used": [
- "urn:5c04b2ac-9263-4f7e-84b9-e4b1c26db771"
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:84104bd3-82ce-4004-b61b-6770c8563513",
+ "@id": "urn:3dalline-kygdvilF",
"Label": "3dAllineate",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped",
"Parameters": {},
"Used": [
- "urn:b0574ba8-bc8b-49a7-9b9f-aa4783c7800b"
+ "bids::anat_final.$subj+tlrc",
+ "bids::warp.anat.Xat.1D"
]
},
{
- "@id": "urn:4bbd25ac-bbe4-49bf-8e89-d892ecfe2ae9",
+ "@id": "urn:3dmerge-soXKeMFe",
"Label": "3dmerge",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc",
"Parameters": {},
"Used": [
- "urn:375eb646-fef7-4012-935b-ac8f7b28dca1",
- "urn:52b4e335-e4b8-4778-824e-0640913d61fd"
+ "bids::pb02.$subj.r$run.volreg+tlrc",
+ "bids::pb03.$subj.r$run.blur"
]
},
{
- "@id": "urn:06d8dd6a-728a-4412-b299-f8fb915c2fc9",
+ "@id": "urn:3dautoma-zXzILOFI",
"Label": "3dAutomask",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:c99d5a17-11c4-4165-bf0d-0a0b536a3fcc"
+ "bids::pb03.$subj.r$run.blur+tlrc"
]
},
{
- "@id": "urn:b8f972d9-f226-43b2-91a6-6c23a9e2d752",
+ "@id": "urn:3dmaskto-KORdJ9qp",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:40819247-1fcc-4b66-acaf-9f3e6e6333fa",
+ "@id": "urn:3dresamp-M7iURngw",
"Label": "3dresample",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat",
"Parameters": {},
"Used": [
- "urn:5b94b6ab-5880-496b-8f90-d0158d2e2d73",
- "urn:5c04b2ac-9263-4f7e-84b9-e4b1c26db771"
+ "bids::full_mask.$subj+tlrc",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:94d92ce2-3775-4ebf-893b-44c9e3d6dc68",
+ "@id": "urn:3dmaskto-hJBLuYfU",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj",
"Parameters": {},
"Used": [
- "urn:32b98972-d2ee-4e72-8597-71810714a976"
+ "bids::rm.resam.anat+tlrc"
]
},
{
- "@id": "urn:5caaba6c-e58e-47fb-8216-4f7e6345a328",
+ "@id": "urn:3dabover-wyTw56Ux",
"Label": "3dABoverlap",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt",
"Parameters": {},
"Used": [
- "urn:a7cf4d8b-0646-448e-9f96-fa0ee0c60dd7",
- "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb"
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee"
]
},
{
- "@id": "urn:fb9b46cd-af5c-4e0d-a6a0-437314eb72ab",
+ "@id": "urn:3ddot-9UcoOjaJ",
"Label": "3ddot",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt",
"Parameters": {},
"Used": [
- "urn:a7cf4d8b-0646-448e-9f96-fa0ee0c60dd7",
- "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb"
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee"
]
},
{
- "@id": "urn:cd3b4ccd-e2c1-44f1-b372-4b7152273b09",
+ "@id": "urn:3dresamp-KD4OLtse",
"Label": "3dresample",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc",
"Parameters": {},
"Used": [
- "urn:5b94b6ab-5880-496b-8f90-d0158d2e2d73",
- "urn:eb23f479-d3a4-4687-93f2-ff639fff3aaf"
+ "bids::/Users/u1591557/abin/TT_N27+tlrc",
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:573da5fb-2825-437b-b7e4-0de6289e15e3",
+ "@id": "urn:3dmaskto-r1L37Z4x",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group",
"Parameters": {},
"Used": [
- "urn:76ae161f-4380-481d-979a-2cef8e7cdd9e"
+ "bids::rm.resam.group+tlrc"
]
},
{
- "@id": "urn:0d5637ef-3522-47f3-8fbe-129a0ffa7c36",
+ "@id": "urn:3dtstat-90PVF6gg",
"Label": "3dTstat",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:c99d5a17-11c4-4165-bf0d-0a0b536a3fcc"
+ "bids::pb03.$subj.r$run.blur+tlrc"
]
},
{
- "@id": "urn:4fed7ac4-779c-4b17-8c30-5c636dc89acd",
+ "@id": "urn:3dcalc-FaDTKvWb",
"Label": "3dcalc",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale",
"Parameters": {},
"Used": [
- "urn:36d562e7-c693-4a28-bdd0-17e2c4b39660",
- "urn:37683ca5-1963-41df-b40c-cd03888b8d3f",
- "urn:c99d5a17-11c4-4165-bf0d-0a0b536a3fcc"
+ "bids::mask_epi_extents+tlrc",
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::rm.mean_r$run+tlrc"
]
},
{
- "@id": "urn:70c07c46-ffd5-4ef3-819e-2ee6f5265dd5",
+ "@id": "urn:1dtoolpy-ZfaCxzZ6",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D",
"Parameters": {},
"Used": [
- "urn:20222870-633f-4598-b671-960cf3d572fa"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:60e7c949-5bcd-48b7-8190-ecf305162390",
+ "@id": "urn:1dtoolpy-MZXwlLDw",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D",
"Parameters": {},
"Used": [
- "urn:20222870-633f-4598-b671-960cf3d572fa"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:aaf5527f-f67f-4c8c-afec-3544e99943ae",
+ "@id": "urn:1dtoolpy-kv2PqQbU",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}",
"Parameters": {},
"Used": [
- "urn:20222870-633f-4598-b671-960cf3d572fa"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:9aff8a3b-3ab3-40d1-b5a4-c720945178d9",
+ "@id": "urn:3ddeconv-hvXpUiR6",
"Label": "3dDeconvolve",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'TENT(0,12,7)' -stim_label 1 tone_counting -stim_times 2 stimuli/tone_counting_probe_onsets.txt 'TENT(0,14,8)' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -iresp 1 iresp_tone_counting.$subj -iresp 2 iresp_probe.$subj -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj",
"Parameters": {},
"Used": [
- "urn:7836b94e-365d-4c9f-98c2-98f8219f9924"
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD"
]
},
{
- "@id": "urn:e215ad6e-d4e7-4b13-9ba1-5353b1dddee0",
+ "@id": "urn:1dtoolpy-EJgI912b",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt",
"Parameters": {},
"Used": [
- "urn:3bf36bd4-a425-4266-9c15-e89373b35211"
+ "bids::X.xmat.1D"
]
},
{
- "@id": "urn:b185efef-8306-47df-9b4e-4d359d1ed28a",
+ "@id": "urn:timingto-MqFbTXF0",
"Label": "timing_tool.py",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "timing_tool.py -multi_timing stimuli/tone_counting_onset_times.txt stimuli/tone_counting_probe_onsets.txt -tr 2.0 -warn_tr_stats |& tee out.TENT_warn.txt",
"Parameters": {
"-multi_timing": "stimuli/tone_counting_onset_times.txt",
@@ -412,164 +413,166 @@
"-warn_tr_stats": "|&"
},
"Used": [
- "urn:84f0b77a-0276-4ce9-9370-78ab87dbbe31"
+ "bids::stimuli/tone_counting_probe_onsets.txt"
]
},
{
- "@id": "urn:6bf38f81-d157-48c7-809c-9d6fdbd4ea47",
+ "@id": "urn:3dtcat-nqcTZGqw",
"Label": "3dTcat",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD",
"Parameters": {},
"Used": [
- "urn:7836b94e-365d-4c9f-98c2-98f8219f9924"
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD"
]
},
{
- "@id": "urn:89e387c3-e856-481e-8055-7ae25e760a36",
+ "@id": "urn:3dtstat-6VWqNLos",
"Label": "3dTstat",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:1033b2b2-fd65-4e68-9c8d-cd59ef44b50c"
+ "bids::all_runs.$subj+tlrc%22[$ktrs]%22"
]
},
{
- "@id": "urn:bba0a903-5eff-4d42-9e42-8c0758430f9b",
+ "@id": "urn:3dtstat-DWshRU94",
"Label": "3dTstat",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:377e3ee2-d526-4e90-b489-8992ce228785"
+ "bids::errts.$%7Bsubj%7D+tlrc%22[$ktrs]%22"
]
},
{
- "@id": "urn:f04d7a27-d1d5-4be0-b103-38bdcd5eb0e3",
+ "@id": "urn:3dcalc-jnLuhj7l",
"Label": "3dcalc",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj",
"Parameters": {},
"Used": [
- "urn:3d3d3da7-c4d4-4abb-8999-8252f6323c18",
- "urn:5b94b6ab-5880-496b-8f90-d0158d2e2d73",
- "urn:81c37383-2699-4e08-9b37-d05476f53749"
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.noise.all+tlrc",
+ "bids::rm.signal.all+tlrc"
]
},
{
- "@id": "urn:31c9b029-310d-4021-aa62-c0dbd25fc2e0",
+ "@id": "urn:3dtnorm-LoxTEe0B",
"Label": "3dTnorm",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc",
"Parameters": {},
"Used": [
- "urn:1790034e-03d6-44e2-9434-fa01a361bc8e"
+ "bids::errts.$%7Bsubj%7D+tlrc"
]
},
{
- "@id": "urn:e681cd2e-df3c-4488-a64d-0261a6b46929",
+ "@id": "urn:3dmaskav-13pJnuBU",
"Label": "3dmaskave",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D",
"Parameters": {},
- "Used": []
+ "Used": [
+ "bids::full_mask.$subj+tlrc"
+ ]
},
{
- "@id": "urn:55fc28fb-de6a-46a5-9b3a-8e8ddfddbff8",
+ "@id": "urn:3dtstat-b94l3K8y",
"Label": "3dTstat",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D",
"Parameters": {},
"Used": [
- "urn:6c569e45-9361-462c-bded-a5959c6c2e84"
+ "bids::out.gcor.1D"
]
},
{
- "@id": "urn:c88080b6-995a-41c4-88ce-a7d6c176e52f",
+ "@id": "urn:3dcalc-Zb2vG85e",
"Label": "3dcalc",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP",
"Parameters": {},
"Used": [
- "urn:413711a9-eae9-4ace-9bb6-e4d09cea35d8",
- "urn:d62cb163-faad-415d-b1a8-afb62b829694"
+ "bids::gmean.errts.unit.1D",
+ "bids::rm.errts.unit+tlrc"
]
},
{
- "@id": "urn:7cb60c42-3c85-481f-9aca-b86d2fc5dbd0",
+ "@id": "urn:3dtstat-qIv85HKI",
"Label": "3dTstat",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc",
"Parameters": {},
"Used": [
- "urn:d1b4cbde-57bb-48bc-b03c-333cbba29eca"
+ "bids::rm.DP+tlrc"
]
},
{
- "@id": "urn:601dd07b-c372-4753-ae81-340c406e60c7",
+ "@id": "urn:3dtstat-vZlmpAJf",
"Label": "3dTstat",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"",
"Parameters": {},
"Used": [
- "urn:fd3b323c-a128-4acd-b36a-af036f954577"
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:35e8fbfa-42f0-43c2-9d95-995255ab0223",
+ "@id": "urn:1dcat-IjsgTPfv",
"Label": "1dcat",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D",
"Parameters": {},
"Used": [
- "urn:fd3b323c-a128-4acd-b36a-af036f954577"
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:e8c8f0ca-ae02-4f1d-955c-d73f5c5f4a89",
+ "@id": "urn:3dfwhmx-cZWCstBL",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D",
"Parameters": {},
"Used": [
- "urn:5b94b6ab-5880-496b-8f90-d0158d2e2d73"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:212a98ba-e6e1-4edb-a72f-352f455c2f01",
+ "@id": "urn:3dfwhmx-CC6HkIhP",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D",
"Parameters": {},
"Used": [
- "urn:5b94b6ab-5880-496b-8f90-d0158d2e2d73"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:f80e3c61-fdee-42ff-bc7a-b3bdc1dafba4",
+ "@id": "urn:3dclusts-a80eHKzD",
"Label": "3dClustSim",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim",
"Parameters": {},
"Used": [
- "urn:5b94b6ab-5880-496b-8f90-d0158d2e2d73"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:476b8803-80cd-43c7-8ad8-fd6bd664a6b0",
+ "@id": "urn:genepire-uCkxUTJ8",
"Label": "gen_epi_review.py",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD",
"Parameters": {},
"Used": [
- "urn:e7b671f3-5938-4982-9518-9fc1f631d613"
+ "bids::pb00.$subj.r*.tcat+orig.HEAD"
]
},
{
- "@id": "urn:9f99c103-7de0-43ce-b4d8-fd4eda8b8506",
+ "@id": "urn:genssrev-v1XRw400",
"Label": "gen_ss_review_scripts.py",
- "AssociatedWith": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
+ "AssociatedWith": "urn:afni-KInB335j",
"Command": "gen_ss_review_scripts.py -mot_limit 0.3 -exit0",
"Parameters": {
"-mot_limit": "0.3",
@@ -580,22 +583,22 @@
],
"Entities": [
{
- "@id": "urn:f1bef987-0aa6-4482-a0af-4af6044db240",
+ "@id": "bids::$output_dir",
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"AtLocation": "$output_dir",
- "GeneratedBy": "urn:5d66c68e-3383-423b-a9a7-bc6dd08e0d21",
+ "GeneratedBy": "urn:makedire-rMBB43ru",
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{
- "@id": "urn:ea055e9f-2674-43d5-a9c6-1c5265d24cfa",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:208eefab-d051-4765-bff4-67f1743005b2"
+ "GeneratedBy": "urn:makedire-pCcQt8Hm"
},
{
- "@id": "urn:fa2f1c7b-7751-4b85-b51c-c0c7ff606a4e",
+ "@id": "bids::afni_tent_basis_function/tone_counting_onset_times.txt",
"Label": "tone_counting_onset_times.txt",
"AtLocation": "./afni_tent_basis_function/tone_counting_onset_times.txt",
"digest": {
@@ -603,7 +606,7 @@
}
},
{
- "@id": "urn:7c5a9367-dab4-4e86-97df-749978bfe8cb",
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"Label": "tone_counting_probe_onsets.txt",
"AtLocation": "./afni_tent_basis_function/tone_counting_probe_onsets.txt",
"digest": {
@@ -611,13 +614,13 @@
}
},
{
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+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:9b52e42b-e126-46e8-8f25-8f5aaaa31b85"
+ "GeneratedBy": "urn:cp-4seTsodx"
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{
- "@id": "urn:792ea18a-543c-4720-bb39-266ed3d5a6f2",
+ "@id": "bids::afni_tent_basis_function/sub-01_T1w.nii.gz",
"Label": "sub-01_T1w.nii.gz",
"AtLocation": "./afni_tent_basis_function/sub-01_T1w.nii.gz",
"digest": {
@@ -625,13 +628,13 @@
}
},
{
- "@id": "urn:4ecb4806-6c75-4308-ad7c-0e14b9b89a9f",
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"AtLocation": "$output_dir/sub-01_T1w",
- "GeneratedBy": "urn:5bbc1c18-26eb-4371-a51f-6060dc8d9342"
+ "GeneratedBy": "urn:3dcopy-YpRyxDa0"
},
{
- "@id": "urn:2e21b4e4-5935-4855-8b93-dd5e88819342",
+ "@id": "bids::afni_tent_basis_function/sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Label": "sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "./afni_tent_basis_function/sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"digest": {
@@ -639,13 +642,13 @@
}
},
{
- "@id": "urn:b344a607-bd81-4876-9108-440c30497751",
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"AtLocation": "$output_dir/pb00.$subj.r01.tcat",
- "GeneratedBy": "urn:08254780-9d70-4efc-8615-576ba6205e13"
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- "@id": "urn:8c4fb7bc-b852-4995-9c0d-f57f3bc4ff9d",
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"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -653,16 +656,16 @@
}
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{
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"AtLocation": "outcount.r$run.1D",
- "GeneratedBy": "urn:497d8112-4d30-4d69-8445-f21e9299b37d",
+ "GeneratedBy": "urn:3dtoutco-9zsBBDsR",
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{
- "@id": "urn:a11d9f65-21e9-4639-956e-2670338fb5a4",
+ "@id": "bids::outcount.r*.1D",
"Label": "outcount.r*.1D",
"AtLocation": "outcount.r*.1D",
"digest": {
@@ -670,25 +673,25 @@
}
},
{
- "@id": "urn:e5d28661-d83f-4e8e-a350-8605712fa18e",
+ "@id": "bids::outcount_rall.1D",
"Label": "outcount_rall.1D",
"AtLocation": "outcount_rall.1D",
- "GeneratedBy": "urn:33ed22a7-1c99-4461-8c48-648b04cd652a",
+ "GeneratedBy": "urn:cat-kqzAufE3",
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{
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+ "@id": "bids::pb01.$subj.r$run.tshift",
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"AtLocation": "pb01.$subj.r$run.tshift",
- "GeneratedBy": "urn:e1684662-ca16-489b-91c8-d1c156f0d690",
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{
- "@id": "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9",
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"AtLocation": "sub-01_T1w+orig",
"digest": {
@@ -696,7 +699,7 @@
}
},
{
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"Label": "pb01.$subj.r01.tshift",
"AtLocation": "pb01.$subj.r01.tshift+orig",
"digest": {
@@ -704,16 +707,16 @@
}
},
{
- "@id": "urn:37f82981-5933-4f9e-9690-5aacde57b42e",
+ "@id": "bids::_al_junk",
"Label": "_al_junk",
"AtLocation": "_al_junk",
- "GeneratedBy": "urn:c4a68c32-0925-45db-89b7-3831e4e76e01",
+ "GeneratedBy": "urn:alignepi-TEeGO0Xs",
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{
- "@id": "urn:aa1738e1-fffa-413c-b8ed-5027efbeb699",
+ "@id": "bids::TT_N27+tlrc",
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"AtLocation": "TT_N27+tlrc",
"digest": {
@@ -721,7 +724,7 @@
}
},
{
- "@id": "urn:a78d4805-0251-477e-af6b-e6c89ff27f3b",
+ "@id": "bids::sub-01_T1w_ns+orig",
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"AtLocation": "sub-01_T1w_ns+orig",
"digest": {
@@ -729,7 +732,7 @@
}
},
{
- "@id": "urn:e06a687b-df2b-48e6-8c5f-a2c14a0b1980",
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"AtLocation": "sub-01_T1w_ns+tlrc::WARP_DATA",
"digest": {
@@ -737,16 +740,16 @@
}
},
{
- "@id": "urn:b0574ba8-bc8b-49a7-9b9f-aa4783c7800b",
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"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:0cb803af-3a44-41a2-8c2c-049d588667e8",
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{
- "@id": "urn:b51223eb-e691-4d0b-9b2b-21688c76b1f1",
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"AtLocation": "pb01.$subj.r$run.tshift+orig",
"digest": {
@@ -754,34 +757,34 @@
}
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{
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"AtLocation": "mat.r$run.vr.aff12.1D",
- "GeneratedBy": "urn:04ed6b15-acd8-4153-bd79-745075ff58fb",
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{
- "@id": "urn:f5266e11-6d2d-4f7c-bf3c-85b21c458104",
+ "@id": "bids::rm.epi.all1",
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"AtLocation": "rm.epi.all1",
- "GeneratedBy": "urn:5a0983f2-8f5b-4f8c-a9b9-1dd457e1bcea",
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{
- "@id": "urn:695559a1-9da1-4abf-8ffd-18797ec1ce59",
+ "@id": "bids::mat.r$run.warp.aff12.1D",
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"AtLocation": "mat.r$run.warp.aff12.1D",
- "GeneratedBy": "urn:7583d6d9-67d6-4bbc-a100-f16a38448de8",
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{
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+ "@id": "bids::sub-01_T1w_ns+tlrc",
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"AtLocation": "sub-01_T1w_ns+tlrc",
"digest": {
@@ -789,16 +792,16 @@
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},
{
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"AtLocation": "rm.epi.nomask.r$run",
- "GeneratedBy": "urn:09658342-b347-432e-a0ca-39ead0b8b6bb",
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{
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@@ -806,16 +809,16 @@
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@@ -823,16 +826,16 @@
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@@ -840,16 +843,16 @@
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@@ -857,16 +860,16 @@
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@@ -874,7 +877,7 @@
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@@ -882,34 +885,42 @@
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@@ -917,7 +928,7 @@
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@@ -925,7 +936,7 @@
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@@ -933,25 +944,25 @@
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@@ -959,16 +970,16 @@
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@@ -976,16 +987,16 @@
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@@ -993,7 +1004,7 @@
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@@ -1001,7 +1012,7 @@
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@@ -1009,16 +1020,16 @@
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@@ -1026,25 +1037,25 @@
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@@ -1052,34 +1063,34 @@
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@@ -1087,16 +1098,16 @@
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@@ -1104,25 +1115,25 @@
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@@ -1130,16 +1141,16 @@
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@@ -1147,16 +1158,16 @@
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@@ -1164,7 +1175,7 @@
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@@ -1172,16 +1183,16 @@
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@@ -1189,25 +1200,25 @@
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@@ -1215,16 +1226,16 @@
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},
{
- "@id": "urn:d62cb163-faad-415d-b1a8-afb62b829694",
+ "@id": "bids::rm.errts.unit+tlrc",
"Label": "rm.errts.unit",
"AtLocation": "rm.errts.unit+tlrc",
"digest": {
@@ -1232,16 +1243,16 @@
}
},
{
- "@id": "urn:f5c9f82a-b785-4bbf-87ef-489a139ab78b",
+ "@id": "bids::rm.DP",
"Label": "rm.DP",
"AtLocation": "rm.DP",
- "GeneratedBy": "urn:c88080b6-995a-41c4-88ce-a7d6c176e52f",
+ "GeneratedBy": "urn:3dcalc-Zb2vG85e",
"digest": {
"sha256": "06a0bfbc609c1a06ecf93c479a3288d2911c7f5f3e93cf49c5d26f721c2035ed"
}
},
{
- "@id": "urn:d1b4cbde-57bb-48bc-b03c-333cbba29eca",
+ "@id": "bids::rm.DP+tlrc",
"Label": "rm.DP",
"AtLocation": "rm.DP+tlrc",
"digest": {
@@ -1249,16 +1260,16 @@
}
},
{
- "@id": "urn:14031aea-2c77-49f0-bf28-aa68bf199afa",
+ "@id": "bids::corr_brain",
"Label": "corr_brain",
"AtLocation": "corr_brain",
- "GeneratedBy": "urn:7cb60c42-3c85-481f-9aca-b86d2fc5dbd0",
+ "GeneratedBy": "urn:3dtstat-qIv85HKI",
"digest": {
"sha256": "74e3aeae0da338b871ab5dc9e8859a4e81fcf1b3c0042cd22fe337eb7baf5eae"
}
},
{
- "@id": "urn:fd3b323c-a128-4acd-b36a-af036f954577",
+ "@id": "bids::X.nocensor.xmat.1D%22[$reg_cols]%22",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D\"[$reg_cols]\"",
"digest": {
@@ -1266,52 +1277,52 @@
}
},
{
- "@id": "urn:a5426e27-b44f-4ee5-9f79-99f13c820e2d",
+ "@id": "bids::sum_ideal.1D",
"Label": "sum_ideal.1D",
"AtLocation": "sum_ideal.1D",
- "GeneratedBy": "urn:601dd07b-c372-4753-ae81-340c406e60c7",
+ "GeneratedBy": "urn:3dtstat-vZlmpAJf",
"digest": {
"sha256": "b2dccadcd84b2d26ec9685c4d1846baf2f11b867f31c36a08748d1c85467b01a"
}
},
{
- "@id": "urn:4ab0a510-1e34-41b9-a913-9db8b8c40537",
+ "@id": "bids::X.stim.xmat.1D",
"Label": "X.stim.xmat.1D",
"AtLocation": "X.stim.xmat.1D",
- "GeneratedBy": "urn:35e8fbfa-42f0-43c2-9d95-995255ab0223",
+ "GeneratedBy": "urn:1dcat-IjsgTPfv",
"digest": {
"sha256": "7c61b2f4bbb9eb0cecb19f81faa3a79b94d547b7fb4087ed18e368619e0004e6"
}
},
{
- "@id": "urn:0b66eade-b9cf-457f-a7a8-520a4b9771de",
+ "@id": "bids::blur.epits.1D",
"Label": "blur.epits.1D",
"AtLocation": "blur.epits.1D",
- "GeneratedBy": "urn:e8c8f0ca-ae02-4f1d-955c-d73f5c5f4a89",
+ "GeneratedBy": "urn:3dfwhmx-cZWCstBL",
"digest": {
"sha256": "623e70a42214e56babc1f1dca156e0b11ba09865dbd6ca9549d54ca2fc601515"
}
},
{
- "@id": "urn:e0cf6796-f3d4-4408-801a-580d81d2167d",
+ "@id": "bids::blur.errts.1D",
"Label": "blur.errts.1D",
"AtLocation": "blur.errts.1D",
- "GeneratedBy": "urn:212a98ba-e6e1-4edb-a72f-352f455c2f01",
+ "GeneratedBy": "urn:3dfwhmx-CC6HkIhP",
"digest": {
"sha256": "73969700079b5d3275536ac7eaf0e17571d7e74ec49553b6940f90d5718fc800"
}
},
{
- "@id": "urn:3f7a5206-52c1-41b7-aa5a-aad9f9eccf59",
+ "@id": "bids::ClustSim",
"Label": "ClustSim",
"AtLocation": "ClustSim",
- "GeneratedBy": "urn:f80e3c61-fdee-42ff-bc7a-b3bdc1dafba4",
+ "GeneratedBy": "urn:3dclusts-a80eHKzD",
"digest": {
"sha256": "2e0cdba2c91902ba12d742a39cb20df66cfd705ba8de767fbf68aae8eb65c6f0"
}
},
{
- "@id": "urn:e7b671f3-5938-4982-9518-9fc1f631d613",
+ "@id": "bids::pb00.$subj.r*.tcat+orig.HEAD",
"Label": "pb00.$subj.r*.tcat",
"AtLocation": "pb00.$subj.r*.tcat+orig.HEAD",
"digest": {
@@ -1319,10 +1330,10 @@
}
},
{
- "@id": "urn:c9b570f8-3272-4cb8-91fc-a33ea9a79491",
+ "@id": "bids::-exit0",
"Label": "-exit0",
"AtLocation": "-exit0",
- "GeneratedBy": "urn:9f99c103-7de0-43ce-b4d8-fd4eda8b8506",
+ "GeneratedBy": "urn:genssrev-v1XRw400",
"digest": {
"sha256": "871a4d3513ed2924cbb10c1c15a196eac4a46a05bdcc248e3bcdb23327b3ad90"
}
diff --git a/examples/from_parsers/afni/afni_hrf_tent_proc.png b/examples/from_parsers/afni/afni_hrf_tent_proc.png
index 8e81a00d0..7de99440e 100644
Binary files a/examples/from_parsers/afni/afni_hrf_tent_proc.png and b/examples/from_parsers/afni/afni_hrf_tent_proc.png differ
diff --git a/examples/from_parsers/afni/afni_hrf_tent_proc_block.jsonld b/examples/from_parsers/afni/afni_hrf_tent_proc_block.jsonld
index bc0d27b02..63f146f27 100644
--- a/examples/from_parsers/afni/afni_hrf_tent_proc_block.jsonld
+++ b/examples/from_parsers/afni/afni_hrf_tent_proc_block.jsonld
@@ -4,186 +4,188 @@
"Records": {
"Software": [
{
- "@id": "urn:4b96e2d7-8c88-43d1-99a1-792255a1e144",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:afni-uASy2GCl",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
- "Version": "afni24"
+ "Version": "afni24",
+ "AltIdentifier": "RRID:SCR_005927"
}
],
"Activities": [
{
- "@id": "urn:269c8fba-0d96-4b17-b05d-2924e2e82b5b",
+ "@id": "urn:autobloc-3YGfBr3I",
"Label": "auto block: setup",
- "AssociatedWith": "urn:4b96e2d7-8c88-43d1-99a1-792255a1e144",
+ "AssociatedWith": "urn:afni-uASy2GCl",
"Command": "mkdir $output_dir; mkdir $output_dir/stimuli; cp ./afni_tent_basis_function/tone_counting_onset_times.txt ./afni_tent_basis_function/tone_counting_probe_onsets.txt $output_dir/stimuli; 3dcopy ./afni_tent_basis_function/sub-01_T1w.nii.gz $output_dir/sub-01_T1w; ",
"Used": [
- "urn:50bdb27a-fefd-4bc4-b12f-e03609ea2f44",
- "urn:a51008db-25b7-4e5b-9dd4-3332e54c1340",
- "urn:3d0dda92-91be-4978-95fe-28b76df35115"
+ "bids::afni_tent_basis_function/tone_counting_onset_times.txt",
+ "bids::afni_tent_basis_function/tone_counting_probe_onsets.txt",
+ "bids::afni_tent_basis_function/sub-01_T1w.nii.gz"
]
},
{
- "@id": "urn:f6cfe28a-e166-4752-92f0-f7162e671ba1",
+ "@id": "urn:autobloc-phrCjl2z",
"Label": "auto block: tcat",
- "AssociatedWith": "urn:4b96e2d7-8c88-43d1-99a1-792255a1e144",
+ "AssociatedWith": "urn:afni-uASy2GCl",
"Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat ./afni_tent_basis_function/sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ",
"Used": [
- "urn:5b37350c-ccb1-45a0-b9fd-45e607e4718d"
+ "bids::afni_tent_basis_function/sub-01_task-tonecounting_bold.nii.gz'[0..$]'"
]
},
{
- "@id": "urn:da01af5f-48f5-4a6e-bffe-3a21d518055f",
+ "@id": "urn:autobloc-5kWFbgC7",
"Label": "auto block: outcount",
- "AssociatedWith": "urn:4b96e2d7-8c88-43d1-99a1-792255a1e144",
+ "AssociatedWith": "urn:afni-uASy2GCl",
"Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ",
"Used": [
- "urn:4aed242b-89cb-413f-a4af-892df17b2585",
- "urn:df45ffb2-0fc0-4ac6-b8e5-4e20a863bc34"
+ "bids::pb00.$subj.r$run.tcat+orig",
+ "bids::outcount.r*.1D"
]
},
{
- "@id": "urn:52abab30-8200-46c1-a7d5-5cd13fa04669",
+ "@id": "urn:tshift-24rSnNu6",
"Label": "tshift",
- "AssociatedWith": "urn:4b96e2d7-8c88-43d1-99a1-792255a1e144",
+ "AssociatedWith": "urn:afni-uASy2GCl",
"Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ",
"Used": [
- "urn:4aed242b-89cb-413f-a4af-892df17b2585"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:dc948196-03a1-4379-8a06-ef7ad0b5aecd",
+ "@id": "urn:align-dHze0nqH",
"Label": "align",
- "AssociatedWith": "urn:4b96e2d7-8c88-43d1-99a1-792255a1e144",
+ "AssociatedWith": "urn:afni-uASy2GCl",
"Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ",
"Used": [
- "urn:20bb5ec6-2f0e-43b7-862c-bcae7b5f0c2f",
- "urn:9e5b02ef-3ed2-4f0f-96ec-59134e367424"
+ "bids::pb01.$subj.r01.tshift+orig",
+ "bids::sub-01_T1w+orig"
]
},
{
- "@id": "urn:8f7535aa-ce58-4d25-a40e-0a992e5fa51b",
+ "@id": "urn:tlrc-0RmnlSoq",
"Label": "tlrc",
- "AssociatedWith": "urn:4b96e2d7-8c88-43d1-99a1-792255a1e144",
+ "AssociatedWith": "urn:afni-uASy2GCl",
"Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ",
"Used": [
- "urn:c6ed5643-9338-4f2c-ac91-1d0e6af17437",
- "urn:ee78b807-2592-4d04-a5fe-a598c79a8f54",
- "urn:fbe8da44-f727-45b4-acea-f9c466ce910f"
+ "bids::TT_N27+tlrc",
+ "bids::sub-01_T1w_ns+orig",
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:482e756c-1735-4552-aa69-a61ebd059d85",
+ "@id": "urn:volreg-9AcKgwvI",
"Label": "volreg",
- "AssociatedWith": "urn:4b96e2d7-8c88-43d1-99a1-792255a1e144",
+ "AssociatedWith": "urn:afni-uASy2GCl",
"Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig; 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1; cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D; 3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run; 3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run; 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc; cat dfile.r*.1D > dfile_rall.1D; 3dcopy rm.epi.min.r01+tlrc mask_epi_extents; 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg; 3dcopy sub-01_T1w_ns+tlrc anat_final.$subj; 3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped; ",
"Used": [
- "urn:489ee359-4af7-4f70-b93c-6fd638b112b3",
- "urn:489ee359-4af7-4f70-b93c-6fd638b112b3",
- "urn:fbe8da44-f727-45b4-acea-f9c466ce910f",
- "urn:489ee359-4af7-4f70-b93c-6fd638b112b3",
- "urn:da97f2d0-d3e2-463f-b3b1-b405e013599e",
- "urn:da97f2d0-d3e2-463f-b3b1-b405e013599e",
- "urn:e88ac25a-1920-4693-b775-d9aa77d9e2b5",
- "urn:77b1a6d4-2c81-4425-86ca-3199c1c5a801",
- "urn:5e7a05e8-f457-47a2-8924-d55827fda455",
- "urn:d8b82d32-0f19-46cb-9355-082f1a0568eb",
- "urn:2d19aac9-48f4-41ee-b21f-e77731c5a2ed",
- "urn:c38d3fd6-4413-4aeb-af2c-a4ba9e52d1ea",
- "urn:da97f2d0-d3e2-463f-b3b1-b405e013599e",
- "urn:1430ed23-73d6-42db-8269-2236d93df758"
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.epi.all1+orig",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.epi.1.r$run+tlrc",
+ "bids::dfile.r*.1D",
+ "bids::rm.epi.min.r01+tlrc",
+ "bids::mask_epi_extents+tlrc",
+ "bids::rm.epi.nomask.r$run+tlrc",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::anat_final.$subj+tlrc",
+ "bids::warp.anat.Xat.1D"
]
},
{
- "@id": "urn:a77e2980-084e-420a-8251-6b6f8ec74d3d",
+ "@id": "urn:blur-XGkqFpmY",
"Label": "blur",
- "AssociatedWith": "urn:4b96e2d7-8c88-43d1-99a1-792255a1e144",
+ "AssociatedWith": "urn:afni-uASy2GCl",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc; ",
"Used": [
- "urn:2c5bec6e-f8bb-4c29-9ba0-2c37fff9df0f",
- "urn:a507c349-230f-4c60-a6c5-16b82223b1f5"
+ "bids::pb02.$subj.r$run.volreg+tlrc",
+ "bids::pb03.$subj.r$run.blur"
]
},
{
- "@id": "urn:42aaf4db-e512-4c9e-b00a-cc6d61a29c6d",
+ "@id": "urn:mask-3eXfLybE",
"Label": "mask",
- "AssociatedWith": "urn:4b96e2d7-8c88-43d1-99a1-792255a1e144",
+ "AssociatedWith": "urn:afni-uASy2GCl",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc; 3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj; 3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj; 3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt; 3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt; 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group; ",
"Used": [
- "urn:aad6fc92-8eef-49f4-9fa8-d8c2f463412a",
- "urn:17a72a6f-17b3-484f-bd82-73ac77bb2582",
- "urn:da97f2d0-d3e2-463f-b3b1-b405e013599e",
- "urn:e266a5e3-6b72-4e1b-9f60-d17a1bbc757e",
- "urn:5a5791ee-c6d4-4622-aef5-6f0645ea1f06",
- "urn:e53e3355-9001-471d-a597-e07049ea64f4",
- "urn:5a5791ee-c6d4-4622-aef5-6f0645ea1f06",
- "urn:e53e3355-9001-471d-a597-e07049ea64f4",
- "urn:17a72a6f-17b3-484f-bd82-73ac77bb2582",
- "urn:88a41a1d-66fb-452e-b388-09adadae62aa",
- "urn:d0988a04-e775-488c-aeeb-43257f04f61e"
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.resam.anat+tlrc",
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee",
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee",
+ "bids::/Users/u1591557/abin/TT_N27+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.resam.group+tlrc"
]
},
{
- "@id": "urn:a9f3eaa0-878b-4b96-9cae-1f2f9bb7d00f",
+ "@id": "urn:scale-34hey5xA",
"Label": "scale",
- "AssociatedWith": "urn:4b96e2d7-8c88-43d1-99a1-792255a1e144",
+ "AssociatedWith": "urn:afni-uASy2GCl",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc; 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale; ",
"Used": [
- "urn:aad6fc92-8eef-49f4-9fa8-d8c2f463412a",
- "urn:58e14c3c-a6ae-4ea7-b8e3-405904f13da6",
- "urn:aad6fc92-8eef-49f4-9fa8-d8c2f463412a",
- "urn:c38d3fd6-4413-4aeb-af2c-a4ba9e52d1ea"
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::mask_epi_extents+tlrc",
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::rm.mean_r$run+tlrc"
]
},
{
- "@id": "urn:9f864701-7bb6-4ce8-b2ce-2d262e2ddccb",
+ "@id": "urn:regress-4r98WB2m",
"Label": "regress",
- "AssociatedWith": "urn:4b96e2d7-8c88-43d1-99a1-792255a1e144",
+ "AssociatedWith": "urn:afni-uASy2GCl",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}; 3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'TENT(0,12,7)' -stim_label 1 tone_counting -stim_times 2 stimuli/tone_counting_probe_onsets.txt 'TENT(0,14,8)' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -iresp 1 iresp_tone_counting.$subj -iresp 2 iresp_probe.$subj -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj; 1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt; timing_tool.py -multi_timing stimuli/tone_counting_onset_times.txt stimuli/tone_counting_probe_onsets.txt -tr 2.0 -warn_tr_stats |& tee out.TENT_warn.txt; 3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD; 3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"; 3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"; 3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj; 3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc; 3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D; 3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D; 3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP; 3dTstat -sum -prefix corr_brain rm.DP+tlrc; 3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"; 1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D; ",
"Used": [
- "urn:640b9809-dad4-4832-9ce8-182ffd348e71",
- "urn:640b9809-dad4-4832-9ce8-182ffd348e71",
- "urn:640b9809-dad4-4832-9ce8-182ffd348e71",
- "urn:8a4a9ff9-1d14-470a-8bd4-1d72ba71ad58",
- "urn:afd8fd7e-3ef8-4c37-85cf-c087a46b6b6a",
- "urn:8a4a9ff9-1d14-470a-8bd4-1d72ba71ad58",
- "urn:80ead96e-5334-44ca-a43c-763052f7e42d",
- "urn:b9b34fc0-689e-4f12-b23e-3a571f9bf148",
- "urn:17a72a6f-17b3-484f-bd82-73ac77bb2582",
- "urn:65a7f84d-c002-49ad-a484-8d09adb63e08",
- "urn:a01d75ac-c17f-4f91-9f22-81e6b3027a66",
- "urn:e461db18-e9c3-4b8d-b479-84c6dada49e4",
- "urn:ee7a4504-7361-41ed-af89-d735a28b1750",
- "urn:b25ebbae-2818-4e59-b180-df976d627315",
- "urn:f7c63cb0-d328-435b-a9f2-edaf795c5aff",
- "urn:7c4915b1-ff35-4a5e-a569-440e5a5fc1dc",
- "urn:7c4915b1-ff35-4a5e-a569-440e5a5fc1dc"
+ "bids::dfile_rall.1D",
+ "bids::dfile_rall.1D",
+ "bids::dfile_rall.1D",
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD",
+ "bids::stimuli/tone_counting_probe_onsets.txt",
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD",
+ "bids::all_runs.$subj+tlrc%22[$ktrs]%22",
+ "bids::errts.$%7Bsubj%7D+tlrc%22[$ktrs]%22",
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.noise.all+tlrc",
+ "bids::rm.signal.all+tlrc",
+ "bids::errts.$%7Bsubj%7D+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::out.gcor.1D",
+ "bids::rm.errts.unit+tlrc",
+ "bids::rm.DP+tlrc",
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22",
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:02c24147-6006-4aca-90ca-7d5d71e7a3e7",
+ "@id": "urn:bluresti-4mrz2v5M",
"Label": "blur estimation",
- "AssociatedWith": "urn:4b96e2d7-8c88-43d1-99a1-792255a1e144",
+ "AssociatedWith": "urn:afni-uASy2GCl",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D; 3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D; 3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim; ",
"Used": [
- "urn:17a72a6f-17b3-484f-bd82-73ac77bb2582",
- "urn:17a72a6f-17b3-484f-bd82-73ac77bb2582",
- "urn:17a72a6f-17b3-484f-bd82-73ac77bb2582"
+ "bids::full_mask.$subj+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:7bfd59ea-0347-411d-bf0e-18104d70adef",
+ "@id": "urn:autobloc-c0QvQZQU",
"Label": "auto block: generate review scripts",
- "AssociatedWith": "urn:4b96e2d7-8c88-43d1-99a1-792255a1e144",
+ "AssociatedWith": "urn:afni-uASy2GCl",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD; gen_ss_review_scripts.py -mot_limit 0.3 -exit0; ",
"Used": [
- "urn:326203db-7e6d-4f53-9c88-902808ba180d"
+ "bids::pb00.$subj.r*.tcat+orig.HEAD"
]
}
],
"Entities": [
{
- "@id": "urn:a51008db-25b7-4e5b-9dd4-3332e54c1340",
+ "@id": "bids::afni_tent_basis_function/tone_counting_onset_times.txt",
"Label": "tone_counting_onset_times.txt",
"AtLocation": "./afni_tent_basis_function/tone_counting_onset_times.txt",
"digest": {
@@ -191,7 +193,7 @@
}
},
{
- "@id": "urn:50bdb27a-fefd-4bc4-b12f-e03609ea2f44",
+ "@id": "bids::afni_tent_basis_function/tone_counting_probe_onsets.txt",
"Label": "tone_counting_probe_onsets.txt",
"AtLocation": "./afni_tent_basis_function/tone_counting_probe_onsets.txt",
"digest": {
@@ -199,7 +201,7 @@
}
},
{
- "@id": "urn:3d0dda92-91be-4978-95fe-28b76df35115",
+ "@id": "bids::afni_tent_basis_function/sub-01_T1w.nii.gz",
"Label": "sub-01_T1w.nii.gz",
"AtLocation": "./afni_tent_basis_function/sub-01_T1w.nii.gz",
"digest": {
@@ -207,34 +209,34 @@
}
},
{
- "@id": "urn:8a8fc13d-f4c7-485c-a2f7-f49f774d29de",
+ "@id": "bids::$output_dir",
"Label": "$output_dir",
"AtLocation": "$output_dir",
- "GeneratedBy": "urn:269c8fba-0d96-4b17-b05d-2924e2e82b5b",
+ "GeneratedBy": "urn:autobloc-3YGfBr3I",
"digest": {
"sha256": "9fa4c635e6533ddf2fed54295920052818d948c3ffe97bc753bd7336b453f8cb"
}
},
{
- "@id": "urn:1088143c-d7d4-4f9d-98ed-a958a30f0650",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:269c8fba-0d96-4b17-b05d-2924e2e82b5b"
+ "GeneratedBy": "urn:autobloc-3YGfBr3I"
},
{
- "@id": "urn:14ce5791-494b-4a0b-a1a6-701796a26de3",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:269c8fba-0d96-4b17-b05d-2924e2e82b5b"
+ "GeneratedBy": "urn:autobloc-3YGfBr3I"
},
{
- "@id": "urn:56a41cb2-9d52-42bc-bbba-a4eecabc8257",
+ "@id": "bids::$output_dir/sub-01_T1w",
"Label": "sub-01_T1w",
"AtLocation": "$output_dir/sub-01_T1w",
- "GeneratedBy": "urn:269c8fba-0d96-4b17-b05d-2924e2e82b5b"
+ "GeneratedBy": "urn:autobloc-3YGfBr3I"
},
{
- "@id": "urn:5b37350c-ccb1-45a0-b9fd-45e607e4718d",
+ "@id": "bids::afni_tent_basis_function/sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Label": "sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "./afni_tent_basis_function/sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"digest": {
@@ -242,13 +244,13 @@
}
},
{
- "@id": "urn:d2b04583-62a4-4acb-a5b7-533bf65853b2",
+ "@id": "bids::$output_dir/pb00.$subj.r01.tcat",
"Label": "pb00.$subj.r01.tcat",
"AtLocation": "$output_dir/pb00.$subj.r01.tcat",
- "GeneratedBy": "urn:f6cfe28a-e166-4752-92f0-f7162e671ba1"
+ "GeneratedBy": "urn:autobloc-phrCjl2z"
},
{
- "@id": "urn:4aed242b-89cb-413f-a4af-892df17b2585",
+ "@id": "bids::pb00.$subj.r$run.tcat+orig",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -256,7 +258,7 @@
}
},
{
- "@id": "urn:df45ffb2-0fc0-4ac6-b8e5-4e20a863bc34",
+ "@id": "bids::outcount.r*.1D",
"Label": "outcount.r*.1D",
"AtLocation": "outcount.r*.1D",
"digest": {
@@ -264,25 +266,25 @@
}
},
{
- "@id": "urn:40085074-470f-40a7-8592-5cfde205f538",
+ "@id": "bids::outcount.r$run.1D",
"Label": "outcount.r$run.1D",
"AtLocation": "outcount.r$run.1D",
- "GeneratedBy": "urn:da01af5f-48f5-4a6e-bffe-3a21d518055f",
+ "GeneratedBy": "urn:autobloc-5kWFbgC7",
"digest": {
"sha256": "63d9f539e5470badc625d557109f68bc4eecbb02ca2667483739d52f95e5d0dd"
}
},
{
- "@id": "urn:0eed29c2-767d-42bf-9aa3-d1747f773e3a",
+ "@id": "bids::outcount_rall.1D",
"Label": "outcount_rall.1D",
"AtLocation": "outcount_rall.1D",
- "GeneratedBy": "urn:da01af5f-48f5-4a6e-bffe-3a21d518055f",
+ "GeneratedBy": "urn:autobloc-5kWFbgC7",
"digest": {
"sha256": "cb887fd5e4d5e9acb3a24820d0f7a62ed38a5ffb0fdedd373440ac0219fb186a"
}
},
{
- "@id": "urn:4aed242b-89cb-413f-a4af-892df17b2585",
+ "@id": "bids::pb00.$subj.r$run.tcat+orig",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -290,16 +292,16 @@
}
},
{
- "@id": "urn:69d846d5-f7c6-4c06-a249-6e6214cbbf0f",
+ "@id": "bids::pb01.$subj.r$run.tshift",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift",
- "GeneratedBy": "urn:52abab30-8200-46c1-a7d5-5cd13fa04669",
+ "GeneratedBy": "urn:tshift-24rSnNu6",
"digest": {
"sha256": "c6bf01cea8d2eac1d7a866f80b865c6e7d4b4e012dbb63d480ac9a8551162d72"
}
},
{
- "@id": "urn:9e5b02ef-3ed2-4f0f-96ec-59134e367424",
+ "@id": "bids::sub-01_T1w+orig",
"Label": "sub-01_T1w",
"AtLocation": "sub-01_T1w+orig",
"digest": {
@@ -307,7 +309,7 @@
}
},
{
- "@id": "urn:20bb5ec6-2f0e-43b7-862c-bcae7b5f0c2f",
+ "@id": "bids::pb01.$subj.r01.tshift+orig",
"Label": "pb01.$subj.r01.tshift",
"AtLocation": "pb01.$subj.r01.tshift+orig",
"digest": {
@@ -315,16 +317,16 @@
}
},
{
- "@id": "urn:96b316d6-37f1-4855-92ad-1ee08a6fb44a",
+ "@id": "bids::_al_junk",
"Label": "_al_junk",
"AtLocation": "_al_junk",
- "GeneratedBy": "urn:dc948196-03a1-4379-8a06-ef7ad0b5aecd",
+ "GeneratedBy": "urn:align-dHze0nqH",
"digest": {
"sha256": "bd785a075a4c6446e1e54de9e628913f7f1c814e86b69a9fbfe933209e6d37b5"
}
},
{
- "@id": "urn:c6ed5643-9338-4f2c-ac91-1d0e6af17437",
+ "@id": "bids::TT_N27+tlrc",
"Label": "TT_N27",
"AtLocation": "TT_N27+tlrc",
"digest": {
@@ -332,7 +334,7 @@
}
},
{
- "@id": "urn:ee78b807-2592-4d04-a5fe-a598c79a8f54",
+ "@id": "bids::sub-01_T1w_ns+orig",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+orig",
"digest": {
@@ -340,7 +342,7 @@
}
},
{
- "@id": "urn:fbe8da44-f727-45b4-acea-f9c466ce910f",
+ "@id": "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc::WARP_DATA",
"digest": {
@@ -348,16 +350,16 @@
}
},
{
- "@id": "urn:1430ed23-73d6-42db-8269-2236d93df758",
+ "@id": "bids::warp.anat.Xat.1D",
"Label": "warp.anat.Xat.1D",
"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:8f7535aa-ce58-4d25-a40e-0a992e5fa51b",
+ "GeneratedBy": "urn:tlrc-0RmnlSoq",
"digest": {
"sha256": "800633fb5b4e9be64078bc181c4d5510ffb73fc5cccaf364c7fb6a294aa06728"
}
},
{
- "@id": "urn:fbe8da44-f727-45b4-acea-f9c466ce910f",
+ "@id": "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc::WARP_DATA",
"digest": {
@@ -365,16 +367,16 @@
}
},
{
- "@id": "urn:1430ed23-73d6-42db-8269-2236d93df758",
+ "@id": "bids::warp.anat.Xat.1D",
"Label": "warp.anat.Xat.1D",
"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:8f7535aa-ce58-4d25-a40e-0a992e5fa51b",
+ "GeneratedBy": "urn:tlrc-0RmnlSoq",
"digest": {
"sha256": "800633fb5b4e9be64078bc181c4d5510ffb73fc5cccaf364c7fb6a294aa06728"
}
},
{
- "@id": "urn:489ee359-4af7-4f70-b93c-6fd638b112b3",
+ "@id": "bids::pb01.$subj.r$run.tshift+orig",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift+orig",
"digest": {
@@ -382,7 +384,7 @@
}
},
{
- "@id": "urn:da97f2d0-d3e2-463f-b3b1-b405e013599e",
+ "@id": "bids::sub-01_T1w_ns+tlrc",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc",
"digest": {
@@ -390,7 +392,7 @@
}
},
{
- "@id": "urn:e88ac25a-1920-4693-b775-d9aa77d9e2b5",
+ "@id": "bids::rm.epi.all1+orig",
"Label": "rm.epi.all1",
"AtLocation": "rm.epi.all1+orig",
"digest": {
@@ -398,7 +400,7 @@
}
},
{
- "@id": "urn:77b1a6d4-2c81-4425-86ca-3199c1c5a801",
+ "@id": "bids::rm.epi.1.r$run+tlrc",
"Label": "rm.epi.1.r$run",
"AtLocation": "rm.epi.1.r$run+tlrc",
"digest": {
@@ -406,7 +408,7 @@
}
},
{
- "@id": "urn:5e7a05e8-f457-47a2-8924-d55827fda455",
+ "@id": "bids::dfile.r*.1D",
"Label": "dfile.r*.1D",
"AtLocation": "dfile.r*.1D",
"digest": {
@@ -414,7 +416,7 @@
}
},
{
- "@id": "urn:d8b82d32-0f19-46cb-9355-082f1a0568eb",
+ "@id": "bids::rm.epi.min.r01+tlrc",
"Label": "rm.epi.min.r01",
"AtLocation": "rm.epi.min.r01+tlrc",
"digest": {
@@ -422,7 +424,7 @@
}
},
{
- "@id": "urn:2d19aac9-48f4-41ee-b21f-e77731c5a2ed",
+ "@id": "bids::rm.epi.nomask.r$run+tlrc",
"Label": "rm.epi.nomask.r$run",
"AtLocation": "rm.epi.nomask.r$run+tlrc",
"digest": {
@@ -430,7 +432,7 @@
}
},
{
- "@id": "urn:c38d3fd6-4413-4aeb-af2c-a4ba9e52d1ea",
+ "@id": "bids::mask_epi_extents+tlrc",
"Label": "mask_epi_extents",
"AtLocation": "mask_epi_extents+tlrc",
"digest": {
@@ -438,97 +440,105 @@
}
},
{
- "@id": "urn:3135e215-2b94-4562-8b8e-a48f87f57f2d",
+ "@id": "bids::anat_final.$subj+tlrc",
+ "Label": "anat_final.$subj",
+ "AtLocation": "anat_final.$subj+tlrc",
+ "digest": {
+ "sha256": "94eb1853614cc085b22772c011f119f6a0ad7ec06cba2850587762e7f1a6eae6"
+ }
+ },
+ {
+ "@id": "bids::mat.r$run.vr.aff12.1D",
"Label": "mat.r$run.vr.aff12.1D",
"AtLocation": "mat.r$run.vr.aff12.1D",
- "GeneratedBy": "urn:482e756c-1735-4552-aa69-a61ebd059d85",
+ "GeneratedBy": "urn:volreg-9AcKgwvI",
"digest": {
"sha256": "2e6e6c2ce8089cfa3c6e11dc72fca0cc8497f7a55faae2ced402de4867466c91"
}
},
{
- "@id": "urn:bd3ca465-bdf8-4c4b-bb01-4fb8ab6d1942",
+ "@id": "bids::rm.epi.all1",
"Label": "rm.epi.all1",
"AtLocation": "rm.epi.all1",
- "GeneratedBy": "urn:482e756c-1735-4552-aa69-a61ebd059d85",
+ "GeneratedBy": "urn:volreg-9AcKgwvI",
"digest": {
"sha256": "1023e3c16cecdbdc73ea456bcf33c2e5bb4f1e07094b73d29022d651e5fa3f85"
}
},
{
- "@id": "urn:dfe0e715-e555-4e6f-aa5c-8b7fcf92bf1f",
+ "@id": "bids::rm.epi.nomask.r$run",
"Label": "rm.epi.nomask.r$run",
"AtLocation": "rm.epi.nomask.r$run",
- "GeneratedBy": "urn:482e756c-1735-4552-aa69-a61ebd059d85",
+ "GeneratedBy": "urn:volreg-9AcKgwvI",
"digest": {
"sha256": "03d6cba0426c5545e350e6b63a19b0e46f8dfa2223fd08691753e8914a479e36"
}
},
{
- "@id": "urn:bd192b25-b688-4062-a17d-1fda0f6bdc79",
+ "@id": "bids::rm.epi.1.r$run",
"Label": "rm.epi.1.r$run",
"AtLocation": "rm.epi.1.r$run",
- "GeneratedBy": "urn:482e756c-1735-4552-aa69-a61ebd059d85",
+ "GeneratedBy": "urn:volreg-9AcKgwvI",
"digest": {
"sha256": "b1b9128c103ea246625db1a35e6f474a221ca6c1105a30df38aefdc4d5421e84"
}
},
{
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@@ -536,7 +546,7 @@
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@@ -544,7 +554,7 @@
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@@ -552,7 +562,7 @@
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@@ -560,7 +570,7 @@
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@@ -568,7 +578,7 @@
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@@ -576,7 +586,7 @@
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@@ -584,7 +594,7 @@
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@@ -592,7 +602,7 @@
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{
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@@ -600,7 +610,7 @@
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@@ -608,61 +618,61 @@
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@@ -670,7 +680,7 @@
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@@ -678,7 +688,7 @@
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@@ -686,34 +696,34 @@
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@@ -721,7 +731,7 @@
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@@ -729,7 +739,7 @@
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@@ -737,7 +747,7 @@
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@@ -745,7 +755,7 @@
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@@ -753,7 +763,7 @@
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@@ -761,7 +771,7 @@
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@@ -769,7 +779,7 @@
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@@ -777,7 +787,7 @@
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@@ -785,7 +795,7 @@
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@@ -793,7 +803,7 @@
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@@ -801,7 +811,7 @@
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@@ -809,124 +819,124 @@
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+ "@id": "bids::sum_ideal.1D",
"Label": "sum_ideal.1D",
"AtLocation": "sum_ideal.1D",
- "GeneratedBy": "urn:9f864701-7bb6-4ce8-b2ce-2d262e2ddccb",
+ "GeneratedBy": "urn:regress-4r98WB2m",
"digest": {
"sha256": "b2dccadcd84b2d26ec9685c4d1846baf2f11b867f31c36a08748d1c85467b01a"
}
},
{
- "@id": "urn:29e4cde7-2a6d-4eea-b111-f5ef59fa37e5",
+ "@id": "bids::X.stim.xmat.1D",
"Label": "X.stim.xmat.1D",
"AtLocation": "X.stim.xmat.1D",
- "GeneratedBy": "urn:9f864701-7bb6-4ce8-b2ce-2d262e2ddccb",
+ "GeneratedBy": "urn:regress-4r98WB2m",
"digest": {
"sha256": "7c61b2f4bbb9eb0cecb19f81faa3a79b94d547b7fb4087ed18e368619e0004e6"
}
},
{
- "@id": "urn:17a72a6f-17b3-484f-bd82-73ac77bb2582",
+ "@id": "bids::full_mask.$subj+tlrc",
"Label": "full_mask.$subj",
"AtLocation": "full_mask.$subj+tlrc",
"digest": {
@@ -934,34 +944,34 @@
}
},
{
- "@id": "urn:909efc3d-f27c-4252-ae34-a7ee61b99437",
+ "@id": "bids::blur.epits.1D",
"Label": "blur.epits.1D",
"AtLocation": "blur.epits.1D",
- "GeneratedBy": "urn:02c24147-6006-4aca-90ca-7d5d71e7a3e7",
+ "GeneratedBy": "urn:bluresti-4mrz2v5M",
"digest": {
"sha256": "623e70a42214e56babc1f1dca156e0b11ba09865dbd6ca9549d54ca2fc601515"
}
},
{
- "@id": "urn:38e524db-cce5-4263-884b-660ca792543f",
+ "@id": "bids::blur.errts.1D",
"Label": "blur.errts.1D",
"AtLocation": "blur.errts.1D",
- "GeneratedBy": "urn:02c24147-6006-4aca-90ca-7d5d71e7a3e7",
+ "GeneratedBy": "urn:bluresti-4mrz2v5M",
"digest": {
"sha256": "73969700079b5d3275536ac7eaf0e17571d7e74ec49553b6940f90d5718fc800"
}
},
{
- "@id": "urn:eaf3b170-c710-4fec-b825-95943f0d52c5",
+ "@id": "bids::ClustSim",
"Label": "ClustSim",
"AtLocation": "ClustSim",
- "GeneratedBy": "urn:02c24147-6006-4aca-90ca-7d5d71e7a3e7",
+ "GeneratedBy": "urn:bluresti-4mrz2v5M",
"digest": {
"sha256": "2e0cdba2c91902ba12d742a39cb20df66cfd705ba8de767fbf68aae8eb65c6f0"
}
},
{
- "@id": "urn:326203db-7e6d-4f53-9c88-902808ba180d",
+ "@id": "bids::pb00.$subj.r*.tcat+orig.HEAD",
"Label": "pb00.$subj.r*.tcat",
"AtLocation": "pb00.$subj.r*.tcat+orig.HEAD",
"digest": {
@@ -969,10 +979,10 @@
}
},
{
- "@id": "urn:9274c0b4-0087-4c70-9ddf-f04828990ad0",
+ "@id": "bids::-exit0",
"Label": "-exit0",
"AtLocation": "-exit0",
- "GeneratedBy": "urn:7bfd59ea-0347-411d-bf0e-18104d70adef",
+ "GeneratedBy": "urn:autobloc-c0QvQZQU",
"digest": {
"sha256": "871a4d3513ed2924cbb10c1c15a196eac4a46a05bdcc248e3bcdb23327b3ad90"
}
diff --git a/examples/from_parsers/afni/afni_hrf_tent_proc_block.png b/examples/from_parsers/afni/afni_hrf_tent_proc_block.png
index e261cc557..cd40a4257 100644
Binary files a/examples/from_parsers/afni/afni_hrf_tent_proc_block.png and b/examples/from_parsers/afni/afni_hrf_tent_proc_block.png differ
diff --git a/examples/from_parsers/afni/afni_other_template_proc.jsonld b/examples/from_parsers/afni/afni_other_template_proc.jsonld
index be9e14ef4..a0464b8f4 100644
--- a/examples/from_parsers/afni/afni_other_template_proc.jsonld
+++ b/examples/from_parsers/afni/afni_other_template_proc.jsonld
@@ -4,578 +4,581 @@
"Records": {
"Software": [
{
- "@id": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:afni-OtBYYGL9",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
- "Version": "afni24"
+ "Version": "afni24",
+ "AltIdentifier": "RRID:SCR_005927"
}
],
"Activities": [
{
- "@id": "urn:3c1c1553-6286-4be5-810b-d7bb1aad3ec1",
+ "@id": "urn:makedire-kLuppHkS",
"Label": "Make directory",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "mkdir $output_dir",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:3562deaa-5b0a-48b1-8eaa-afe1d78e7fc4",
+ "@id": "urn:makedire-lTaUmSAd",
"Label": "Make directory",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "mkdir $output_dir/stimuli",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:45a21908-a486-4dab-9e3f-3e855a3c19f6",
+ "@id": "urn:cp-dk0J9D1k",
"Label": "cp",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "cp ./afni_other_template/tone_counting_onset_times.txt ./afni_other_template/tone_counting_probe_duration.txt $output_dir/stimuli",
"Parameters": {},
"Used": [
- "urn:08fd597b-f4a7-45bd-979f-e58fef88f940",
- "urn:8b8d48c4-1094-4364-890c-10a4a9ead464"
+ "bids::afni_other_template/tone_counting_onset_times.txt",
+ "bids::afni_other_template/tone_counting_probe_duration.txt"
]
},
{
- "@id": "urn:7038bb21-462d-49e4-8648-b1f551beb4f9",
+ "@id": "urn:3dcopy-WCNzhSPt",
"Label": "3dcopy",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "3dcopy ./afni_other_template/sub-01_T1w.nii.gz $output_dir/sub-01_T1w",
"Parameters": {},
"Used": [
- "urn:5121e8ee-779f-4958-a088-9628349736cf"
+ "bids::afni_other_template/sub-01_T1w.nii.gz"
]
},
{
- "@id": "urn:2249bbef-f91d-41b1-ae95-d63b67759bbc",
+ "@id": "urn:3dtcat-lB2O2RCN",
"Label": "3dTcat",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat ./afni_other_template/sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Parameters": {},
"Used": [
- "urn:a4d31d13-6da8-4850-9575-5de3a1280498"
+ "bids::afni_other_template/sub-01_task-tonecounting_bold.nii.gz'[0..$]'"
]
},
{
- "@id": "urn:9a4a7929-932f-46fe-a3fe-77c45a06d74b",
+ "@id": "urn:3dtoutco-deMvTxSG",
"Label": "3dToutcount",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D",
"Parameters": {},
"Used": [
- "urn:10aafe1c-8130-438e-a532-2e58da437e99"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:03e05b5e-ee1f-43a2-9cb8-3b3034c2c122",
+ "@id": "urn:cat-eIpwJEgR",
"Label": "cat",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "cat outcount.r*.1D > outcount_rall.1D",
"Parameters": {},
"Used": [
- "urn:9b70dc38-50f3-4284-ae87-9649561e21e9"
+ "bids::outcount.r*.1D"
]
},
{
- "@id": "urn:62f97f3b-0511-4475-ac31-0099f01800fa",
+ "@id": "urn:3dtshift-2qIKy4sQ",
"Label": "3dTshift",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig",
"Parameters": {},
"Used": [
- "urn:10aafe1c-8130-438e-a532-2e58da437e99"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:b9a3f24e-6935-416e-a55d-0902e4eb5784",
+ "@id": "urn:alignepi-henTELhM",
"Label": "align_epi_anat.py",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off",
"Parameters": {},
"Used": [
- "urn:273e3231-0307-4f6b-ad9f-71c617e36b55",
- "urn:6bca44aa-e57a-4b10-bc56-9a2b0922c588"
+ "bids::pb01.$subj.r01.tshift+orig",
+ "bids::sub-01_T1w+orig"
]
},
{
- "@id": "urn:5bdc542e-3b26-4f1c-8d64-4b0b147b00a1",
+ "@id": "urn:autotlrc-7zuBWBEN",
"Label": "@auto_tlrc",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "@auto_tlrc -base TT_icbm452+tlrc -input sub-01_T1w_ns+orig -no_ss",
"Parameters": {},
"Used": [
- "urn:1a481e22-c17b-41ed-806a-aef76c109975",
- "urn:704c3a83-6508-4dcc-a911-ca32105c0e68"
+ "bids::TT_icbm452+tlrc",
+ "bids::sub-01_T1w_ns+orig"
]
},
{
- "@id": "urn:d4d47077-2a58-44c1-9a2a-a65f80dda07a",
+ "@id": "urn:catmatve-FtabqVUy",
"Label": "cat_matvec",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D",
"Parameters": {},
"Used": [
- "urn:eb18da33-1c19-4e8e-a0e5-78055b53b9e5"
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:56fe0b52-3b78-42fc-82ad-c7c01409aded",
+ "@id": "urn:3dvolreg-tRffTRPI",
"Label": "3dvolreg",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig",
"Parameters": {},
"Used": [
- "urn:a36ed554-5488-48fc-be06-70df64cc8ec0"
+ "bids::pb01.$subj.r$run.tshift+orig"
]
},
{
- "@id": "urn:b1a8e4d7-aaf9-4932-a2d4-bcd2f284903d",
+ "@id": "urn:3dcalc-uliTn0Km",
"Label": "3dcalc",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1",
"Parameters": {},
"Used": [
- "urn:a36ed554-5488-48fc-be06-70df64cc8ec0"
+ "bids::pb01.$subj.r$run.tshift+orig"
]
},
{
- "@id": "urn:2ada9729-6572-4dff-b711-2397a07617e3",
+ "@id": "urn:catmatve-z3tnuXYu",
"Label": "cat_matvec",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D",
"Parameters": {},
"Used": [
- "urn:eb18da33-1c19-4e8e-a0e5-78055b53b9e5"
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:f19716f5-039f-45fe-a46d-a39bde4da5fe",
+ "@id": "urn:3dalline-q1cVmk64",
"Label": "3dAllineate",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run",
"Parameters": {},
"Used": [
- "urn:5ef078c2-8950-457e-8bd2-92ee4e015f36",
- "urn:99c997b4-e99a-468e-9bb5-e3157f75c708",
- "urn:a36ed554-5488-48fc-be06-70df64cc8ec0"
+ "bids::mat.r$run.warp.aff12.1D",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:0914339d-cb34-404f-a5a8-73ead044ffae",
+ "@id": "urn:3dalline-s2NW7rWx",
"Label": "3dAllineate",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run",
"Parameters": {},
"Used": [
- "urn:5ef078c2-8950-457e-8bd2-92ee4e015f36",
- "urn:68db26d2-85c8-4e1c-82ef-57b20a491822",
- "urn:99c997b4-e99a-468e-9bb5-e3157f75c708"
+ "bids::mat.r$run.warp.aff12.1D",
+ "bids::rm.epi.all1+orig",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:5efcfaa0-9adb-4029-913f-25636acc25d1",
+ "@id": "urn:3dtstat-UGtBTEHb",
"Label": "3dTstat",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc",
"Parameters": {},
"Used": [
- "urn:0ac3c052-6f41-4547-870f-93b91ef0a84c"
+ "bids::rm.epi.1.r$run+tlrc"
]
},
{
- "@id": "urn:b12172b5-b120-4960-9e98-588064fe5d3d",
+ "@id": "urn:cat-KcIw3qKJ",
"Label": "cat",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "cat dfile.r*.1D > dfile_rall.1D",
"Parameters": {},
"Used": [
- "urn:b771dcfe-c85d-41b2-95d1-8040d6be5ea8"
+ "bids::dfile.r*.1D"
]
},
{
- "@id": "urn:6bfc4ae6-5c3a-4973-a4f8-1a23e1780ca3",
+ "@id": "urn:3dcopy-NOULEl6u",
"Label": "3dcopy",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents",
"Parameters": {},
"Used": [
- "urn:38872af1-a4bd-45a0-a592-b4555d33e8d3"
+ "bids::rm.epi.min.r01+tlrc"
]
},
{
- "@id": "urn:20ffe775-1cac-4507-b351-59b11f4615eb",
+ "@id": "urn:3dcalc-VzmVGent",
"Label": "3dcalc",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg",
"Parameters": {},
"Used": [
- "urn:6994398e-bc35-4415-9880-afd5e50c2276",
- "urn:78c5f0b6-e85c-4a57-8482-2c7215257822"
+ "bids::mask_epi_extents+tlrc",
+ "bids::rm.epi.nomask.r$run+tlrc"
]
},
{
- "@id": "urn:9c77fa9f-9cdc-4543-8a8d-38275793aeb0",
+ "@id": "urn:3dcopy-vIF4FBjA",
"Label": "3dcopy",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj",
"Parameters": {},
"Used": [
- "urn:99c997b4-e99a-468e-9bb5-e3157f75c708"
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:339f5128-3ff0-4e59-a183-937ead1f4756",
+ "@id": "urn:3dalline-lN5R4jHH",
"Label": "3dAllineate",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped",
"Parameters": {},
"Used": [
- "urn:cc327189-2989-42fc-94e7-b5d178a5013c"
+ "bids::anat_final.$subj+tlrc",
+ "bids::warp.anat.Xat.1D"
]
},
{
- "@id": "urn:0d46e72a-feab-4f6a-ba4f-10c89aa837dd",
+ "@id": "urn:3dmerge-vYzWDJi5",
"Label": "3dmerge",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc",
"Parameters": {},
"Used": [
- "urn:c6a9dd36-7589-4de6-8fa2-2fdcd43dfe88",
- "urn:c825f79e-70a4-49f9-871b-614b6f2037d2"
+ "bids::pb02.$subj.r$run.volreg+tlrc",
+ "bids::pb03.$subj.r$run.blur"
]
},
{
- "@id": "urn:6687424b-809a-4438-be40-6a6c62056b73",
+ "@id": "urn:3dautoma-4FNaiTgs",
"Label": "3dAutomask",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:130f1168-701b-4ae0-a70d-f5fd03e3e729"
+ "bids::pb03.$subj.r$run.blur+tlrc"
]
},
{
- "@id": "urn:2b1ff054-4323-4a81-a8b2-ab40230aae81",
+ "@id": "urn:3dmaskto-fja1GfuR",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:734090d0-c29c-41e6-b2f3-9ebcef2a771c",
+ "@id": "urn:3dresamp-ogTu8kZg",
"Label": "3dresample",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat",
"Parameters": {},
"Used": [
- "urn:8c983441-d454-42c9-a6c2-0ac8fd4e7844",
- "urn:99c997b4-e99a-468e-9bb5-e3157f75c708"
+ "bids::full_mask.$subj+tlrc",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:b3680a68-0f93-4b8e-a17c-8b4847593adf",
+ "@id": "urn:3dmaskto-5803fP7R",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj",
"Parameters": {},
"Used": [
- "urn:025f40a3-cd87-42e1-8012-f0f99da7b63f"
+ "bids::rm.resam.anat+tlrc"
]
},
{
- "@id": "urn:f5f40dd2-8ee4-4318-861b-9070b035cd17",
+ "@id": "urn:3dabover-UqFFmbFO",
"Label": "3dABoverlap",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt",
"Parameters": {},
"Used": [
- "urn:5942de21-999c-4019-8e04-6978dbabc03c",
- "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13"
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee"
]
},
{
- "@id": "urn:d1ec081b-dca9-4e34-b453-c9369a7d8f14",
+ "@id": "urn:3ddot-owooRRUE",
"Label": "3ddot",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt",
"Parameters": {},
"Used": [
- "urn:5942de21-999c-4019-8e04-6978dbabc03c",
- "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13"
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee"
]
},
{
- "@id": "urn:5a331a8f-133d-42f1-9cd8-db061bfd5b10",
+ "@id": "urn:3dresamp-iPUhLb1K",
"Label": "3dresample",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_icbm452+tlrc",
"Parameters": {},
"Used": [
- "urn:4bbd2eb8-4451-41fa-ab75-72b4178166f0",
- "urn:8c983441-d454-42c9-a6c2-0ac8fd4e7844"
+ "bids::/Users/u1591557/abin/TT_icbm452+tlrc",
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:580d3f39-2ed1-4d19-a7cb-afc1dca96dcd",
+ "@id": "urn:3dmaskto-vS1tRDqd",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group",
"Parameters": {},
"Used": [
- "urn:3ef69f43-addd-4b3e-a08d-72e58ac1cc5e"
+ "bids::rm.resam.group+tlrc"
]
},
{
- "@id": "urn:e7b3d762-06a3-4ab8-b5a0-36d56b8ca686",
+ "@id": "urn:3dtstat-Y5RmSFCv",
"Label": "3dTstat",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:130f1168-701b-4ae0-a70d-f5fd03e3e729"
+ "bids::pb03.$subj.r$run.blur+tlrc"
]
},
{
- "@id": "urn:cf862659-769f-4670-a1c9-e8942ea215d6",
+ "@id": "urn:3dcalc-K4X4DN9L",
"Label": "3dcalc",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale",
"Parameters": {},
"Used": [
- "urn:130f1168-701b-4ae0-a70d-f5fd03e3e729",
- "urn:6994398e-bc35-4415-9880-afd5e50c2276",
- "urn:7f2241be-00ff-42bb-a0ff-019307d039e3"
+ "bids::mask_epi_extents+tlrc",
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::rm.mean_r$run+tlrc"
]
},
{
- "@id": "urn:3cc4966c-5bed-4213-8972-39f8b5539223",
+ "@id": "urn:1dtoolpy-2AWzqdum",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D",
"Parameters": {},
"Used": [
- "urn:1e601f81-5617-42ef-af6a-fe9946483903"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:d16e1d03-91c1-44be-b2e2-01f8510acb7c",
+ "@id": "urn:1dtoolpy-SGulyxie",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D",
"Parameters": {},
"Used": [
- "urn:1e601f81-5617-42ef-af6a-fe9946483903"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:e6fbf256-8d35-47ec-876b-0357ad3e8ea9",
+ "@id": "urn:1dtoolpy-NB1SjVzV",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}",
"Parameters": {},
"Used": [
- "urn:1e601f81-5617-42ef-af6a-fe9946483903"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:01c14a4b-ed94-4cd7-aecf-b1cf5dbd0636",
+ "@id": "urn:3ddeconv-OoMAmZgE",
"Label": "3dDeconvolve",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj",
"Parameters": {},
"Used": [
- "urn:b0870209-65e9-4f07-bb0e-04a01421ebca"
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD"
]
},
{
- "@id": "urn:5ede64d7-ed6a-43e8-9d84-48c85ba3337d",
+ "@id": "urn:1dtoolpy-so1G4GNe",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt",
"Parameters": {},
"Used": [
- "urn:f66a5afb-048b-42f9-9463-57d589c88e3f"
+ "bids::X.xmat.1D"
]
},
{
- "@id": "urn:3b5a7e2d-88da-4698-9bd2-d28b7924cca7",
+ "@id": "urn:3dtcat-iIu57VXs",
"Label": "3dTcat",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD",
"Parameters": {},
"Used": [
- "urn:b0870209-65e9-4f07-bb0e-04a01421ebca"
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD"
]
},
{
- "@id": "urn:a8c28eb9-afad-491e-a43e-db03a1be3b6a",
+ "@id": "urn:3dtstat-7859jRZO",
"Label": "3dTstat",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:1e5f7ab0-fe79-4408-9285-7703f62ada81"
+ "bids::all_runs.$subj+tlrc%22[$ktrs]%22"
]
},
{
- "@id": "urn:b85d2b6f-cd72-46a9-9170-9e771394d1c3",
+ "@id": "urn:3dtstat-DkShidOa",
"Label": "3dTstat",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:a526b97a-55a5-4dc9-b3f9-814e2a95b0fe"
+ "bids::errts.$%7Bsubj%7D+tlrc%22[$ktrs]%22"
]
},
{
- "@id": "urn:e131bee9-ce48-4f8f-b464-6b794de8d1bb",
+ "@id": "urn:3dcalc-2J9dUflw",
"Label": "3dcalc",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj",
"Parameters": {},
"Used": [
- "urn:8c983441-d454-42c9-a6c2-0ac8fd4e7844",
- "urn:8d2f96db-47a1-47c6-b087-1619a32013c5",
- "urn:dee7b627-8bbc-4dbc-ab35-5cbe42b58957"
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.noise.all+tlrc",
+ "bids::rm.signal.all+tlrc"
]
},
{
- "@id": "urn:f8f82bba-8f80-41cb-b392-8fc935ddc6dd",
+ "@id": "urn:3dtnorm-pMUJuYjw",
"Label": "3dTnorm",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc",
"Parameters": {},
"Used": [
- "urn:97b11942-b410-490b-ad9c-02daf8206251"
+ "bids::errts.$%7Bsubj%7D+tlrc"
]
},
{
- "@id": "urn:199f626c-2d13-4c2a-b33b-34c7dc9aa47f",
+ "@id": "urn:3dmaskav-dvsD2epu",
"Label": "3dmaskave",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D",
"Parameters": {},
- "Used": []
+ "Used": [
+ "bids::full_mask.$subj+tlrc"
+ ]
},
{
- "@id": "urn:64a62b27-c7d0-4419-9538-7329af3dd622",
+ "@id": "urn:3dtstat-ktjNDoNF",
"Label": "3dTstat",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D",
"Parameters": {},
"Used": [
- "urn:a909d3a6-899d-4094-8057-76e748420573"
+ "bids::out.gcor.1D"
]
},
{
- "@id": "urn:0f15b38a-e271-450e-b7c3-14c46bfb8783",
+ "@id": "urn:3dcalc-SnxiqcDb",
"Label": "3dcalc",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP",
"Parameters": {},
"Used": [
- "urn:04ac1ef8-d5a2-4352-ab0a-d06ffa23be2b",
- "urn:8eeb9194-ceb7-49f9-8dae-c6dcc96a815c"
+ "bids::gmean.errts.unit.1D",
+ "bids::rm.errts.unit+tlrc"
]
},
{
- "@id": "urn:f19d6328-24e2-42c1-ad5d-1fc16a1931d0",
+ "@id": "urn:3dtstat-TQOy4xl8",
"Label": "3dTstat",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc",
"Parameters": {},
"Used": [
- "urn:9b37a68c-a27c-46e1-aa03-71a61fa288e5"
+ "bids::rm.DP+tlrc"
]
},
{
- "@id": "urn:5d7ec244-9551-4cb8-99be-7c1dad861e6c",
+ "@id": "urn:1dcat-4G6OUj2l",
"Label": "1dcat",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D",
"Parameters": {},
"Used": [
- "urn:a54b8921-42d3-47d2-a1ab-b3a0180ec2d4"
+ "bids::X.nocensor.xmat.1D'[3]'"
]
},
{
- "@id": "urn:b3121925-d672-4712-af45-24dbda16034d",
+ "@id": "urn:1dcat-gLkoyvOA",
"Label": "1dcat",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D",
"Parameters": {},
"Used": [
- "urn:2337b5ba-1b0e-478b-922a-f3823ffa09f3"
+ "bids::X.nocensor.xmat.1D'[4]'"
]
},
{
- "@id": "urn:1f07ea58-80fc-4ffe-944d-a5da07ab3038",
+ "@id": "urn:3dtstat-2ERP6fmu",
"Label": "3dTstat",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"",
"Parameters": {},
"Used": [
- "urn:b5713225-c925-41a4-8859-f1a45cb98b2f"
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:b8adece9-f65d-4d61-be15-5c33519b0f64",
+ "@id": "urn:1dcat-utdtUqJM",
"Label": "1dcat",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D",
"Parameters": {},
"Used": [
- "urn:b5713225-c925-41a4-8859-f1a45cb98b2f"
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:fd8de9a6-9747-4705-b203-874e9188fdfa",
+ "@id": "urn:3dfwhmx-5IqPC8kh",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D",
"Parameters": {},
"Used": [
- "urn:8c983441-d454-42c9-a6c2-0ac8fd4e7844"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:1abb0280-d736-438e-ab98-9bf91c2f4d5c",
+ "@id": "urn:3dfwhmx-NkxUKdaX",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D",
"Parameters": {},
"Used": [
- "urn:8c983441-d454-42c9-a6c2-0ac8fd4e7844"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:d43ba11a-f577-40fb-9530-87f9e2e7a6b6",
+ "@id": "urn:3dclusts-l5YDzEfr",
"Label": "3dClustSim",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim",
"Parameters": {},
"Used": [
- "urn:8c983441-d454-42c9-a6c2-0ac8fd4e7844"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:7852bcb8-5b20-4e3d-b988-b3d0a7cd856a",
+ "@id": "urn:genepire-29FksSzA",
"Label": "gen_epi_review.py",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD",
"Parameters": {},
"Used": [
- "urn:403fd3a8-2563-4e0c-857b-1bebc80b2d71"
+ "bids::pb00.$subj.r*.tcat+orig.HEAD"
]
},
{
- "@id": "urn:09be8e24-44e4-445c-a6a3-1fcee09bc3c6",
+ "@id": "urn:genssrev-n8NqP2Tq",
"Label": "gen_ss_review_scripts.py",
- "AssociatedWith": "urn:23bd1471-95b0-43c4-a5fa-bc085934d2e7",
+ "AssociatedWith": "urn:afni-OtBYYGL9",
"Command": "gen_ss_review_scripts.py -mot_limit 0.3 -exit0",
"Parameters": {
"-mot_limit": "0.3",
@@ -586,22 +589,22 @@
],
"Entities": [
{
- "@id": "urn:11f44ec4-ef4a-4148-851c-9470e7743b03",
+ "@id": "bids::$output_dir",
"Label": "$output_dir",
"AtLocation": "$output_dir",
- "GeneratedBy": "urn:3c1c1553-6286-4be5-810b-d7bb1aad3ec1",
+ "GeneratedBy": "urn:makedire-kLuppHkS",
"digest": {
"sha256": "9fa4c635e6533ddf2fed54295920052818d948c3ffe97bc753bd7336b453f8cb"
}
},
{
- "@id": "urn:8c0997e2-70f3-4866-a94d-51aa75171c3d",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:3562deaa-5b0a-48b1-8eaa-afe1d78e7fc4"
+ "GeneratedBy": "urn:makedire-lTaUmSAd"
},
{
- "@id": "urn:08fd597b-f4a7-45bd-979f-e58fef88f940",
+ "@id": "bids::afni_other_template/tone_counting_onset_times.txt",
"Label": "tone_counting_onset_times.txt",
"AtLocation": "./afni_other_template/tone_counting_onset_times.txt",
"digest": {
@@ -609,7 +612,7 @@
}
},
{
- "@id": "urn:8b8d48c4-1094-4364-890c-10a4a9ead464",
+ "@id": "bids::afni_other_template/tone_counting_probe_duration.txt",
"Label": "tone_counting_probe_duration.txt",
"AtLocation": "./afni_other_template/tone_counting_probe_duration.txt",
"digest": {
@@ -617,13 +620,13 @@
}
},
{
- "@id": "urn:7535c27a-c9e2-4406-b1d6-e8f46b6698db",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:45a21908-a486-4dab-9e3f-3e855a3c19f6"
+ "GeneratedBy": "urn:cp-dk0J9D1k"
},
{
- "@id": "urn:5121e8ee-779f-4958-a088-9628349736cf",
+ "@id": "bids::afni_other_template/sub-01_T1w.nii.gz",
"Label": "sub-01_T1w.nii.gz",
"AtLocation": "./afni_other_template/sub-01_T1w.nii.gz",
"digest": {
@@ -631,13 +634,13 @@
}
},
{
- "@id": "urn:3f1da5fc-6379-4555-a10d-e8797e678e28",
+ "@id": "bids::$output_dir/sub-01_T1w",
"Label": "sub-01_T1w",
"AtLocation": "$output_dir/sub-01_T1w",
- "GeneratedBy": "urn:7038bb21-462d-49e4-8648-b1f551beb4f9"
+ "GeneratedBy": "urn:3dcopy-WCNzhSPt"
},
{
- "@id": "urn:a4d31d13-6da8-4850-9575-5de3a1280498",
+ "@id": "bids::afni_other_template/sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Label": "sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "./afni_other_template/sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"digest": {
@@ -645,13 +648,13 @@
}
},
{
- "@id": "urn:695ea24d-a640-456f-ad93-86de46c462f6",
+ "@id": "bids::$output_dir/pb00.$subj.r01.tcat",
"Label": "pb00.$subj.r01.tcat",
"AtLocation": "$output_dir/pb00.$subj.r01.tcat",
- "GeneratedBy": "urn:2249bbef-f91d-41b1-ae95-d63b67759bbc"
+ "GeneratedBy": "urn:3dtcat-lB2O2RCN"
},
{
- "@id": "urn:10aafe1c-8130-438e-a532-2e58da437e99",
+ "@id": "bids::pb00.$subj.r$run.tcat+orig",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -659,16 +662,16 @@
}
},
{
- "@id": "urn:0041442d-735f-4ffe-8ae4-29004a1b4dfb",
+ "@id": "bids::outcount.r$run.1D",
"Label": "outcount.r$run.1D",
"AtLocation": "outcount.r$run.1D",
- "GeneratedBy": "urn:9a4a7929-932f-46fe-a3fe-77c45a06d74b",
+ "GeneratedBy": "urn:3dtoutco-deMvTxSG",
"digest": {
"sha256": "63d9f539e5470badc625d557109f68bc4eecbb02ca2667483739d52f95e5d0dd"
}
},
{
- "@id": "urn:9b70dc38-50f3-4284-ae87-9649561e21e9",
+ "@id": "bids::outcount.r*.1D",
"Label": "outcount.r*.1D",
"AtLocation": "outcount.r*.1D",
"digest": {
@@ -676,25 +679,25 @@
}
},
{
- "@id": "urn:7935d373-23a0-4ddf-9106-346d23889ad4",
+ "@id": "bids::outcount_rall.1D",
"Label": "outcount_rall.1D",
"AtLocation": "outcount_rall.1D",
- "GeneratedBy": "urn:03e05b5e-ee1f-43a2-9cb8-3b3034c2c122",
+ "GeneratedBy": "urn:cat-eIpwJEgR",
"digest": {
"sha256": "cb887fd5e4d5e9acb3a24820d0f7a62ed38a5ffb0fdedd373440ac0219fb186a"
}
},
{
- "@id": "urn:cd1e1f54-9b8d-481a-ab46-dba06afac2a6",
+ "@id": "bids::pb01.$subj.r$run.tshift",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift",
- "GeneratedBy": "urn:62f97f3b-0511-4475-ac31-0099f01800fa",
+ "GeneratedBy": "urn:3dtshift-2qIKy4sQ",
"digest": {
"sha256": "c6bf01cea8d2eac1d7a866f80b865c6e7d4b4e012dbb63d480ac9a8551162d72"
}
},
{
- "@id": "urn:6bca44aa-e57a-4b10-bc56-9a2b0922c588",
+ "@id": "bids::sub-01_T1w+orig",
"Label": "sub-01_T1w",
"AtLocation": "sub-01_T1w+orig",
"digest": {
@@ -702,7 +705,7 @@
}
},
{
- "@id": "urn:273e3231-0307-4f6b-ad9f-71c617e36b55",
+ "@id": "bids::pb01.$subj.r01.tshift+orig",
"Label": "pb01.$subj.r01.tshift",
"AtLocation": "pb01.$subj.r01.tshift+orig",
"digest": {
@@ -710,16 +713,16 @@
}
},
{
- "@id": "urn:53fd3582-ea72-482e-bf09-f3bdea960188",
+ "@id": "bids::_al_junk",
"Label": "_al_junk",
"AtLocation": "_al_junk",
- "GeneratedBy": "urn:b9a3f24e-6935-416e-a55d-0902e4eb5784",
+ "GeneratedBy": "urn:alignepi-henTELhM",
"digest": {
"sha256": "bd785a075a4c6446e1e54de9e628913f7f1c814e86b69a9fbfe933209e6d37b5"
}
},
{
- "@id": "urn:704c3a83-6508-4dcc-a911-ca32105c0e68",
+ "@id": "bids::TT_icbm452+tlrc",
"Label": "TT_icbm452",
"AtLocation": "TT_icbm452+tlrc",
"digest": {
@@ -727,7 +730,7 @@
}
},
{
- "@id": "urn:1a481e22-c17b-41ed-806a-aef76c109975",
+ "@id": "bids::sub-01_T1w_ns+orig",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+orig",
"digest": {
@@ -735,7 +738,7 @@
}
},
{
- "@id": "urn:eb18da33-1c19-4e8e-a0e5-78055b53b9e5",
+ "@id": "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc::WARP_DATA",
"digest": {
@@ -743,16 +746,16 @@
}
},
{
- "@id": "urn:cc327189-2989-42fc-94e7-b5d178a5013c",
+ "@id": "bids::warp.anat.Xat.1D",
"Label": "warp.anat.Xat.1D",
"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:d4d47077-2a58-44c1-9a2a-a65f80dda07a",
+ "GeneratedBy": "urn:catmatve-FtabqVUy",
"digest": {
"sha256": "800633fb5b4e9be64078bc181c4d5510ffb73fc5cccaf364c7fb6a294aa06728"
}
},
{
- "@id": "urn:a36ed554-5488-48fc-be06-70df64cc8ec0",
+ "@id": "bids::pb01.$subj.r$run.tshift+orig",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift+orig",
"digest": {
@@ -760,34 +763,34 @@
}
},
{
- "@id": "urn:55d1580e-1e33-4f71-889f-ca3253de9185",
+ "@id": "bids::mat.r$run.vr.aff12.1D",
"Label": "mat.r$run.vr.aff12.1D",
"AtLocation": "mat.r$run.vr.aff12.1D",
- "GeneratedBy": "urn:56fe0b52-3b78-42fc-82ad-c7c01409aded",
+ "GeneratedBy": "urn:3dvolreg-tRffTRPI",
"digest": {
"sha256": "2e6e6c2ce8089cfa3c6e11dc72fca0cc8497f7a55faae2ced402de4867466c91"
}
},
{
- "@id": "urn:18751749-1537-427c-9605-143c97185e93",
+ "@id": "bids::rm.epi.all1",
"Label": "rm.epi.all1",
"AtLocation": "rm.epi.all1",
- "GeneratedBy": "urn:b1a8e4d7-aaf9-4932-a2d4-bcd2f284903d",
+ "GeneratedBy": "urn:3dcalc-uliTn0Km",
"digest": {
"sha256": "1023e3c16cecdbdc73ea456bcf33c2e5bb4f1e07094b73d29022d651e5fa3f85"
}
},
{
- "@id": "urn:5ef078c2-8950-457e-8bd2-92ee4e015f36",
+ "@id": "bids::mat.r$run.warp.aff12.1D",
"Label": "mat.r$run.warp.aff12.1D",
"AtLocation": "mat.r$run.warp.aff12.1D",
- "GeneratedBy": "urn:2ada9729-6572-4dff-b711-2397a07617e3",
+ "GeneratedBy": "urn:catmatve-z3tnuXYu",
"digest": {
"sha256": "7c536b6f582a067c718f9e5ea2566cb535c73b43b4e15116c4c46045734d6eee"
}
},
{
- "@id": "urn:99c997b4-e99a-468e-9bb5-e3157f75c708",
+ "@id": "bids::sub-01_T1w_ns+tlrc",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc",
"digest": {
@@ -795,16 +798,16 @@
}
},
{
- "@id": "urn:21785f36-0629-4cc3-a83b-2de18aac9d52",
+ "@id": "bids::rm.epi.nomask.r$run",
"Label": "rm.epi.nomask.r$run",
"AtLocation": "rm.epi.nomask.r$run",
- "GeneratedBy": "urn:f19716f5-039f-45fe-a46d-a39bde4da5fe",
+ "GeneratedBy": "urn:3dalline-q1cVmk64",
"digest": {
"sha256": "03d6cba0426c5545e350e6b63a19b0e46f8dfa2223fd08691753e8914a479e36"
}
},
{
- "@id": "urn:68db26d2-85c8-4e1c-82ef-57b20a491822",
+ "@id": "bids::rm.epi.all1+orig",
"Label": "rm.epi.all1",
"AtLocation": "rm.epi.all1+orig",
"digest": {
@@ -812,16 +815,16 @@
}
},
{
- "@id": "urn:dc7e9182-537e-4e7e-8b63-8ce1b3041ae9",
+ "@id": "bids::rm.epi.1.r$run",
"Label": "rm.epi.1.r$run",
"AtLocation": "rm.epi.1.r$run",
- "GeneratedBy": "urn:0914339d-cb34-404f-a5a8-73ead044ffae",
+ "GeneratedBy": "urn:3dalline-s2NW7rWx",
"digest": {
"sha256": "b1b9128c103ea246625db1a35e6f474a221ca6c1105a30df38aefdc4d5421e84"
}
},
{
- "@id": "urn:0ac3c052-6f41-4547-870f-93b91ef0a84c",
+ "@id": "bids::rm.epi.1.r$run+tlrc",
"Label": "rm.epi.1.r$run",
"AtLocation": "rm.epi.1.r$run+tlrc",
"digest": {
@@ -829,16 +832,16 @@
}
},
{
- "@id": "urn:eb92f9df-ef75-491e-928e-c8328bd4532d",
+ "@id": "bids::rm.epi.min.r$run",
"Label": "rm.epi.min.r$run",
"AtLocation": "rm.epi.min.r$run",
- "GeneratedBy": "urn:5efcfaa0-9adb-4029-913f-25636acc25d1",
+ "GeneratedBy": "urn:3dtstat-UGtBTEHb",
"digest": {
"sha256": "b4418a96ddbbf25afdfd01ed0506ddebe009011ba18aed10137f994260fd1a66"
}
},
{
- "@id": "urn:b771dcfe-c85d-41b2-95d1-8040d6be5ea8",
+ "@id": "bids::dfile.r*.1D",
"Label": "dfile.r*.1D",
"AtLocation": "dfile.r*.1D",
"digest": {
@@ -846,16 +849,16 @@
}
},
{
- "@id": "urn:1e601f81-5617-42ef-af6a-fe9946483903",
+ "@id": "bids::dfile_rall.1D",
"Label": "dfile_rall.1D",
"AtLocation": "dfile_rall.1D",
- "GeneratedBy": "urn:b12172b5-b120-4960-9e98-588064fe5d3d",
+ "GeneratedBy": "urn:cat-KcIw3qKJ",
"digest": {
"sha256": "011e7296870a1ac7e15377fb0d529ed68710bb16b138bef6aeb6c645f437dcf2"
}
},
{
- "@id": "urn:38872af1-a4bd-45a0-a592-b4555d33e8d3",
+ "@id": "bids::rm.epi.min.r01+tlrc",
"Label": "rm.epi.min.r01",
"AtLocation": "rm.epi.min.r01+tlrc",
"digest": {
@@ -863,16 +866,16 @@
}
},
{
- "@id": "urn:e910de43-3fa5-4f82-bf5d-87a1382af00d",
+ "@id": "bids::mask_epi_extents",
"Label": "mask_epi_extents",
"AtLocation": "mask_epi_extents",
- "GeneratedBy": "urn:6bfc4ae6-5c3a-4973-a4f8-1a23e1780ca3",
+ "GeneratedBy": "urn:3dcopy-NOULEl6u",
"digest": {
"sha256": "a69dd71209516ec24e2b3364072ed54adff16619459b1c369866210ec642e987"
}
},
{
- "@id": "urn:78c5f0b6-e85c-4a57-8482-2c7215257822",
+ "@id": "bids::rm.epi.nomask.r$run+tlrc",
"Label": "rm.epi.nomask.r$run",
"AtLocation": "rm.epi.nomask.r$run+tlrc",
"digest": {
@@ -880,7 +883,7 @@
}
},
{
- "@id": "urn:6994398e-bc35-4415-9880-afd5e50c2276",
+ "@id": "bids::mask_epi_extents+tlrc",
"Label": "mask_epi_extents",
"AtLocation": "mask_epi_extents+tlrc",
"digest": {
@@ -888,34 +891,42 @@
}
},
{
- "@id": "urn:146e65ce-01ff-4b1b-93a6-8d9697dc5f58",
+ "@id": "bids::pb02.$subj.r$run.volreg",
"Label": "pb02.$subj.r$run.volreg",
"AtLocation": "pb02.$subj.r$run.volreg",
- "GeneratedBy": "urn:20ffe775-1cac-4507-b351-59b11f4615eb",
+ "GeneratedBy": "urn:3dcalc-VzmVGent",
"digest": {
"sha256": "8821927190ac1b3f8f9d9a5ec74f6468ae6c1cb736e58e5de2cdbe3543d5cc0c"
}
},
{
- "@id": "urn:c137464a-c04b-4db9-8189-34c3690525ad",
+ "@id": "bids::anat_final.$subj",
"Label": "anat_final.$subj",
"AtLocation": "anat_final.$subj",
- "GeneratedBy": "urn:9c77fa9f-9cdc-4543-8a8d-38275793aeb0",
+ "GeneratedBy": "urn:3dcopy-vIF4FBjA",
"digest": {
"sha256": "69b750d004bdba337de0b4ffa683bd92bc8f34b854d320327839ad264b28c4c5"
}
},
{
- "@id": "urn:7e44b770-8d71-419f-acc7-53ddd529ea51",
+ "@id": "bids::anat_final.$subj+tlrc",
+ "Label": "anat_final.$subj",
+ "AtLocation": "anat_final.$subj+tlrc",
+ "digest": {
+ "sha256": "94eb1853614cc085b22772c011f119f6a0ad7ec06cba2850587762e7f1a6eae6"
+ }
+ },
+ {
+ "@id": "bids::anat_w_skull_warped",
"Label": "anat_w_skull_warped",
"AtLocation": "anat_w_skull_warped",
- "GeneratedBy": "urn:339f5128-3ff0-4e59-a183-937ead1f4756",
+ "GeneratedBy": "urn:3dalline-lN5R4jHH",
"digest": {
"sha256": "462fdb8cd2b882e250fee3c6adb7acf0b0b9a9edb3e1cadf9d45d16180871105"
}
},
{
- "@id": "urn:c6a9dd36-7589-4de6-8fa2-2fdcd43dfe88",
+ "@id": "bids::pb03.$subj.r$run.blur",
"Label": "pb03.$subj.r$run.blur",
"AtLocation": "pb03.$subj.r$run.blur",
"digest": {
@@ -923,7 +934,7 @@
}
},
{
- "@id": "urn:c825f79e-70a4-49f9-871b-614b6f2037d2",
+ "@id": "bids::pb02.$subj.r$run.volreg+tlrc",
"Label": "pb02.$subj.r$run.volreg",
"AtLocation": "pb02.$subj.r$run.volreg+tlrc",
"digest": {
@@ -931,7 +942,7 @@
}
},
{
- "@id": "urn:130f1168-701b-4ae0-a70d-f5fd03e3e729",
+ "@id": "bids::pb03.$subj.r$run.blur+tlrc",
"Label": "pb03.$subj.r$run.blur",
"AtLocation": "pb03.$subj.r$run.blur+tlrc",
"digest": {
@@ -939,25 +950,25 @@
}
},
{
- "@id": "urn:c04a8817-03a1-42de-bceb-57bfcf5274c3",
+ "@id": "bids::rm.mask_r$run",
"Label": "rm.mask_r$run",
"AtLocation": "rm.mask_r$run",
- "GeneratedBy": "urn:6687424b-809a-4438-be40-6a6c62056b73",
+ "GeneratedBy": "urn:3dautoma-4FNaiTgs",
"digest": {
"sha256": "d251275ec819884fd84596da3fa356f3d83709d66170c45ad73c2f14ee830b35"
}
},
{
- "@id": "urn:5c99fbfa-175c-45d4-81cc-ba9545d0077a",
+ "@id": "bids::full_mask.$subj",
"Label": "full_mask.$subj",
"AtLocation": "full_mask.$subj",
- "GeneratedBy": "urn:2b1ff054-4323-4a81-a8b2-ab40230aae81",
+ "GeneratedBy": "urn:3dmaskto-fja1GfuR",
"digest": {
"sha256": "02da8c6ed741c00cb6ccb8da25bf6ca853afb9100b992c854209afde9e30918f"
}
},
{
- "@id": "urn:8c983441-d454-42c9-a6c2-0ac8fd4e7844",
+ "@id": "bids::full_mask.$subj+tlrc",
"Label": "full_mask.$subj",
"AtLocation": "full_mask.$subj+tlrc",
"digest": {
@@ -965,16 +976,16 @@
}
},
{
- "@id": "urn:ddace0ae-fa26-408a-a611-f76c0d6494a6",
+ "@id": "bids::rm.resam.anat",
"Label": "rm.resam.anat",
"AtLocation": "rm.resam.anat",
- "GeneratedBy": "urn:734090d0-c29c-41e6-b2f3-9ebcef2a771c",
+ "GeneratedBy": "urn:3dresamp-ogTu8kZg",
"digest": {
"sha256": "fe716d2bdbce773476ef264f2cd990f7114d7f2d7245c0cbeb10e8abc7feff9b"
}
},
{
- "@id": "urn:025f40a3-cd87-42e1-8012-f0f99da7b63f",
+ "@id": "bids::rm.resam.anat+tlrc",
"Label": "rm.resam.anat",
"AtLocation": "rm.resam.anat+tlrc",
"digest": {
@@ -982,16 +993,16 @@
}
},
{
- "@id": "urn:8f9d2d72-9169-489e-a681-528405d545fb",
+ "@id": "bids::mask_anat.$subj",
"Label": "mask_anat.$subj",
"AtLocation": "mask_anat.$subj",
- "GeneratedBy": "urn:b3680a68-0f93-4b8e-a17c-8b4847593adf",
+ "GeneratedBy": "urn:3dmaskto-5803fP7R",
"digest": {
"sha256": "d3f1becfb7c7d234361e002cc34c3ca5b5333640259f572993b773f6973f0e98"
}
},
{
- "@id": "urn:5942de21-999c-4019-8e04-6978dbabc03c",
+ "@id": "bids::mask_anat.$subj+tlrc",
"Label": "mask_anat.$subj",
"AtLocation": "mask_anat.$subj+tlrc",
"digest": {
@@ -999,7 +1010,7 @@
}
},
{
- "@id": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
+ "@id": "bids::tee",
"Label": "tee",
"AtLocation": "tee",
"digest": {
@@ -1007,7 +1018,7 @@
}
},
{
- "@id": "urn:4bbd2eb8-4451-41fa-ab75-72b4178166f0",
+ "@id": "bids::/Users/u1591557/abin/TT_icbm452+tlrc",
"Label": "TT_icbm452",
"AtLocation": "/Users/u1591557/abin/TT_icbm452+tlrc",
"digest": {
@@ -1015,16 +1026,16 @@
}
},
{
- "@id": "urn:2486d696-f1a8-466b-ba4b-839949c75305",
+ "@id": "bids::rm.resam.group",
"Label": "rm.resam.group",
"AtLocation": "./rm.resam.group",
- "GeneratedBy": "urn:5a331a8f-133d-42f1-9cd8-db061bfd5b10",
+ "GeneratedBy": "urn:3dresamp-iPUhLb1K",
"digest": {
"sha256": "79e954aee237a244a2498f6f7811a10a1c4508563eebd38000c13f2c145942c9"
}
},
{
- "@id": "urn:3ef69f43-addd-4b3e-a08d-72e58ac1cc5e",
+ "@id": "bids::rm.resam.group+tlrc",
"Label": "rm.resam.group",
"AtLocation": "rm.resam.group+tlrc",
"digest": {
@@ -1032,25 +1043,25 @@
}
},
{
- "@id": "urn:0255d49b-7932-4898-932c-f76b2883d865",
+ "@id": "bids::mask_group",
"Label": "mask_group",
"AtLocation": "mask_group",
- "GeneratedBy": "urn:580d3f39-2ed1-4d19-a7cb-afc1dca96dcd",
+ "GeneratedBy": "urn:3dmaskto-vS1tRDqd",
"digest": {
"sha256": "d7093b26470ded8d7e939359017b18d28a2da4c6bb702c1183df20bca614f949"
}
},
{
- "@id": "urn:1228f105-1246-44de-ba34-4b6a2c0574be",
+ "@id": "bids::rm.mean_r$run",
"Label": "rm.mean_r$run",
"AtLocation": "rm.mean_r$run",
- "GeneratedBy": "urn:e7b3d762-06a3-4ab8-b5a0-36d56b8ca686",
+ "GeneratedBy": "urn:3dtstat-Y5RmSFCv",
"digest": {
"sha256": "17047aa0c91933cf57076e6ce78a48ebe5975d6881ca47c8357cbd66e0fde9fb"
}
},
{
- "@id": "urn:7f2241be-00ff-42bb-a0ff-019307d039e3",
+ "@id": "bids::rm.mean_r$run+tlrc",
"Label": "rm.mean_r$run",
"AtLocation": "rm.mean_r$run+tlrc",
"digest": {
@@ -1058,34 +1069,34 @@
}
},
{
- "@id": "urn:6125b559-65da-4d84-91f6-f5e0bb74253d",
+ "@id": "bids::pb04.$subj.r$run.scale",
"Label": "pb04.$subj.r$run.scale",
"AtLocation": "pb04.$subj.r$run.scale",
- "GeneratedBy": "urn:cf862659-769f-4670-a1c9-e8942ea215d6",
+ "GeneratedBy": "urn:3dcalc-K4X4DN9L",
"digest": {
"sha256": "1e6d4160b1a7b120e8201df43aabc22c6fe0e0b0788b12c76c8d63554897a790"
}
},
{
- "@id": "urn:b8510365-9a63-4fce-a710-1fac7f827369",
+ "@id": "bids::motion_demean.1D",
"Label": "motion_demean.1D",
"AtLocation": "motion_demean.1D",
- "GeneratedBy": "urn:3cc4966c-5bed-4213-8972-39f8b5539223",
+ "GeneratedBy": "urn:1dtoolpy-2AWzqdum",
"digest": {
"sha256": "1de1e10c0120caa7b6cf441bd141a5a76716e458676ae56ce693039eecb79c85"
}
},
{
- "@id": "urn:c5509615-585c-4c3e-89d6-842233802aa1",
+ "@id": "bids::motion_deriv.1D",
"Label": "motion_deriv.1D",
"AtLocation": "motion_deriv.1D",
- "GeneratedBy": "urn:d16e1d03-91c1-44be-b2e2-01f8510acb7c",
+ "GeneratedBy": "urn:1dtoolpy-SGulyxie",
"digest": {
"sha256": "47185bf319e91642ad6f2a396a43fc9f8db7b82f2a9aef326bfe4a955120038b"
}
},
{
- "@id": "urn:b0870209-65e9-4f07-bb0e-04a01421ebca",
+ "@id": "bids::pb04.$subj.r*.scale+tlrc.HEAD",
"Label": "pb04.$subj.r*.scale",
"AtLocation": "pb04.$subj.r*.scale+tlrc.HEAD",
"digest": {
@@ -1093,25 +1104,25 @@
}
},
{
- "@id": "urn:f66a5afb-048b-42f9-9463-57d589c88e3f",
+ "@id": "bids::X.xmat.1D",
"Label": "X.xmat.1D",
"AtLocation": "X.xmat.1D",
- "GeneratedBy": "urn:01c14a4b-ed94-4cd7-aecf-b1cf5dbd0636",
+ "GeneratedBy": "urn:3ddeconv-OoMAmZgE",
"digest": {
"sha256": "cdbd4f4edf6fa02a9d7fcf9a3e593893438e9279c9523fbb6993630a83ad5162"
}
},
{
- "@id": "urn:6a709cf3-59bd-4bef-8036-427403483640",
+ "@id": "bids::all_runs.$subj",
"Label": "all_runs.$subj",
"AtLocation": "all_runs.$subj",
- "GeneratedBy": "urn:3b5a7e2d-88da-4698-9bd2-d28b7924cca7",
+ "GeneratedBy": "urn:3dtcat-iIu57VXs",
"digest": {
"sha256": "bcf27fc2e339e751d0ea9bba931674c21fd9d434ff411330f4df55f872a8cc7e"
}
},
{
- "@id": "urn:1e5f7ab0-fe79-4408-9285-7703f62ada81",
+ "@id": "bids::all_runs.$subj+tlrc%22[$ktrs]%22",
"Label": "all_runs.$subj",
"AtLocation": "all_runs.$subj+tlrc\"[$ktrs]\"",
"digest": {
@@ -1119,16 +1130,16 @@
}
},
{
- "@id": "urn:48ef0bfa-2e36-4e1d-b1cd-a8c2ae60de83",
+ "@id": "bids::rm.signal.all",
"Label": "rm.signal.all",
"AtLocation": "rm.signal.all",
- "GeneratedBy": "urn:a8c28eb9-afad-491e-a43e-db03a1be3b6a",
+ "GeneratedBy": "urn:3dtstat-7859jRZO",
"digest": {
"sha256": "bda68a16c0afd5e55d4d7415c8c959e61a9aad7898dd456b0f3bb597363dde31"
}
},
{
- "@id": "urn:a526b97a-55a5-4dc9-b3f9-814e2a95b0fe",
+ "@id": "bids::errts.$%7Bsubj%7D+tlrc%22[$ktrs]%22",
"Label": "errts.${subj}",
"AtLocation": "errts.${subj}+tlrc\"[$ktrs]\"",
"digest": {
@@ -1136,16 +1147,16 @@
}
},
{
- "@id": "urn:7be37559-6bf1-48c8-a499-879e7c0a4005",
+ "@id": "bids::rm.noise.all",
"Label": "rm.noise.all",
"AtLocation": "rm.noise.all",
- "GeneratedBy": "urn:b85d2b6f-cd72-46a9-9170-9e771394d1c3",
+ "GeneratedBy": "urn:3dtstat-DkShidOa",
"digest": {
"sha256": "431314eb75d086ce08373b3a374427969e89414c4a2d607e449c1f6485c547af"
}
},
{
- "@id": "urn:dee7b627-8bbc-4dbc-ab35-5cbe42b58957",
+ "@id": "bids::rm.signal.all+tlrc",
"Label": "rm.signal.all",
"AtLocation": "rm.signal.all+tlrc",
"digest": {
@@ -1153,7 +1164,7 @@
}
},
{
- "@id": "urn:8d2f96db-47a1-47c6-b087-1619a32013c5",
+ "@id": "bids::rm.noise.all+tlrc",
"Label": "rm.noise.all",
"AtLocation": "rm.noise.all+tlrc",
"digest": {
@@ -1161,16 +1172,16 @@
}
},
{
- "@id": "urn:2eaa128d-c17c-4f91-8b9b-8e8937bceee6",
+ "@id": "bids::TSNR.$subj",
"Label": "TSNR.$subj",
"AtLocation": "TSNR.$subj",
- "GeneratedBy": "urn:e131bee9-ce48-4f8f-b464-6b794de8d1bb",
+ "GeneratedBy": "urn:3dcalc-2J9dUflw",
"digest": {
"sha256": "303f183145a1e295686c08335d3b70753777cf0fa0b3f9628cf8de5471359a00"
}
},
{
- "@id": "urn:97b11942-b410-490b-ad9c-02daf8206251",
+ "@id": "bids::errts.$%7Bsubj%7D+tlrc",
"Label": "errts.${subj}",
"AtLocation": "errts.${subj}+tlrc",
"digest": {
@@ -1178,25 +1189,25 @@
}
},
{
- "@id": "urn:4688a0da-b830-4568-ab4d-6194265ae343",
+ "@id": "bids::rm.errts.unit",
"Label": "rm.errts.unit",
"AtLocation": "rm.errts.unit",
- "GeneratedBy": "urn:f8f82bba-8f80-41cb-b392-8fc935ddc6dd",
+ "GeneratedBy": "urn:3dtnorm-pMUJuYjw",
"digest": {
"sha256": "03b570ad773a00f51ab7e6cdedfebdeca45f5356de0c25f9e3be44d7bf2c7151"
}
},
{
- "@id": "urn:8eeb9194-ceb7-49f9-8dae-c6dcc96a815c",
+ "@id": "bids::gmean.errts.unit.1D",
"Label": "gmean.errts.unit.1D",
"AtLocation": "gmean.errts.unit.1D",
- "GeneratedBy": "urn:199f626c-2d13-4c2a-b33b-34c7dc9aa47f",
+ "GeneratedBy": "urn:3dmaskav-dvsD2epu",
"digest": {
"sha256": "a35a66cce2e2d487762823c197ca1edc450a9887f46f125826b69c5021662f95"
}
},
{
- "@id": "urn:a909d3a6-899d-4094-8057-76e748420573",
+ "@id": "bids::out.gcor.1D",
"Label": "out.gcor.1D",
"AtLocation": "out.gcor.1D",
"digest": {
@@ -1204,16 +1215,16 @@
}
},
{
- "@id": "urn:201ec870-0145-4a31-9d4a-0cbac8184ca4",
+ "@id": "urn:uuid:92d36e57-fdf4-41be-ac3f-ff88ff2caa71",
"Label": "-",
"AtLocation": "-",
- "GeneratedBy": "urn:64a62b27-c7d0-4419-9538-7329af3dd622",
+ "GeneratedBy": "urn:3dtstat-ktjNDoNF",
"digest": {
"sha256": "dac304c9f20899ca1ef5aa403e565345fd0ff4ed80c35f82007c9b03a68292b3"
}
},
{
- "@id": "urn:04ac1ef8-d5a2-4352-ab0a-d06ffa23be2b",
+ "@id": "bids::rm.errts.unit+tlrc",
"Label": "rm.errts.unit",
"AtLocation": "rm.errts.unit+tlrc",
"digest": {
@@ -1221,16 +1232,16 @@
}
},
{
- "@id": "urn:ae357776-5485-4889-bb9e-c387428c9166",
+ "@id": "bids::rm.DP",
"Label": "rm.DP",
"AtLocation": "rm.DP",
- "GeneratedBy": "urn:0f15b38a-e271-450e-b7c3-14c46bfb8783",
+ "GeneratedBy": "urn:3dcalc-SnxiqcDb",
"digest": {
"sha256": "06a0bfbc609c1a06ecf93c479a3288d2911c7f5f3e93cf49c5d26f721c2035ed"
}
},
{
- "@id": "urn:9b37a68c-a27c-46e1-aa03-71a61fa288e5",
+ "@id": "bids::rm.DP+tlrc",
"Label": "rm.DP",
"AtLocation": "rm.DP+tlrc",
"digest": {
@@ -1238,16 +1249,16 @@
}
},
{
- "@id": "urn:fba22008-1aa9-4493-997f-2cff7479fcff",
+ "@id": "bids::corr_brain",
"Label": "corr_brain",
"AtLocation": "corr_brain",
- "GeneratedBy": "urn:f19d6328-24e2-42c1-ad5d-1fc16a1931d0",
+ "GeneratedBy": "urn:3dtstat-TQOy4xl8",
"digest": {
"sha256": "74e3aeae0da338b871ab5dc9e8859a4e81fcf1b3c0042cd22fe337eb7baf5eae"
}
},
{
- "@id": "urn:a54b8921-42d3-47d2-a1ab-b3a0180ec2d4",
+ "@id": "bids::X.nocensor.xmat.1D'[3]'",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D'[3]'",
"digest": {
@@ -1255,16 +1266,16 @@
}
},
{
- "@id": "urn:63e9e22e-6a3c-4664-91c2-76c0146eb36e",
+ "@id": "bids::ideal_tone_counting.1D",
"Label": "ideal_tone_counting.1D",
"AtLocation": "ideal_tone_counting.1D",
- "GeneratedBy": "urn:5d7ec244-9551-4cb8-99be-7c1dad861e6c",
+ "GeneratedBy": "urn:1dcat-4G6OUj2l",
"digest": {
"sha256": "9bb1cabac5ce7ca19dffa5cd6336a9bf82d362fea2ce9341978406e421b5333c"
}
},
{
- "@id": "urn:2337b5ba-1b0e-478b-922a-f3823ffa09f3",
+ "@id": "bids::X.nocensor.xmat.1D'[4]'",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D'[4]'",
"digest": {
@@ -1272,16 +1283,16 @@
}
},
{
- "@id": "urn:78c653e8-e20d-4eb7-82e7-c91622e60556",
+ "@id": "bids::ideal_probe.1D",
"Label": "ideal_probe.1D",
"AtLocation": "ideal_probe.1D",
- "GeneratedBy": "urn:b3121925-d672-4712-af45-24dbda16034d",
+ "GeneratedBy": "urn:1dcat-gLkoyvOA",
"digest": {
"sha256": "705d93afa8b6ded9f4f572db3f967b54e9906942669af51dd8287a9863bb4288"
}
},
{
- "@id": "urn:b5713225-c925-41a4-8859-f1a45cb98b2f",
+ "@id": "bids::X.nocensor.xmat.1D%22[$reg_cols]%22",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D\"[$reg_cols]\"",
"digest": {
@@ -1289,52 +1300,52 @@
}
},
{
- "@id": "urn:970956ae-ef48-4c77-b7bf-2eaaed636b16",
+ "@id": "bids::sum_ideal.1D",
"Label": "sum_ideal.1D",
"AtLocation": "sum_ideal.1D",
- "GeneratedBy": "urn:1f07ea58-80fc-4ffe-944d-a5da07ab3038",
+ "GeneratedBy": "urn:3dtstat-2ERP6fmu",
"digest": {
"sha256": "b2dccadcd84b2d26ec9685c4d1846baf2f11b867f31c36a08748d1c85467b01a"
}
},
{
- "@id": "urn:4ecbb73d-2077-4d41-85ef-8d76176486f4",
+ "@id": "bids::X.stim.xmat.1D",
"Label": "X.stim.xmat.1D",
"AtLocation": "X.stim.xmat.1D",
- "GeneratedBy": "urn:b8adece9-f65d-4d61-be15-5c33519b0f64",
+ "GeneratedBy": "urn:1dcat-utdtUqJM",
"digest": {
"sha256": "7c61b2f4bbb9eb0cecb19f81faa3a79b94d547b7fb4087ed18e368619e0004e6"
}
},
{
- "@id": "urn:7ece0046-69d0-453f-b841-4914e61a6f52",
+ "@id": "bids::blur.epits.1D",
"Label": "blur.epits.1D",
"AtLocation": "blur.epits.1D",
- "GeneratedBy": "urn:fd8de9a6-9747-4705-b203-874e9188fdfa",
+ "GeneratedBy": "urn:3dfwhmx-5IqPC8kh",
"digest": {
"sha256": "623e70a42214e56babc1f1dca156e0b11ba09865dbd6ca9549d54ca2fc601515"
}
},
{
- "@id": "urn:fd80192e-6ca9-4f86-97ad-12b807eae30f",
+ "@id": "bids::blur.errts.1D",
"Label": "blur.errts.1D",
"AtLocation": "blur.errts.1D",
- "GeneratedBy": "urn:1abb0280-d736-438e-ab98-9bf91c2f4d5c",
+ "GeneratedBy": "urn:3dfwhmx-NkxUKdaX",
"digest": {
"sha256": "73969700079b5d3275536ac7eaf0e17571d7e74ec49553b6940f90d5718fc800"
}
},
{
- "@id": "urn:52627452-6a11-4548-851b-68d0c1c1247a",
+ "@id": "bids::ClustSim",
"Label": "ClustSim",
"AtLocation": "ClustSim",
- "GeneratedBy": "urn:d43ba11a-f577-40fb-9530-87f9e2e7a6b6",
+ "GeneratedBy": "urn:3dclusts-l5YDzEfr",
"digest": {
"sha256": "2e0cdba2c91902ba12d742a39cb20df66cfd705ba8de767fbf68aae8eb65c6f0"
}
},
{
- "@id": "urn:403fd3a8-2563-4e0c-857b-1bebc80b2d71",
+ "@id": "bids::pb00.$subj.r*.tcat+orig.HEAD",
"Label": "pb00.$subj.r*.tcat",
"AtLocation": "pb00.$subj.r*.tcat+orig.HEAD",
"digest": {
@@ -1342,10 +1353,10 @@
}
},
{
- "@id": "urn:e00697fb-7e8b-4090-8a45-79be638ae447",
+ "@id": "bids::-exit0",
"Label": "-exit0",
"AtLocation": "-exit0",
- "GeneratedBy": "urn:09be8e24-44e4-445c-a6a3-1fcee09bc3c6",
+ "GeneratedBy": "urn:genssrev-n8NqP2Tq",
"digest": {
"sha256": "871a4d3513ed2924cbb10c1c15a196eac4a46a05bdcc248e3bcdb23327b3ad90"
}
diff --git a/examples/from_parsers/afni/afni_other_template_proc.png b/examples/from_parsers/afni/afni_other_template_proc.png
index 7b78a9cb5..260db6ad8 100644
Binary files a/examples/from_parsers/afni/afni_other_template_proc.png and b/examples/from_parsers/afni/afni_other_template_proc.png differ
diff --git a/examples/from_parsers/afni/afni_other_template_proc_block.jsonld b/examples/from_parsers/afni/afni_other_template_proc_block.jsonld
index 4e367698d..e50c06381 100644
--- a/examples/from_parsers/afni/afni_other_template_proc_block.jsonld
+++ b/examples/from_parsers/afni/afni_other_template_proc_block.jsonld
@@ -4,187 +4,189 @@
"Records": {
"Software": [
{
- "@id": "urn:4a0a738c-5446-434b-b37e-185850b2c815",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:afni-YYVukVUa",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
- "Version": "afni24"
+ "Version": "afni24",
+ "AltIdentifier": "RRID:SCR_005927"
}
],
"Activities": [
{
- "@id": "urn:5c3f74df-5e15-416e-8c19-763fdf4fac10",
+ "@id": "urn:autobloc-NCfx652N",
"Label": "auto block: setup",
- "AssociatedWith": "urn:4a0a738c-5446-434b-b37e-185850b2c815",
+ "AssociatedWith": "urn:afni-YYVukVUa",
"Command": "mkdir $output_dir; mkdir $output_dir/stimuli; cp ./afni_other_template/tone_counting_onset_times.txt ./afni_other_template/tone_counting_probe_duration.txt $output_dir/stimuli; 3dcopy ./afni_other_template/sub-01_T1w.nii.gz $output_dir/sub-01_T1w; ",
"Used": [
- "urn:36b08c61-b83f-4357-8020-44cbf06f0fe0",
- "urn:e36061c5-57b1-4a49-ae7e-0484d46f0d41",
- "urn:f8a1c91e-1034-4376-98f7-2013730c5cc8"
+ "bids::afni_other_template/tone_counting_onset_times.txt",
+ "bids::afni_other_template/tone_counting_probe_duration.txt",
+ "bids::afni_other_template/sub-01_T1w.nii.gz"
]
},
{
- "@id": "urn:535bc829-b0d7-4089-a924-ada0c271af18",
+ "@id": "urn:autobloc-1lc3rowI",
"Label": "auto block: tcat",
- "AssociatedWith": "urn:4a0a738c-5446-434b-b37e-185850b2c815",
+ "AssociatedWith": "urn:afni-YYVukVUa",
"Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat ./afni_other_template/sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ",
"Used": [
- "urn:bf65fe1e-ad76-47f9-a992-39f329cd3457"
+ "bids::afni_other_template/sub-01_task-tonecounting_bold.nii.gz'[0..$]'"
]
},
{
- "@id": "urn:adb1b0ff-e8c1-4355-9b01-b20a5b01cf0b",
+ "@id": "urn:autobloc-4CqOaPM0",
"Label": "auto block: outcount",
- "AssociatedWith": "urn:4a0a738c-5446-434b-b37e-185850b2c815",
+ "AssociatedWith": "urn:afni-YYVukVUa",
"Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ",
"Used": [
- "urn:5d41178a-42ce-4693-8b77-8e7c79d0157d",
- "urn:e419e2b5-ff1d-4b58-b687-eccac743696d"
+ "bids::pb00.$subj.r$run.tcat+orig",
+ "bids::outcount.r*.1D"
]
},
{
- "@id": "urn:7e5eb7b6-e0e9-4515-8d8a-332f2753d583",
+ "@id": "urn:tshift-iPalhda0",
"Label": "tshift",
- "AssociatedWith": "urn:4a0a738c-5446-434b-b37e-185850b2c815",
+ "AssociatedWith": "urn:afni-YYVukVUa",
"Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ",
"Used": [
- "urn:5d41178a-42ce-4693-8b77-8e7c79d0157d"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:308ee1ba-15be-4db5-a4f2-9e4ad49adee8",
+ "@id": "urn:align-iJXWvura",
"Label": "align",
- "AssociatedWith": "urn:4a0a738c-5446-434b-b37e-185850b2c815",
+ "AssociatedWith": "urn:afni-YYVukVUa",
"Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ",
"Used": [
- "urn:a6cf3443-a7a0-40c4-9036-dfeb288a68a3",
- "urn:b9c6adb1-025e-452c-b725-c94944c871d2"
+ "bids::pb01.$subj.r01.tshift+orig",
+ "bids::sub-01_T1w+orig"
]
},
{
- "@id": "urn:f19f51ad-5e08-412b-b80a-9023c70693b4",
+ "@id": "urn:tlrc-KjPkMBFn",
"Label": "tlrc",
- "AssociatedWith": "urn:4a0a738c-5446-434b-b37e-185850b2c815",
+ "AssociatedWith": "urn:afni-YYVukVUa",
"Command": "@auto_tlrc -base TT_icbm452+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ",
"Used": [
- "urn:4afc874f-94c0-4c10-9aa6-0817491b5286",
- "urn:934646fa-7bbc-4805-a09f-9f5610ab15fc",
- "urn:4d84c4a2-4d4a-4c24-bebe-a6c923523ebd"
+ "bids::TT_icbm452+tlrc",
+ "bids::sub-01_T1w_ns+orig",
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:5a7ec459-4af7-4ecb-9669-f5681bfecdf9",
+ "@id": "urn:volreg-GdAJQq8f",
"Label": "volreg",
- "AssociatedWith": "urn:4a0a738c-5446-434b-b37e-185850b2c815",
+ "AssociatedWith": "urn:afni-YYVukVUa",
"Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig; 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1; cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D; 3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run; 3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run; 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc; cat dfile.r*.1D > dfile_rall.1D; 3dcopy rm.epi.min.r01+tlrc mask_epi_extents; 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg; 3dcopy sub-01_T1w_ns+tlrc anat_final.$subj; 3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped; ",
"Used": [
- "urn:ce34796c-ecbb-473e-aabd-9aaac62ef33c",
- "urn:ce34796c-ecbb-473e-aabd-9aaac62ef33c",
- "urn:4d84c4a2-4d4a-4c24-bebe-a6c923523ebd",
- "urn:a6beb099-d9b4-462b-9aee-41068713356a",
- "urn:ce34796c-ecbb-473e-aabd-9aaac62ef33c",
- "urn:21e521a1-5a90-48de-bc39-16737d89f891",
- "urn:a6beb099-d9b4-462b-9aee-41068713356a",
- "urn:63d224d0-eb64-4a30-a939-811117bae908",
- "urn:50e20ccc-b165-4f42-9835-b7ed07183397",
- "urn:5a12057b-7894-4658-8885-bf8772cdd0cf",
- "urn:660fe90e-75ea-435d-8db6-d226d404baef",
- "urn:9d077082-757f-4630-99ce-4cea132a877d",
- "urn:a6beb099-d9b4-462b-9aee-41068713356a",
- "urn:134af596-b966-4d6d-b1de-8e018a339753"
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.epi.all1+orig",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.epi.1.r$run+tlrc",
+ "bids::dfile.r*.1D",
+ "bids::rm.epi.min.r01+tlrc",
+ "bids::mask_epi_extents+tlrc",
+ "bids::rm.epi.nomask.r$run+tlrc",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::anat_final.$subj+tlrc",
+ "bids::warp.anat.Xat.1D"
]
},
{
- "@id": "urn:0571739d-afb1-4fc4-85a8-64b608b3ddc1",
+ "@id": "urn:blur-s3bO7HKu",
"Label": "blur",
- "AssociatedWith": "urn:4a0a738c-5446-434b-b37e-185850b2c815",
+ "AssociatedWith": "urn:afni-YYVukVUa",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc; ",
"Used": [
- "urn:33ff81af-1444-46c3-a060-f926d0ced8ae",
- "urn:d4539ad2-b6b6-447b-b595-4c432dfba73a"
+ "bids::pb02.$subj.r$run.volreg+tlrc",
+ "bids::pb03.$subj.r$run.blur"
]
},
{
- "@id": "urn:8fff7e64-4f79-487c-8d5e-d71cf1c63f20",
+ "@id": "urn:mask-j7YojExy",
"Label": "mask",
- "AssociatedWith": "urn:4a0a738c-5446-434b-b37e-185850b2c815",
+ "AssociatedWith": "urn:afni-YYVukVUa",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc; 3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj; 3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj; 3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt; 3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt; 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_icbm452+tlrc; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group; ",
"Used": [
- "urn:39fdeb1b-1b9e-48d6-967e-ba216bc07d04",
- "urn:a6beb099-d9b4-462b-9aee-41068713356a",
- "urn:c72a767c-6c04-48a4-840f-8f8fce9c046f",
- "urn:f48bc076-8f2e-47d0-b651-3a12200ba777",
- "urn:30934d7f-fa54-4dc4-92c2-0692dcc79bf8",
- "urn:bfc94b09-104e-4f77-bc9c-6a254b2b3237",
- "urn:30934d7f-fa54-4dc4-92c2-0692dcc79bf8",
- "urn:bfc94b09-104e-4f77-bc9c-6a254b2b3237",
- "urn:abc626d1-00a7-4658-8345-e262989b746d",
- "urn:c72a767c-6c04-48a4-840f-8f8fce9c046f",
- "urn:360c6e24-8ef1-4e78-a20c-4f1e6ebabc67"
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.resam.anat+tlrc",
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee",
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee",
+ "bids::/Users/u1591557/abin/TT_icbm452+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.resam.group+tlrc"
]
},
{
- "@id": "urn:30df620a-6022-4cb7-8b04-92b6ee439617",
+ "@id": "urn:scale-Tm1YtRxv",
"Label": "scale",
- "AssociatedWith": "urn:4a0a738c-5446-434b-b37e-185850b2c815",
+ "AssociatedWith": "urn:afni-YYVukVUa",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc; 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale; ",
"Used": [
- "urn:39fdeb1b-1b9e-48d6-967e-ba216bc07d04",
- "urn:1d237c07-a52d-4a05-81d5-bbabc95bf4d5",
- "urn:39fdeb1b-1b9e-48d6-967e-ba216bc07d04",
- "urn:9d077082-757f-4630-99ce-4cea132a877d"
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::mask_epi_extents+tlrc",
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::rm.mean_r$run+tlrc"
]
},
{
- "@id": "urn:ac0a1582-d0e6-4c06-8f3c-f7e2371d9d71",
+ "@id": "urn:regress-fsFkOQmi",
"Label": "regress",
- "AssociatedWith": "urn:4a0a738c-5446-434b-b37e-185850b2c815",
+ "AssociatedWith": "urn:afni-YYVukVUa",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}; 3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj; 1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt; 3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD; 3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"; 3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"; 3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj; 3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc; 3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D; 3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D; 3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP; 3dTstat -sum -prefix corr_brain rm.DP+tlrc; 1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D; 1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D; 3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"; 1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D; ",
"Used": [
- "urn:80fe1888-cba7-45c4-b609-c42f8b9ed545",
- "urn:80fe1888-cba7-45c4-b609-c42f8b9ed545",
- "urn:80fe1888-cba7-45c4-b609-c42f8b9ed545",
- "urn:b38636c2-8db1-4744-9952-28a75ff3368d",
- "urn:b38636c2-8db1-4744-9952-28a75ff3368d",
- "urn:5ecaa27a-d8dc-48bf-acb6-e3c9283ad0b8",
- "urn:d78dd409-4c35-499c-9671-cf9bfce87925",
- "urn:3190be3b-d808-4789-a6b2-90c5db0bb314",
- "urn:c72a767c-6c04-48a4-840f-8f8fce9c046f",
- "urn:f0423d9e-54a2-4f80-a53f-e1dd94b3a947",
- "urn:454dc845-1967-46e8-9b90-69b929477b23",
- "urn:198081c3-d54d-4afa-8c05-56a43bd2ec90",
- "urn:1bf86114-bffa-44fe-a6e3-93a863200efc",
- "urn:3459f83d-9b42-4196-9684-d7762bb4bd34",
- "urn:c73fa496-d31f-4802-97a4-ed7e422f2b73",
- "urn:aa7b2f0c-211d-402d-9e28-14a87872319f",
- "urn:6b561749-90cb-4ca3-b23e-29c9ffbe9085",
- "urn:6b561749-90cb-4ca3-b23e-29c9ffbe9085"
+ "bids::dfile_rall.1D",
+ "bids::dfile_rall.1D",
+ "bids::dfile_rall.1D",
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD",
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD",
+ "bids::all_runs.$subj+tlrc%22[$ktrs]%22",
+ "bids::errts.$%7Bsubj%7D+tlrc%22[$ktrs]%22",
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.noise.all+tlrc",
+ "bids::rm.signal.all+tlrc",
+ "bids::errts.$%7Bsubj%7D+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::out.gcor.1D",
+ "bids::rm.errts.unit+tlrc",
+ "bids::rm.DP+tlrc",
+ "bids::X.nocensor.xmat.1D'[3]'",
+ "bids::X.nocensor.xmat.1D'[4]'",
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22",
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:d2838435-2817-4d99-8c5e-4adbd8852f73",
+ "@id": "urn:bluresti-a9WkYy7D",
"Label": "blur estimation",
- "AssociatedWith": "urn:4a0a738c-5446-434b-b37e-185850b2c815",
+ "AssociatedWith": "urn:afni-YYVukVUa",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D; 3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D; 3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim; ",
"Used": [
- "urn:c72a767c-6c04-48a4-840f-8f8fce9c046f",
- "urn:c72a767c-6c04-48a4-840f-8f8fce9c046f",
- "urn:c72a767c-6c04-48a4-840f-8f8fce9c046f"
+ "bids::full_mask.$subj+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:1f3aa16c-dba5-4a6a-be1f-070a6dd46a7c",
+ "@id": "urn:autobloc-iR03faH6",
"Label": "auto block: generate review scripts",
- "AssociatedWith": "urn:4a0a738c-5446-434b-b37e-185850b2c815",
+ "AssociatedWith": "urn:afni-YYVukVUa",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD; gen_ss_review_scripts.py -mot_limit 0.3 -exit0; ",
"Used": [
- "urn:91bcc4fd-63dd-4ccd-b200-8f3db9ecd468"
+ "bids::pb00.$subj.r*.tcat+orig.HEAD"
]
}
],
"Entities": [
{
- "@id": "urn:e36061c5-57b1-4a49-ae7e-0484d46f0d41",
+ "@id": "bids::afni_other_template/tone_counting_onset_times.txt",
"Label": "tone_counting_onset_times.txt",
"AtLocation": "./afni_other_template/tone_counting_onset_times.txt",
"digest": {
@@ -192,7 +194,7 @@
}
},
{
- "@id": "urn:36b08c61-b83f-4357-8020-44cbf06f0fe0",
+ "@id": "bids::afni_other_template/tone_counting_probe_duration.txt",
"Label": "tone_counting_probe_duration.txt",
"AtLocation": "./afni_other_template/tone_counting_probe_duration.txt",
"digest": {
@@ -200,7 +202,7 @@
}
},
{
- "@id": "urn:f8a1c91e-1034-4376-98f7-2013730c5cc8",
+ "@id": "bids::afni_other_template/sub-01_T1w.nii.gz",
"Label": "sub-01_T1w.nii.gz",
"AtLocation": "./afni_other_template/sub-01_T1w.nii.gz",
"digest": {
@@ -208,34 +210,34 @@
}
},
{
- "@id": "urn:07fce6f9-2f95-4236-86c2-f8cdad14a55a",
+ "@id": "bids::$output_dir",
"Label": "$output_dir",
"AtLocation": "$output_dir",
- "GeneratedBy": "urn:5c3f74df-5e15-416e-8c19-763fdf4fac10",
+ "GeneratedBy": "urn:autobloc-NCfx652N",
"digest": {
"sha256": "9fa4c635e6533ddf2fed54295920052818d948c3ffe97bc753bd7336b453f8cb"
}
},
{
- "@id": "urn:51456d55-6d51-492d-a67a-47de6460190c",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:5c3f74df-5e15-416e-8c19-763fdf4fac10"
+ "GeneratedBy": "urn:autobloc-NCfx652N"
},
{
- "@id": "urn:40dbdf46-570c-41fc-95d3-253dbe2e58c5",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:5c3f74df-5e15-416e-8c19-763fdf4fac10"
+ "GeneratedBy": "urn:autobloc-NCfx652N"
},
{
- "@id": "urn:93bf1748-0d66-4de9-8727-daad0227f807",
+ "@id": "bids::$output_dir/sub-01_T1w",
"Label": "sub-01_T1w",
"AtLocation": "$output_dir/sub-01_T1w",
- "GeneratedBy": "urn:5c3f74df-5e15-416e-8c19-763fdf4fac10"
+ "GeneratedBy": "urn:autobloc-NCfx652N"
},
{
- "@id": "urn:bf65fe1e-ad76-47f9-a992-39f329cd3457",
+ "@id": "bids::afni_other_template/sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Label": "sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "./afni_other_template/sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"digest": {
@@ -243,13 +245,13 @@
}
},
{
- "@id": "urn:ce42a61b-ef8f-4e71-8f12-7425fa64d4d5",
+ "@id": "bids::$output_dir/pb00.$subj.r01.tcat",
"Label": "pb00.$subj.r01.tcat",
"AtLocation": "$output_dir/pb00.$subj.r01.tcat",
- "GeneratedBy": "urn:535bc829-b0d7-4089-a924-ada0c271af18"
+ "GeneratedBy": "urn:autobloc-1lc3rowI"
},
{
- "@id": "urn:5d41178a-42ce-4693-8b77-8e7c79d0157d",
+ "@id": "bids::pb00.$subj.r$run.tcat+orig",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -257,7 +259,7 @@
}
},
{
- "@id": "urn:e419e2b5-ff1d-4b58-b687-eccac743696d",
+ "@id": "bids::outcount.r*.1D",
"Label": "outcount.r*.1D",
"AtLocation": "outcount.r*.1D",
"digest": {
@@ -265,25 +267,25 @@
}
},
{
- "@id": "urn:5a7d3988-7a4e-412a-a2a9-f6f681725a3b",
+ "@id": "bids::outcount.r$run.1D",
"Label": "outcount.r$run.1D",
"AtLocation": "outcount.r$run.1D",
- "GeneratedBy": "urn:adb1b0ff-e8c1-4355-9b01-b20a5b01cf0b",
+ "GeneratedBy": "urn:autobloc-4CqOaPM0",
"digest": {
"sha256": "63d9f539e5470badc625d557109f68bc4eecbb02ca2667483739d52f95e5d0dd"
}
},
{
- "@id": "urn:8039243e-1237-4865-a4b3-f4d38e1cee10",
+ "@id": "bids::outcount_rall.1D",
"Label": "outcount_rall.1D",
"AtLocation": "outcount_rall.1D",
- "GeneratedBy": "urn:adb1b0ff-e8c1-4355-9b01-b20a5b01cf0b",
+ "GeneratedBy": "urn:autobloc-4CqOaPM0",
"digest": {
"sha256": "cb887fd5e4d5e9acb3a24820d0f7a62ed38a5ffb0fdedd373440ac0219fb186a"
}
},
{
- "@id": "urn:5d41178a-42ce-4693-8b77-8e7c79d0157d",
+ "@id": "bids::pb00.$subj.r$run.tcat+orig",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -291,16 +293,16 @@
}
},
{
- "@id": "urn:b90fa097-6626-4a52-92fa-1011aacdd585",
+ "@id": "bids::pb01.$subj.r$run.tshift",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift",
- "GeneratedBy": "urn:7e5eb7b6-e0e9-4515-8d8a-332f2753d583",
+ "GeneratedBy": "urn:tshift-iPalhda0",
"digest": {
"sha256": "c6bf01cea8d2eac1d7a866f80b865c6e7d4b4e012dbb63d480ac9a8551162d72"
}
},
{
- "@id": "urn:a6cf3443-a7a0-40c4-9036-dfeb288a68a3",
+ "@id": "bids::sub-01_T1w+orig",
"Label": "sub-01_T1w",
"AtLocation": "sub-01_T1w+orig",
"digest": {
@@ -308,7 +310,7 @@
}
},
{
- "@id": "urn:b9c6adb1-025e-452c-b725-c94944c871d2",
+ "@id": "bids::pb01.$subj.r01.tshift+orig",
"Label": "pb01.$subj.r01.tshift",
"AtLocation": "pb01.$subj.r01.tshift+orig",
"digest": {
@@ -316,16 +318,16 @@
}
},
{
- "@id": "urn:c84b6522-8dec-4ded-aa5d-84852adab29c",
+ "@id": "bids::_al_junk",
"Label": "_al_junk",
"AtLocation": "_al_junk",
- "GeneratedBy": "urn:308ee1ba-15be-4db5-a4f2-9e4ad49adee8",
+ "GeneratedBy": "urn:align-iJXWvura",
"digest": {
"sha256": "bd785a075a4c6446e1e54de9e628913f7f1c814e86b69a9fbfe933209e6d37b5"
}
},
{
- "@id": "urn:934646fa-7bbc-4805-a09f-9f5610ab15fc",
+ "@id": "bids::TT_icbm452+tlrc",
"Label": "TT_icbm452",
"AtLocation": "TT_icbm452+tlrc",
"digest": {
@@ -333,7 +335,7 @@
}
},
{
- "@id": "urn:4afc874f-94c0-4c10-9aa6-0817491b5286",
+ "@id": "bids::sub-01_T1w_ns+orig",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+orig",
"digest": {
@@ -341,7 +343,7 @@
}
},
{
- "@id": "urn:4d84c4a2-4d4a-4c24-bebe-a6c923523ebd",
+ "@id": "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc::WARP_DATA",
"digest": {
@@ -349,16 +351,16 @@
}
},
{
- "@id": "urn:134af596-b966-4d6d-b1de-8e018a339753",
+ "@id": "bids::warp.anat.Xat.1D",
"Label": "warp.anat.Xat.1D",
"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:f19f51ad-5e08-412b-b80a-9023c70693b4",
+ "GeneratedBy": "urn:tlrc-KjPkMBFn",
"digest": {
"sha256": "800633fb5b4e9be64078bc181c4d5510ffb73fc5cccaf364c7fb6a294aa06728"
}
},
{
- "@id": "urn:4d84c4a2-4d4a-4c24-bebe-a6c923523ebd",
+ "@id": "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc::WARP_DATA",
"digest": {
@@ -366,16 +368,16 @@
}
},
{
- "@id": "urn:134af596-b966-4d6d-b1de-8e018a339753",
+ "@id": "bids::warp.anat.Xat.1D",
"Label": "warp.anat.Xat.1D",
"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:f19f51ad-5e08-412b-b80a-9023c70693b4",
+ "GeneratedBy": "urn:tlrc-KjPkMBFn",
"digest": {
"sha256": "800633fb5b4e9be64078bc181c4d5510ffb73fc5cccaf364c7fb6a294aa06728"
}
},
{
- "@id": "urn:ce34796c-ecbb-473e-aabd-9aaac62ef33c",
+ "@id": "bids::pb01.$subj.r$run.tshift+orig",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift+orig",
"digest": {
@@ -383,7 +385,7 @@
}
},
{
- "@id": "urn:a6beb099-d9b4-462b-9aee-41068713356a",
+ "@id": "bids::sub-01_T1w_ns+tlrc",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc",
"digest": {
@@ -391,7 +393,7 @@
}
},
{
- "@id": "urn:21e521a1-5a90-48de-bc39-16737d89f891",
+ "@id": "bids::rm.epi.all1+orig",
"Label": "rm.epi.all1",
"AtLocation": "rm.epi.all1+orig",
"digest": {
@@ -399,7 +401,7 @@
}
},
{
- "@id": "urn:63d224d0-eb64-4a30-a939-811117bae908",
+ "@id": "bids::rm.epi.1.r$run+tlrc",
"Label": "rm.epi.1.r$run",
"AtLocation": "rm.epi.1.r$run+tlrc",
"digest": {
@@ -407,7 +409,7 @@
}
},
{
- "@id": "urn:50e20ccc-b165-4f42-9835-b7ed07183397",
+ "@id": "bids::dfile.r*.1D",
"Label": "dfile.r*.1D",
"AtLocation": "dfile.r*.1D",
"digest": {
@@ -415,7 +417,7 @@
}
},
{
- "@id": "urn:5a12057b-7894-4658-8885-bf8772cdd0cf",
+ "@id": "bids::rm.epi.min.r01+tlrc",
"Label": "rm.epi.min.r01",
"AtLocation": "rm.epi.min.r01+tlrc",
"digest": {
@@ -423,7 +425,7 @@
}
},
{
- "@id": "urn:660fe90e-75ea-435d-8db6-d226d404baef",
+ "@id": "bids::rm.epi.nomask.r$run+tlrc",
"Label": "rm.epi.nomask.r$run",
"AtLocation": "rm.epi.nomask.r$run+tlrc",
"digest": {
@@ -431,7 +433,7 @@
}
},
{
- "@id": "urn:9d077082-757f-4630-99ce-4cea132a877d",
+ "@id": "bids::mask_epi_extents+tlrc",
"Label": "mask_epi_extents",
"AtLocation": "mask_epi_extents+tlrc",
"digest": {
@@ -439,97 +441,105 @@
}
},
{
- "@id": "urn:e9d6c052-dd8d-4200-8d7b-befe83645890",
+ "@id": "bids::anat_final.$subj+tlrc",
+ "Label": "anat_final.$subj",
+ "AtLocation": "anat_final.$subj+tlrc",
+ "digest": {
+ "sha256": "94eb1853614cc085b22772c011f119f6a0ad7ec06cba2850587762e7f1a6eae6"
+ }
+ },
+ {
+ "@id": "bids::mat.r$run.vr.aff12.1D",
"Label": "mat.r$run.vr.aff12.1D",
"AtLocation": "mat.r$run.vr.aff12.1D",
- "GeneratedBy": "urn:5a7ec459-4af7-4ecb-9669-f5681bfecdf9",
+ "GeneratedBy": "urn:volreg-GdAJQq8f",
"digest": {
"sha256": "2e6e6c2ce8089cfa3c6e11dc72fca0cc8497f7a55faae2ced402de4867466c91"
}
},
{
- "@id": "urn:226d8aa2-90c8-464e-8eee-e3633304c512",
+ "@id": "bids::rm.epi.all1",
"Label": "rm.epi.all1",
"AtLocation": "rm.epi.all1",
- "GeneratedBy": "urn:5a7ec459-4af7-4ecb-9669-f5681bfecdf9",
+ "GeneratedBy": "urn:volreg-GdAJQq8f",
"digest": {
"sha256": "1023e3c16cecdbdc73ea456bcf33c2e5bb4f1e07094b73d29022d651e5fa3f85"
}
},
{
- "@id": "urn:f55ea7eb-d8d5-4913-a6fa-ee8e7ae533e4",
+ "@id": "bids::rm.epi.nomask.r$run",
"Label": "rm.epi.nomask.r$run",
"AtLocation": "rm.epi.nomask.r$run",
- "GeneratedBy": "urn:5a7ec459-4af7-4ecb-9669-f5681bfecdf9",
+ "GeneratedBy": "urn:volreg-GdAJQq8f",
"digest": {
"sha256": "03d6cba0426c5545e350e6b63a19b0e46f8dfa2223fd08691753e8914a479e36"
}
},
{
- "@id": "urn:785b12bd-eb4a-4628-9c56-943156440438",
+ "@id": "bids::rm.epi.1.r$run",
"Label": "rm.epi.1.r$run",
"AtLocation": "rm.epi.1.r$run",
- "GeneratedBy": "urn:5a7ec459-4af7-4ecb-9669-f5681bfecdf9",
+ "GeneratedBy": "urn:volreg-GdAJQq8f",
"digest": {
"sha256": "b1b9128c103ea246625db1a35e6f474a221ca6c1105a30df38aefdc4d5421e84"
}
},
{
- "@id": "urn:0f7bef4b-4af1-49fc-b13d-3a8b6a9f8dc7",
+ "@id": "bids::rm.epi.min.r$run",
"Label": "rm.epi.min.r$run",
"AtLocation": "rm.epi.min.r$run",
- "GeneratedBy": "urn:5a7ec459-4af7-4ecb-9669-f5681bfecdf9",
+ "GeneratedBy": "urn:volreg-GdAJQq8f",
"digest": {
"sha256": "b4418a96ddbbf25afdfd01ed0506ddebe009011ba18aed10137f994260fd1a66"
}
},
{
- "@id": "urn:80fe1888-cba7-45c4-b609-c42f8b9ed545",
+ "@id": "bids::dfile_rall.1D",
"Label": "dfile_rall.1D",
"AtLocation": "dfile_rall.1D",
- "GeneratedBy": "urn:5a7ec459-4af7-4ecb-9669-f5681bfecdf9",
+ "GeneratedBy": "urn:volreg-GdAJQq8f",
"digest": {
"sha256": "011e7296870a1ac7e15377fb0d529ed68710bb16b138bef6aeb6c645f437dcf2"
}
},
{
- "@id": "urn:f58acb68-39c7-4175-81a0-f7b8353c7746",
+ "@id": "bids::mask_epi_extents",
"Label": "mask_epi_extents",
"AtLocation": "mask_epi_extents",
- "GeneratedBy": "urn:5a7ec459-4af7-4ecb-9669-f5681bfecdf9",
+ "GeneratedBy": "urn:volreg-GdAJQq8f",
"digest": {
"sha256": "a69dd71209516ec24e2b3364072ed54adff16619459b1c369866210ec642e987"
}
},
{
- "@id": "urn:18a22981-1713-456d-b688-a8619a182a84",
+ "@id": "bids::pb02.$subj.r$run.volreg",
"Label": "pb02.$subj.r$run.volreg",
"AtLocation": "pb02.$subj.r$run.volreg",
- "GeneratedBy": "urn:5a7ec459-4af7-4ecb-9669-f5681bfecdf9",
+ "GeneratedBy": "urn:volreg-GdAJQq8f",
"digest": {
"sha256": "8821927190ac1b3f8f9d9a5ec74f6468ae6c1cb736e58e5de2cdbe3543d5cc0c"
}
},
{
- "@id": "urn:9a733674-9bbb-4197-a3b3-6b052060bb4e",
+ "@id": "bids::anat_final.$subj",
"Label": "anat_final.$subj",
"AtLocation": "anat_final.$subj",
- "GeneratedBy": "urn:5a7ec459-4af7-4ecb-9669-f5681bfecdf9",
+ "GeneratedBy": "urn:volreg-GdAJQq8f",
"digest": {
"sha256": "69b750d004bdba337de0b4ffa683bd92bc8f34b854d320327839ad264b28c4c5"
}
},
{
- "@id": "urn:09b0869a-34b6-4e96-8b33-d3180f5c63ee",
+ "@id": "bids::anat_w_skull_warped",
"Label": "anat_w_skull_warped",
"AtLocation": "anat_w_skull_warped",
- "GeneratedBy": "urn:5a7ec459-4af7-4ecb-9669-f5681bfecdf9",
+ "GeneratedBy": "urn:volreg-GdAJQq8f",
"digest": {
"sha256": "462fdb8cd2b882e250fee3c6adb7acf0b0b9a9edb3e1cadf9d45d16180871105"
}
},
{
- "@id": "urn:33ff81af-1444-46c3-a060-f926d0ced8ae",
+ "@id": "bids::pb03.$subj.r$run.blur",
"Label": "pb03.$subj.r$run.blur",
"AtLocation": "pb03.$subj.r$run.blur",
"digest": {
@@ -537,7 +547,7 @@
}
},
{
- "@id": "urn:d4539ad2-b6b6-447b-b595-4c432dfba73a",
+ "@id": "bids::pb02.$subj.r$run.volreg+tlrc",
"Label": "pb02.$subj.r$run.volreg",
"AtLocation": "pb02.$subj.r$run.volreg+tlrc",
"digest": {
@@ -545,7 +555,7 @@
}
},
{
- "@id": "urn:a6beb099-d9b4-462b-9aee-41068713356a",
+ "@id": "bids::sub-01_T1w_ns+tlrc",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc",
"digest": {
@@ -553,7 +563,7 @@
}
},
{
- "@id": "urn:39fdeb1b-1b9e-48d6-967e-ba216bc07d04",
+ "@id": "bids::pb03.$subj.r$run.blur+tlrc",
"Label": "pb03.$subj.r$run.blur",
"AtLocation": "pb03.$subj.r$run.blur+tlrc",
"digest": {
@@ -561,7 +571,7 @@
}
},
{
- "@id": "urn:c72a767c-6c04-48a4-840f-8f8fce9c046f",
+ "@id": "bids::full_mask.$subj+tlrc",
"Label": "full_mask.$subj",
"AtLocation": "full_mask.$subj+tlrc",
"digest": {
@@ -569,7 +579,7 @@
}
},
{
- "@id": "urn:f48bc076-8f2e-47d0-b651-3a12200ba777",
+ "@id": "bids::rm.resam.anat+tlrc",
"Label": "rm.resam.anat",
"AtLocation": "rm.resam.anat+tlrc",
"digest": {
@@ -577,7 +587,7 @@
}
},
{
- "@id": "urn:30934d7f-fa54-4dc4-92c2-0692dcc79bf8",
+ "@id": "bids::mask_anat.$subj+tlrc",
"Label": "mask_anat.$subj",
"AtLocation": "mask_anat.$subj+tlrc",
"digest": {
@@ -585,7 +595,7 @@
}
},
{
- "@id": "urn:bfc94b09-104e-4f77-bc9c-6a254b2b3237",
+ "@id": "bids::tee",
"Label": "tee",
"AtLocation": "tee",
"digest": {
@@ -593,7 +603,7 @@
}
},
{
- "@id": "urn:abc626d1-00a7-4658-8345-e262989b746d",
+ "@id": "bids::/Users/u1591557/abin/TT_icbm452+tlrc",
"Label": "TT_icbm452",
"AtLocation": "/Users/u1591557/abin/TT_icbm452+tlrc",
"digest": {
@@ -601,7 +611,7 @@
}
},
{
- "@id": "urn:360c6e24-8ef1-4e78-a20c-4f1e6ebabc67",
+ "@id": "bids::rm.resam.group+tlrc",
"Label": "rm.resam.group",
"AtLocation": "rm.resam.group+tlrc",
"digest": {
@@ -609,61 +619,61 @@
}
},
{
- "@id": "urn:68c80596-8a3a-41ec-abd1-1b5cb9f3908f",
+ "@id": "bids::rm.mask_r$run",
"Label": "rm.mask_r$run",
"AtLocation": "rm.mask_r$run",
- "GeneratedBy": "urn:8fff7e64-4f79-487c-8d5e-d71cf1c63f20",
+ "GeneratedBy": "urn:mask-j7YojExy",
"digest": {
"sha256": "d251275ec819884fd84596da3fa356f3d83709d66170c45ad73c2f14ee830b35"
}
},
{
- "@id": "urn:1abaf4b3-3b8b-47a5-9bef-ea9e15727931",
+ "@id": "bids::full_mask.$subj",
"Label": "full_mask.$subj",
"AtLocation": "full_mask.$subj",
- "GeneratedBy": "urn:8fff7e64-4f79-487c-8d5e-d71cf1c63f20",
+ "GeneratedBy": "urn:mask-j7YojExy",
"digest": {
"sha256": "02da8c6ed741c00cb6ccb8da25bf6ca853afb9100b992c854209afde9e30918f"
}
},
{
- "@id": "urn:8ddb5caa-1d83-4fa7-81bc-bc33c94e9de0",
+ "@id": "bids::rm.resam.anat",
"Label": "rm.resam.anat",
"AtLocation": "rm.resam.anat",
- "GeneratedBy": "urn:8fff7e64-4f79-487c-8d5e-d71cf1c63f20",
+ "GeneratedBy": "urn:mask-j7YojExy",
"digest": {
"sha256": "fe716d2bdbce773476ef264f2cd990f7114d7f2d7245c0cbeb10e8abc7feff9b"
}
},
{
- "@id": "urn:63ad4bc7-4d97-46bc-b872-48b4e3cc971d",
+ "@id": "bids::mask_anat.$subj",
"Label": "mask_anat.$subj",
"AtLocation": "mask_anat.$subj",
- "GeneratedBy": "urn:8fff7e64-4f79-487c-8d5e-d71cf1c63f20",
+ "GeneratedBy": "urn:mask-j7YojExy",
"digest": {
"sha256": "d3f1becfb7c7d234361e002cc34c3ca5b5333640259f572993b773f6973f0e98"
}
},
{
- "@id": "urn:64836f0e-e8b3-40d6-9247-a8e347c4ccdc",
+ "@id": "bids::rm.resam.group",
"Label": "rm.resam.group",
"AtLocation": "./rm.resam.group",
- "GeneratedBy": "urn:8fff7e64-4f79-487c-8d5e-d71cf1c63f20",
+ "GeneratedBy": "urn:mask-j7YojExy",
"digest": {
"sha256": "79e954aee237a244a2498f6f7811a10a1c4508563eebd38000c13f2c145942c9"
}
},
{
- "@id": "urn:0132a039-6f29-43c3-95e5-c1f46d2f6919",
+ "@id": "bids::mask_group",
"Label": "mask_group",
"AtLocation": "mask_group",
- "GeneratedBy": "urn:8fff7e64-4f79-487c-8d5e-d71cf1c63f20",
+ "GeneratedBy": "urn:mask-j7YojExy",
"digest": {
"sha256": "d7093b26470ded8d7e939359017b18d28a2da4c6bb702c1183df20bca614f949"
}
},
{
- "@id": "urn:9d077082-757f-4630-99ce-4cea132a877d",
+ "@id": "bids::mask_epi_extents+tlrc",
"Label": "mask_epi_extents",
"AtLocation": "mask_epi_extents+tlrc",
"digest": {
@@ -671,7 +681,7 @@
}
},
{
- "@id": "urn:39fdeb1b-1b9e-48d6-967e-ba216bc07d04",
+ "@id": "bids::pb03.$subj.r$run.blur+tlrc",
"Label": "pb03.$subj.r$run.blur",
"AtLocation": "pb03.$subj.r$run.blur+tlrc",
"digest": {
@@ -679,7 +689,7 @@
}
},
{
- "@id": "urn:1d237c07-a52d-4a05-81d5-bbabc95bf4d5",
+ "@id": "bids::rm.mean_r$run+tlrc",
"Label": "rm.mean_r$run",
"AtLocation": "rm.mean_r$run+tlrc",
"digest": {
@@ -687,34 +697,34 @@
}
},
{
- "@id": "urn:8e3dccf2-4041-43a7-ae8e-c6693ee12610",
+ "@id": "bids::rm.mean_r$run",
"Label": "rm.mean_r$run",
"AtLocation": "rm.mean_r$run",
- "GeneratedBy": "urn:30df620a-6022-4cb7-8b04-92b6ee439617",
+ "GeneratedBy": "urn:scale-Tm1YtRxv",
"digest": {
"sha256": "17047aa0c91933cf57076e6ce78a48ebe5975d6881ca47c8357cbd66e0fde9fb"
}
},
{
- "@id": "urn:cc63cbf1-a938-4f36-94b0-28d7334c06ff",
+ "@id": "bids::pb04.$subj.r$run.scale",
"Label": "pb04.$subj.r$run.scale",
"AtLocation": "pb04.$subj.r$run.scale",
- "GeneratedBy": "urn:30df620a-6022-4cb7-8b04-92b6ee439617",
+ "GeneratedBy": "urn:scale-Tm1YtRxv",
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}
},
{
- "@id": "urn:80fe1888-cba7-45c4-b609-c42f8b9ed545",
+ "@id": "bids::dfile_rall.1D",
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"AtLocation": "dfile_rall.1D",
- "GeneratedBy": "urn:5a7ec459-4af7-4ecb-9669-f5681bfecdf9",
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{
- "@id": "urn:c72a767c-6c04-48a4-840f-8f8fce9c046f",
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@@ -722,7 +732,7 @@
}
},
{
- "@id": "urn:b38636c2-8db1-4744-9952-28a75ff3368d",
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"digest": {
@@ -730,7 +740,7 @@
}
},
{
- "@id": "urn:5ecaa27a-d8dc-48bf-acb6-e3c9283ad0b8",
+ "@id": "bids::all_runs.$subj+tlrc%22[$ktrs]%22",
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"digest": {
@@ -738,7 +748,7 @@
}
},
{
- "@id": "urn:d78dd409-4c35-499c-9671-cf9bfce87925",
+ "@id": "bids::errts.$%7Bsubj%7D+tlrc%22[$ktrs]%22",
"Label": "errts.${subj}",
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@@ -746,7 +756,7 @@
}
},
{
- "@id": "urn:3190be3b-d808-4789-a6b2-90c5db0bb314",
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@@ -754,7 +764,7 @@
}
},
{
- "@id": "urn:f0423d9e-54a2-4f80-a53f-e1dd94b3a947",
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"AtLocation": "rm.noise.all+tlrc",
"digest": {
@@ -762,7 +772,7 @@
}
},
{
- "@id": "urn:454dc845-1967-46e8-9b90-69b929477b23",
+ "@id": "bids::errts.$%7Bsubj%7D+tlrc",
"Label": "errts.${subj}",
"AtLocation": "errts.${subj}+tlrc",
"digest": {
@@ -770,7 +780,7 @@
}
},
{
- "@id": "urn:198081c3-d54d-4afa-8c05-56a43bd2ec90",
+ "@id": "bids::out.gcor.1D",
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"digest": {
@@ -778,7 +788,7 @@
}
},
{
- "@id": "urn:1bf86114-bffa-44fe-a6e3-93a863200efc",
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"digest": {
@@ -786,7 +796,7 @@
}
},
{
- "@id": "urn:3459f83d-9b42-4196-9684-d7762bb4bd34",
+ "@id": "bids::rm.DP+tlrc",
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"AtLocation": "rm.DP+tlrc",
"digest": {
@@ -794,7 +804,7 @@
}
},
{
- "@id": "urn:c73fa496-d31f-4802-97a4-ed7e422f2b73",
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@@ -802,7 +812,7 @@
}
},
{
- "@id": "urn:aa7b2f0c-211d-402d-9e28-14a87872319f",
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"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D'[4]'",
"digest": {
@@ -810,7 +820,7 @@
}
},
{
- "@id": "urn:6b561749-90cb-4ca3-b23e-29c9ffbe9085",
+ "@id": "bids::X.nocensor.xmat.1D%22[$reg_cols]%22",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D\"[$reg_cols]\"",
"digest": {
@@ -818,133 +828,133 @@
}
},
{
- "@id": "urn:d5c97dfd-bc9a-4c8f-bd4f-fa5162003600",
+ "@id": "bids::motion_demean.1D",
"Label": "motion_demean.1D",
"AtLocation": "motion_demean.1D",
- "GeneratedBy": "urn:ac0a1582-d0e6-4c06-8f3c-f7e2371d9d71",
+ "GeneratedBy": "urn:regress-fsFkOQmi",
"digest": {
"sha256": "1de1e10c0120caa7b6cf441bd141a5a76716e458676ae56ce693039eecb79c85"
}
},
{
- "@id": "urn:1bea0f51-9adc-43ee-8606-9199fe51d37c",
+ "@id": "bids::motion_deriv.1D",
"Label": "motion_deriv.1D",
"AtLocation": "motion_deriv.1D",
- "GeneratedBy": "urn:ac0a1582-d0e6-4c06-8f3c-f7e2371d9d71",
+ "GeneratedBy": "urn:regress-fsFkOQmi",
"digest": {
"sha256": "47185bf319e91642ad6f2a396a43fc9f8db7b82f2a9aef326bfe4a955120038b"
}
},
{
- "@id": "urn:fbee7fb9-d4f2-4e42-a7f6-b373c25c08be",
+ "@id": "bids::all_runs.$subj",
"Label": "all_runs.$subj",
"AtLocation": "all_runs.$subj",
- "GeneratedBy": "urn:ac0a1582-d0e6-4c06-8f3c-f7e2371d9d71",
+ "GeneratedBy": "urn:regress-fsFkOQmi",
"digest": {
"sha256": "bcf27fc2e339e751d0ea9bba931674c21fd9d434ff411330f4df55f872a8cc7e"
}
},
{
- "@id": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "@id": "bids::rm.signal.all",
"Label": "rm.signal.all",
"AtLocation": "rm.signal.all",
- "GeneratedBy": "urn:ac0a1582-d0e6-4c06-8f3c-f7e2371d9d71",
+ "GeneratedBy": "urn:regress-fsFkOQmi",
"digest": {
"sha256": "bda68a16c0afd5e55d4d7415c8c959e61a9aad7898dd456b0f3bb597363dde31"
}
},
{
- "@id": "urn:64758879-6b04-479d-8021-1385b8b85587",
+ "@id": "bids::rm.noise.all",
"Label": "rm.noise.all",
"AtLocation": "rm.noise.all",
- "GeneratedBy": "urn:ac0a1582-d0e6-4c06-8f3c-f7e2371d9d71",
+ "GeneratedBy": "urn:regress-fsFkOQmi",
"digest": {
"sha256": "431314eb75d086ce08373b3a374427969e89414c4a2d607e449c1f6485c547af"
}
},
{
- "@id": "urn:d33474de-c1e1-4d6c-a0f2-db992f31c561",
+ "@id": "bids::TSNR.$subj",
"Label": "TSNR.$subj",
"AtLocation": "TSNR.$subj",
- "GeneratedBy": "urn:ac0a1582-d0e6-4c06-8f3c-f7e2371d9d71",
+ "GeneratedBy": "urn:regress-fsFkOQmi",
"digest": {
"sha256": "303f183145a1e295686c08335d3b70753777cf0fa0b3f9628cf8de5471359a00"
}
},
{
- "@id": "urn:8d876913-9a8e-4df5-b08f-c399d8347398",
+ "@id": "bids::rm.errts.unit",
"Label": "rm.errts.unit",
"AtLocation": "rm.errts.unit",
- "GeneratedBy": "urn:ac0a1582-d0e6-4c06-8f3c-f7e2371d9d71",
+ "GeneratedBy": "urn:regress-fsFkOQmi",
"digest": {
"sha256": "03b570ad773a00f51ab7e6cdedfebdeca45f5356de0c25f9e3be44d7bf2c7151"
}
},
{
- "@id": "urn:8d068463-26b0-4236-8937-fcb1118a01eb",
+ "@id": "urn:uuid:bf3a439e-808c-464e-9cd8-69074082b387",
"Label": "-",
"AtLocation": "-",
- "GeneratedBy": "urn:ac0a1582-d0e6-4c06-8f3c-f7e2371d9d71",
+ "GeneratedBy": "urn:regress-fsFkOQmi",
"digest": {
"sha256": "dac304c9f20899ca1ef5aa403e565345fd0ff4ed80c35f82007c9b03a68292b3"
}
},
{
- "@id": "urn:3c9d6937-f35d-43bb-968a-f06ed6b2a0a8",
+ "@id": "bids::rm.DP",
"Label": "rm.DP",
"AtLocation": "rm.DP",
- "GeneratedBy": "urn:ac0a1582-d0e6-4c06-8f3c-f7e2371d9d71",
+ "GeneratedBy": "urn:regress-fsFkOQmi",
"digest": {
"sha256": "06a0bfbc609c1a06ecf93c479a3288d2911c7f5f3e93cf49c5d26f721c2035ed"
}
},
{
- "@id": "urn:24a27a0a-d8aa-421e-b5f2-6d2b89af0b86",
+ "@id": "bids::corr_brain",
"Label": "corr_brain",
"AtLocation": "corr_brain",
- "GeneratedBy": "urn:ac0a1582-d0e6-4c06-8f3c-f7e2371d9d71",
+ "GeneratedBy": "urn:regress-fsFkOQmi",
"digest": {
"sha256": "74e3aeae0da338b871ab5dc9e8859a4e81fcf1b3c0042cd22fe337eb7baf5eae"
}
},
{
- "@id": "urn:4a1f3cd3-d200-41dc-81d3-78b30258701e",
+ "@id": "bids::ideal_tone_counting.1D",
"Label": "ideal_tone_counting.1D",
"AtLocation": "ideal_tone_counting.1D",
- "GeneratedBy": "urn:ac0a1582-d0e6-4c06-8f3c-f7e2371d9d71",
+ "GeneratedBy": "urn:regress-fsFkOQmi",
"digest": {
"sha256": "9bb1cabac5ce7ca19dffa5cd6336a9bf82d362fea2ce9341978406e421b5333c"
}
},
{
- "@id": "urn:13d034fa-73d1-442e-a6c5-5225daf2683f",
+ "@id": "bids::ideal_probe.1D",
"Label": "ideal_probe.1D",
"AtLocation": "ideal_probe.1D",
- "GeneratedBy": "urn:ac0a1582-d0e6-4c06-8f3c-f7e2371d9d71",
+ "GeneratedBy": "urn:regress-fsFkOQmi",
"digest": {
"sha256": "705d93afa8b6ded9f4f572db3f967b54e9906942669af51dd8287a9863bb4288"
}
},
{
- "@id": "urn:a020ff0c-b5e2-4414-a32c-0791ca1dd749",
+ "@id": "bids::sum_ideal.1D",
"Label": "sum_ideal.1D",
"AtLocation": "sum_ideal.1D",
- "GeneratedBy": "urn:ac0a1582-d0e6-4c06-8f3c-f7e2371d9d71",
+ "GeneratedBy": "urn:regress-fsFkOQmi",
"digest": {
"sha256": "b2dccadcd84b2d26ec9685c4d1846baf2f11b867f31c36a08748d1c85467b01a"
}
},
{
- "@id": "urn:34aa4304-4007-4181-a467-db010e088b05",
+ "@id": "bids::X.stim.xmat.1D",
"Label": "X.stim.xmat.1D",
"AtLocation": "X.stim.xmat.1D",
- "GeneratedBy": "urn:ac0a1582-d0e6-4c06-8f3c-f7e2371d9d71",
+ "GeneratedBy": "urn:regress-fsFkOQmi",
"digest": {
"sha256": "7c61b2f4bbb9eb0cecb19f81faa3a79b94d547b7fb4087ed18e368619e0004e6"
}
},
{
- "@id": "urn:c72a767c-6c04-48a4-840f-8f8fce9c046f",
+ "@id": "bids::full_mask.$subj+tlrc",
"Label": "full_mask.$subj",
"AtLocation": "full_mask.$subj+tlrc",
"digest": {
@@ -952,34 +962,34 @@
}
},
{
- "@id": "urn:e70ba5ee-87b0-42bd-a44c-5efde9c9bfed",
+ "@id": "bids::blur.epits.1D",
"Label": "blur.epits.1D",
"AtLocation": "blur.epits.1D",
- "GeneratedBy": "urn:d2838435-2817-4d99-8c5e-4adbd8852f73",
+ "GeneratedBy": "urn:bluresti-a9WkYy7D",
"digest": {
"sha256": "623e70a42214e56babc1f1dca156e0b11ba09865dbd6ca9549d54ca2fc601515"
}
},
{
- "@id": "urn:9c34070e-67f7-4161-8228-2532bcf88bc7",
+ "@id": "bids::blur.errts.1D",
"Label": "blur.errts.1D",
"AtLocation": "blur.errts.1D",
- "GeneratedBy": "urn:d2838435-2817-4d99-8c5e-4adbd8852f73",
+ "GeneratedBy": "urn:bluresti-a9WkYy7D",
"digest": {
"sha256": "73969700079b5d3275536ac7eaf0e17571d7e74ec49553b6940f90d5718fc800"
}
},
{
- "@id": "urn:7365d26e-619c-4e80-a058-964fa937d9e5",
+ "@id": "bids::ClustSim",
"Label": "ClustSim",
"AtLocation": "ClustSim",
- "GeneratedBy": "urn:d2838435-2817-4d99-8c5e-4adbd8852f73",
+ "GeneratedBy": "urn:bluresti-a9WkYy7D",
"digest": {
"sha256": "2e0cdba2c91902ba12d742a39cb20df66cfd705ba8de767fbf68aae8eb65c6f0"
}
},
{
- "@id": "urn:91bcc4fd-63dd-4ccd-b200-8f3db9ecd468",
+ "@id": "bids::pb00.$subj.r*.tcat+orig.HEAD",
"Label": "pb00.$subj.r*.tcat",
"AtLocation": "pb00.$subj.r*.tcat+orig.HEAD",
"digest": {
@@ -987,10 +997,10 @@
}
},
{
- "@id": "urn:17c44a15-af08-4f20-80dc-8d6a00fb19a0",
+ "@id": "bids::-exit0",
"Label": "-exit0",
"AtLocation": "-exit0",
- "GeneratedBy": "urn:1f3aa16c-dba5-4a6a-be1f-070a6dd46a7c",
+ "GeneratedBy": "urn:autobloc-iR03faH6",
"digest": {
"sha256": "871a4d3513ed2924cbb10c1c15a196eac4a46a05bdcc248e3bcdb23327b3ad90"
}
diff --git a/examples/from_parsers/afni/afni_other_template_proc_block.png b/examples/from_parsers/afni/afni_other_template_proc_block.png
index 616af2192..a34fc0dce 100644
Binary files a/examples/from_parsers/afni/afni_other_template_proc_block.png and b/examples/from_parsers/afni/afni_other_template_proc_block.png differ
diff --git a/examples/from_parsers/afni/afni_thr_clustfwep05_proc.jsonld b/examples/from_parsers/afni/afni_thr_clustfwep05_proc.jsonld
index 41c51abd1..9d756931d 100644
--- a/examples/from_parsers/afni/afni_thr_clustfwep05_proc.jsonld
+++ b/examples/from_parsers/afni/afni_thr_clustfwep05_proc.jsonld
@@ -4,578 +4,581 @@
"Records": {
"Software": [
{
- "@id": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:afni-mcH6dZNr",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
- "Version": "afni24"
+ "Version": "afni24",
+ "AltIdentifier": "RRID:SCR_005927"
}
],
"Activities": [
{
- "@id": "urn:a0b6b6d8-e7c9-4497-8f03-00bb7ea256c8",
+ "@id": "urn:makedire-FbjuNWop",
"Label": "Make directory",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "mkdir $output_dir",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:2f256f1e-c083-484a-949d-6f728a0acd2c",
+ "@id": "urn:makedire-zEcKY7Zg",
"Label": "Make directory",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "mkdir $output_dir/stimuli",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:dfcf8feb-83e2-4f66-8074-59323dfd273b",
+ "@id": "urn:cp-tfse5Zds",
"Label": "cp",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "cp ./afni_clusterwise_fwe/tone_counting_onset_times.txt ./afni_clusterwise_fwe/tone_counting_probe_duration.txt $output_dir/stimuli",
"Parameters": {},
"Used": [
- "urn:184be230-ca69-44e0-b9d5-937d940c1349",
- "urn:79386b89-5260-48ae-9ca8-585c2ffa0480"
+ "bids::afni_clusterwise_fwe/tone_counting_onset_times.txt",
+ "bids::afni_clusterwise_fwe/tone_counting_probe_duration.txt"
]
},
{
- "@id": "urn:a2fcc21f-bcf1-477c-9b63-18d475287023",
+ "@id": "urn:3dcopy-eaJ6SNxb",
"Label": "3dcopy",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w",
"Parameters": {},
"Used": [
- "urn:d4cb83cd-6bf6-48e2-955f-122e6d0a0439"
+ "bids::sub-01_T1w.nii.gz"
]
},
{
- "@id": "urn:b2713b64-ed9c-4912-bde1-97d522fcdadb",
+ "@id": "urn:3dtcat-FiDxPQrL",
"Label": "3dTcat",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Parameters": {},
"Used": [
- "urn:238b43bf-8fe0-40ba-a54d-1954ced0274f"
+ "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'"
]
},
{
- "@id": "urn:546cf523-f93a-4d49-bf6c-36a419dc196a",
+ "@id": "urn:3dtoutco-4UtqD6kx",
"Label": "3dToutcount",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D",
"Parameters": {},
"Used": [
- "urn:95f9e98f-16a1-4203-add4-aa09068c95cc"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:6dfbc9e7-edf1-4dfb-8913-3084e1f1b1d5",
+ "@id": "urn:cat-ZhJDXyQD",
"Label": "cat",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "cat outcount.r*.1D > outcount_rall.1D",
"Parameters": {},
"Used": [
- "urn:77b2b3c9-72c6-4f55-9698-593ae4c90620"
+ "bids::outcount.r*.1D"
]
},
{
- "@id": "urn:b14377cb-87ee-41ba-9f24-a0fda1eabe1a",
+ "@id": "urn:3dtshift-nIE1uBeo",
"Label": "3dTshift",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig",
"Parameters": {},
"Used": [
- "urn:95f9e98f-16a1-4203-add4-aa09068c95cc"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:8c2bd16c-27f1-4fd7-b9ee-2f6fc3c59e7b",
+ "@id": "urn:alignepi-MMhnKpbM",
"Label": "align_epi_anat.py",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off",
"Parameters": {},
"Used": [
- "urn:77c559d3-63ce-44f4-bb26-91c7ddbe62f6",
- "urn:ab2e43b9-23a9-4498-b928-4a757cf4c869"
+ "bids::pb01.$subj.r01.tshift+orig",
+ "bids::sub-01_T1w+orig"
]
},
{
- "@id": "urn:9c6482f8-d86c-42e8-887e-a01c650d7f9d",
+ "@id": "urn:autotlrc-mKudz3sg",
"Label": "@auto_tlrc",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss",
"Parameters": {},
"Used": [
- "urn:eaf22111-0b26-47af-8627-b1e278e5914a",
- "urn:fd0b7203-0967-4d90-95ec-24ef3e0696f9"
+ "bids::TT_N27+tlrc",
+ "bids::sub-01_T1w_ns+orig"
]
},
{
- "@id": "urn:3199161a-bb31-491f-bd82-4b3283c53d48",
+ "@id": "urn:catmatve-sPOMH5oj",
"Label": "cat_matvec",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D",
"Parameters": {},
"Used": [
- "urn:59104013-7df9-4454-925f-bdb123c22844"
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:2313510a-a7a7-457f-8c2c-53a655cf260c",
+ "@id": "urn:3dvolreg-jfUxbOBp",
"Label": "3dvolreg",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig",
"Parameters": {},
"Used": [
- "urn:a63a5415-2d86-4ea7-995b-f862b8f47f9a"
+ "bids::pb01.$subj.r$run.tshift+orig"
]
},
{
- "@id": "urn:7564cc1a-4e3d-4126-ba65-335ca4eb7193",
+ "@id": "urn:3dcalc-AcOCVbkr",
"Label": "3dcalc",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1",
"Parameters": {},
"Used": [
- "urn:a63a5415-2d86-4ea7-995b-f862b8f47f9a"
+ "bids::pb01.$subj.r$run.tshift+orig"
]
},
{
- "@id": "urn:48149b18-b685-420c-aa12-600700527a8b",
+ "@id": "urn:catmatve-X27tWZ8o",
"Label": "cat_matvec",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D",
"Parameters": {},
"Used": [
- "urn:59104013-7df9-4454-925f-bdb123c22844"
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:5a8ac39b-1335-4c41-889f-60783a5e2b84",
+ "@id": "urn:3dalline-qZCRq4GK",
"Label": "3dAllineate",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run",
"Parameters": {},
"Used": [
- "urn:a63a5415-2d86-4ea7-995b-f862b8f47f9a",
- "urn:d9466a6c-9b6f-4bf0-9164-e9ea186ea434",
- "urn:e65f3ff3-df11-4c71-98a9-d653b6e20e63"
+ "bids::mat.r$run.warp.aff12.1D",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:3689a407-0661-43c1-b0a4-bd37850fd700",
+ "@id": "urn:3dalline-L1ZeQ8Oe",
"Label": "3dAllineate",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run",
"Parameters": {},
"Used": [
- "urn:46d2d540-a591-40b0-85f4-6d99a9fd34cb",
- "urn:d9466a6c-9b6f-4bf0-9164-e9ea186ea434",
- "urn:e65f3ff3-df11-4c71-98a9-d653b6e20e63"
+ "bids::mat.r$run.warp.aff12.1D",
+ "bids::rm.epi.all1+orig",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:5d377cc5-43ba-4030-91de-b34c5c5d5523",
+ "@id": "urn:3dtstat-ibSidOtG",
"Label": "3dTstat",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc",
"Parameters": {},
"Used": [
- "urn:99bcea95-afc5-45e7-88a1-4cbbc4a5fe50"
+ "bids::rm.epi.1.r$run+tlrc"
]
},
{
- "@id": "urn:59a1ea45-0220-470e-939b-f58dd721e19d",
+ "@id": "urn:cat-qgu5dC3S",
"Label": "cat",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "cat dfile.r*.1D > dfile_rall.1D",
"Parameters": {},
"Used": [
- "urn:3e1129c4-1668-4d2a-86a6-ec65ba4cdf22"
+ "bids::dfile.r*.1D"
]
},
{
- "@id": "urn:4eb29210-41a9-45a5-96b6-1222aa0ae290",
+ "@id": "urn:3dcopy-lIVz7ZE9",
"Label": "3dcopy",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents",
"Parameters": {},
"Used": [
- "urn:07996bd3-d168-4ddb-a41a-250a3564c17e"
+ "bids::rm.epi.min.r01+tlrc"
]
},
{
- "@id": "urn:ae9cf233-1cae-4123-a0a2-7d87c41578fa",
+ "@id": "urn:3dcalc-zltI9Eku",
"Label": "3dcalc",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg",
"Parameters": {},
"Used": [
- "urn:a7350c2c-f7d3-4b41-ace6-4cbea8187db7",
- "urn:ec5adfc3-1f39-4145-a708-6aaee3ff4ea1"
+ "bids::mask_epi_extents+tlrc",
+ "bids::rm.epi.nomask.r$run+tlrc"
]
},
{
- "@id": "urn:884190c2-d08b-4691-a22d-6a606a505216",
+ "@id": "urn:3dcopy-JHnQ1OV4",
"Label": "3dcopy",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj",
"Parameters": {},
"Used": [
- "urn:d9466a6c-9b6f-4bf0-9164-e9ea186ea434"
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:810d1d25-c45f-487c-aece-3d12edc22e68",
+ "@id": "urn:3dalline-mIklOZRC",
"Label": "3dAllineate",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped",
"Parameters": {},
"Used": [
- "urn:63557888-6f6f-4d2a-81a1-932de748541d"
+ "bids::anat_final.$subj+tlrc",
+ "bids::warp.anat.Xat.1D"
]
},
{
- "@id": "urn:ce66913e-b094-471b-bcc6-d99a9b2baac6",
+ "@id": "urn:3dmerge-t6gYVDK8",
"Label": "3dmerge",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc",
"Parameters": {},
"Used": [
- "urn:ad54aeea-950d-4781-96b7-9042c66660de",
- "urn:ffda532d-a9a3-4afe-ae56-0c197afed2e5"
+ "bids::pb02.$subj.r$run.volreg+tlrc",
+ "bids::pb03.$subj.r$run.blur"
]
},
{
- "@id": "urn:6f6cc0d2-9b58-407b-8c51-732f0dbaaeda",
+ "@id": "urn:3dautoma-Ix0vEWru",
"Label": "3dAutomask",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:6dac2074-75b1-4e6b-9f4a-37a6d6310631"
+ "bids::pb03.$subj.r$run.blur+tlrc"
]
},
{
- "@id": "urn:d8cc0c56-0ddc-4d6b-aa2b-6b5f38ecee47",
+ "@id": "urn:3dmaskto-nMSxv6HR",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:5470a0ab-86dc-40d7-b2c2-cf0cf4dbb0a8",
+ "@id": "urn:3dresamp-oQ0wyYBD",
"Label": "3dresample",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat",
"Parameters": {},
"Used": [
- "urn:227413e0-9f8c-4ec6-8469-9de994444e70",
- "urn:d9466a6c-9b6f-4bf0-9164-e9ea186ea434"
+ "bids::full_mask.$subj+tlrc",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
+ "@id": "urn:3dmaskto-fTiVoRLQ",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj",
"Parameters": {},
"Used": [
- "urn:413e1783-c57d-416f-9594-1b82ef39aa74"
+ "bids::rm.resam.anat+tlrc"
]
},
{
- "@id": "urn:b5a35ff9-0434-42f2-9b5c-ef7669c25f2b",
+ "@id": "urn:3dabover-i33bsMQT",
"Label": "3dABoverlap",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt",
"Parameters": {},
"Used": [
- "urn:12efd317-2a31-4854-b0c0-60c333623961",
- "urn:f32dd099-a3b9-4889-8fbb-8b2f4df56893"
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee"
]
},
{
- "@id": "urn:1164d63b-cf24-42cc-9f8f-c0ffaee54e74",
+ "@id": "urn:3ddot-X0Yb6q0Q",
"Label": "3ddot",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt",
"Parameters": {},
"Used": [
- "urn:12efd317-2a31-4854-b0c0-60c333623961",
- "urn:f32dd099-a3b9-4889-8fbb-8b2f4df56893"
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee"
]
},
{
- "@id": "urn:0e8e8869-93db-4b86-8b5e-08ad3dc1982b",
+ "@id": "urn:3dresamp-wHMlxr6g",
"Label": "3dresample",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc",
"Parameters": {},
"Used": [
- "urn:227413e0-9f8c-4ec6-8469-9de994444e70",
- "urn:e78802d6-1bb2-429f-bd2e-590f9ca87a83"
+ "bids::/Users/u1591557/abin/TT_N27+tlrc",
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:79564ced-7998-4380-8c8f-3269d12b864f",
+ "@id": "urn:3dmaskto-VdtzEJFq",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group",
"Parameters": {},
"Used": [
- "urn:5d2556b0-25c4-4fcb-8d9e-e104f53f9c3f"
+ "bids::rm.resam.group+tlrc"
]
},
{
- "@id": "urn:493995db-4752-45aa-a7fe-8c271ece8525",
+ "@id": "urn:3dtstat-N8h8WI8V",
"Label": "3dTstat",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:6dac2074-75b1-4e6b-9f4a-37a6d6310631"
+ "bids::pb03.$subj.r$run.blur+tlrc"
]
},
{
- "@id": "urn:1da1246e-8f5c-4ddb-a27f-be71f0701162",
+ "@id": "urn:3dcalc-awdhVElk",
"Label": "3dcalc",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale",
"Parameters": {},
"Used": [
- "urn:6dac2074-75b1-4e6b-9f4a-37a6d6310631",
- "urn:990a8e8f-1603-40d5-9b7e-89e4292d2808",
- "urn:a7350c2c-f7d3-4b41-ace6-4cbea8187db7"
+ "bids::mask_epi_extents+tlrc",
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::rm.mean_r$run+tlrc"
]
},
{
- "@id": "urn:e3fc347c-23da-42f1-9c1e-0adba15a1643",
+ "@id": "urn:1dtoolpy-fGZjwTxy",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D",
"Parameters": {},
"Used": [
- "urn:d6919dba-cce0-4138-93ba-d152dbf4e35e"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:23b55492-978b-4682-9b1f-fdd6e001aa8a",
+ "@id": "urn:1dtoolpy-CyMrv5Xy",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D",
"Parameters": {},
"Used": [
- "urn:d6919dba-cce0-4138-93ba-d152dbf4e35e"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:b0285abd-bd4b-4e1a-8ef5-e5bb34f5165e",
+ "@id": "urn:1dtoolpy-MUeVb72K",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}",
"Parameters": {},
"Used": [
- "urn:d6919dba-cce0-4138-93ba-d152dbf4e35e"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:fa8fea7b-fbf6-4d14-8056-1ab07aa17d8c",
+ "@id": "urn:3ddeconv-LAzXsF8t",
"Label": "3dDeconvolve",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj",
"Parameters": {},
"Used": [
- "urn:96fa5306-ed18-4062-b390-9a7f9e2e366c"
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD"
]
},
{
- "@id": "urn:7bfb70e4-dd28-457b-9115-c026d7b0e481",
+ "@id": "urn:1dtoolpy-AhNNeewD",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt",
"Parameters": {},
"Used": [
- "urn:d0bc9c2c-90c1-4292-8c34-2a60ec1de777"
+ "bids::X.xmat.1D"
]
},
{
- "@id": "urn:354dc113-0efb-4a5c-b8c9-4f90d541ab52",
+ "@id": "urn:3dtcat-1dvxRp0t",
"Label": "3dTcat",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD",
"Parameters": {},
"Used": [
- "urn:96fa5306-ed18-4062-b390-9a7f9e2e366c"
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD"
]
},
{
- "@id": "urn:b369eabd-5b47-4863-b6e4-c205585a5532",
+ "@id": "urn:3dtstat-29NCbF5Q",
"Label": "3dTstat",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:94126632-60e0-4fb2-b4a4-1455377f72ab"
+ "bids::all_runs.$subj+tlrc%22[$ktrs]%22"
]
},
{
- "@id": "urn:8c3dac7c-7b0c-46e3-bd94-66387114869a",
+ "@id": "urn:3dtstat-p1OOFx5l",
"Label": "3dTstat",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:75f301ba-a6be-4b56-8a56-0f77d8d2ef46"
+ "bids::errts.$%7Bsubj%7D+tlrc%22[$ktrs]%22"
]
},
{
- "@id": "urn:3f57ec61-e1a1-43d0-8fb9-75d582643f56",
+ "@id": "urn:3dcalc-vxkvWYQt",
"Label": "3dcalc",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj",
"Parameters": {},
"Used": [
- "urn:227413e0-9f8c-4ec6-8469-9de994444e70",
- "urn:32e033f7-a4dd-4061-9c13-91086c163949",
- "urn:e284c753-a44e-4920-8262-671f46d18dce"
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.noise.all+tlrc",
+ "bids::rm.signal.all+tlrc"
]
},
{
- "@id": "urn:8c8352e6-2511-46a9-8127-c252ae9ce1e7",
+ "@id": "urn:3dtnorm-plidluuV",
"Label": "3dTnorm",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc",
"Parameters": {},
"Used": [
- "urn:1aaaecec-a19d-4eae-9167-db3d5a5330c0"
+ "bids::errts.$%7Bsubj%7D+tlrc"
]
},
{
- "@id": "urn:658a862e-4043-4eca-9aa3-fa687a36306f",
+ "@id": "urn:3dmaskav-dCMQaRZ0",
"Label": "3dmaskave",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D",
"Parameters": {},
- "Used": []
+ "Used": [
+ "bids::full_mask.$subj+tlrc"
+ ]
},
{
- "@id": "urn:d19be31a-0d10-4fd8-bbb9-ecb3b04bb630",
+ "@id": "urn:3dtstat-zRHxYgiC",
"Label": "3dTstat",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D",
"Parameters": {},
"Used": [
- "urn:772cb077-7825-45a0-8ded-70a44fd2dcf5"
+ "bids::out.gcor.1D"
]
},
{
- "@id": "urn:11763a8d-cb69-4341-906a-023ac7c89975",
+ "@id": "urn:3dcalc-yAknuXpJ",
"Label": "3dcalc",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP",
"Parameters": {},
"Used": [
- "urn:0a275e5c-c0d9-4118-b74f-803b5bc6cce4",
- "urn:b5179c0a-3212-4552-8459-4cb76435a9ed"
+ "bids::gmean.errts.unit.1D",
+ "bids::rm.errts.unit+tlrc"
]
},
{
- "@id": "urn:b63a4d9e-da22-432f-9425-14e1858c050d",
+ "@id": "urn:3dtstat-6wWrCL7Q",
"Label": "3dTstat",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc",
"Parameters": {},
"Used": [
- "urn:d367e414-b015-406b-a197-efd7feb66c54"
+ "bids::rm.DP+tlrc"
]
},
{
- "@id": "urn:5bd73eb4-e099-4f85-8323-c5ac5a30be51",
+ "@id": "urn:1dcat-l087IEw3",
"Label": "1dcat",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D",
"Parameters": {},
"Used": [
- "urn:00792443-5789-44db-bbdb-d29db3610079"
+ "bids::X.nocensor.xmat.1D'[3]'"
]
},
{
- "@id": "urn:2fb0b489-c714-44c7-b162-eb7700ec8660",
+ "@id": "urn:1dcat-LyoM8qes",
"Label": "1dcat",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D",
"Parameters": {},
"Used": [
- "urn:edd5c2c1-889a-4d94-a999-b4070f948200"
+ "bids::X.nocensor.xmat.1D'[4]'"
]
},
{
- "@id": "urn:a09a0349-c9d0-4c79-8d0c-60f7a56c2f33",
+ "@id": "urn:3dtstat-zaJyNlVp",
"Label": "3dTstat",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"",
"Parameters": {},
"Used": [
- "urn:3088279e-3972-4eba-a902-ec857b348321"
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:512d926c-8516-47af-88d1-07e903350c49",
+ "@id": "urn:1dcat-xgxysZLI",
"Label": "1dcat",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D",
"Parameters": {},
"Used": [
- "urn:3088279e-3972-4eba-a902-ec857b348321"
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:1adc8260-c1e7-4397-a654-b75bf4ea1d73",
+ "@id": "urn:3dfwhmx-6mRpHZer",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D",
"Parameters": {},
"Used": [
- "urn:227413e0-9f8c-4ec6-8469-9de994444e70"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:21599809-901f-409d-beb8-f9892d2c9091",
+ "@id": "urn:3dfwhmx-j8xguQBu",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D",
"Parameters": {},
"Used": [
- "urn:227413e0-9f8c-4ec6-8469-9de994444e70"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:2ce72d11-51b1-4fef-82d7-02e62be41cfe",
+ "@id": "urn:3dclusts-H3H37Ejv",
"Label": "3dClustSim",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim",
"Parameters": {},
"Used": [
- "urn:227413e0-9f8c-4ec6-8469-9de994444e70"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:87c95662-2ebd-444d-8fa0-4faa70836610",
+ "@id": "urn:genepire-AENVIknc",
"Label": "gen_epi_review.py",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD",
"Parameters": {},
"Used": [
- "urn:17ec0eb3-5e3e-4a09-a2f4-84ca5f8b4752"
+ "bids::pb00.$subj.r*.tcat+orig.HEAD"
]
},
{
- "@id": "urn:88d4bf46-d31e-433c-a6f6-849d5b08a398",
+ "@id": "urn:genssrev-OSEn5lXu",
"Label": "gen_ss_review_scripts.py",
- "AssociatedWith": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "AssociatedWith": "urn:afni-mcH6dZNr",
"Command": "gen_ss_review_scripts.py -mot_limit 0.3 -exit0",
"Parameters": {
"-mot_limit": "0.3",
@@ -586,22 +589,22 @@
],
"Entities": [
{
- "@id": "urn:cffb91c8-2c95-46ce-b44f-baf44b7e488d",
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"Label": "$output_dir",
"AtLocation": "$output_dir",
- "GeneratedBy": "urn:a0b6b6d8-e7c9-4497-8f03-00bb7ea256c8",
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"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:2f256f1e-c083-484a-949d-6f728a0acd2c"
+ "GeneratedBy": "urn:makedire-zEcKY7Zg"
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+ "@id": "bids::afni_clusterwise_fwe/tone_counting_onset_times.txt",
"Label": "tone_counting_onset_times.txt",
"AtLocation": "./afni_clusterwise_fwe/tone_counting_onset_times.txt",
"digest": {
@@ -609,7 +612,7 @@
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"AtLocation": "./afni_clusterwise_fwe/tone_counting_probe_duration.txt",
"digest": {
@@ -617,13 +620,13 @@
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{
- "@id": "urn:5522f531-9075-4d8d-a654-6905c88ca539",
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"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:dfcf8feb-83e2-4f66-8074-59323dfd273b"
+ "GeneratedBy": "urn:cp-tfse5Zds"
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"digest": {
@@ -631,13 +634,13 @@
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{
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"AtLocation": "$output_dir/sub-01_T1w",
- "GeneratedBy": "urn:a2fcc21f-bcf1-477c-9b63-18d475287023"
+ "GeneratedBy": "urn:3dcopy-eaJ6SNxb"
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{
- "@id": "urn:238b43bf-8fe0-40ba-a54d-1954ced0274f",
+ "@id": "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Label": "sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"digest": {
@@ -645,13 +648,13 @@
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{
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"AtLocation": "$output_dir/pb00.$subj.r01.tcat",
- "GeneratedBy": "urn:b2713b64-ed9c-4912-bde1-97d522fcdadb"
+ "GeneratedBy": "urn:3dtcat-FiDxPQrL"
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"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -659,16 +662,16 @@
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{
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"AtLocation": "outcount.r$run.1D",
- "GeneratedBy": "urn:546cf523-f93a-4d49-bf6c-36a419dc196a",
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{
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+ "@id": "bids::outcount.r*.1D",
"Label": "outcount.r*.1D",
"AtLocation": "outcount.r*.1D",
"digest": {
@@ -676,25 +679,25 @@
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- "@id": "urn:9b5c6e54-fbf8-4532-9adb-d5c75ab11be0",
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"Label": "outcount_rall.1D",
"AtLocation": "outcount_rall.1D",
- "GeneratedBy": "urn:6dfbc9e7-edf1-4dfb-8913-3084e1f1b1d5",
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{
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"AtLocation": "pb01.$subj.r$run.tshift",
- "GeneratedBy": "urn:b14377cb-87ee-41ba-9f24-a0fda1eabe1a",
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"digest": {
@@ -702,7 +705,7 @@
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{
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"digest": {
@@ -710,16 +713,16 @@
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{
- "@id": "urn:db45e346-70b9-4be1-8d3c-be40c2aa586b",
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"AtLocation": "_al_junk",
- "GeneratedBy": "urn:8c2bd16c-27f1-4fd7-b9ee-2f6fc3c59e7b",
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{
- "@id": "urn:fd0b7203-0967-4d90-95ec-24ef3e0696f9",
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"digest": {
@@ -727,7 +730,7 @@
}
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{
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"digest": {
@@ -735,7 +738,7 @@
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{
- "@id": "urn:59104013-7df9-4454-925f-bdb123c22844",
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@@ -743,16 +746,16 @@
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{
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"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:3199161a-bb31-491f-bd82-4b3283c53d48",
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@@ -760,34 +763,34 @@
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{
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"AtLocation": "mat.r$run.vr.aff12.1D",
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{
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"AtLocation": "rm.epi.all1",
- "GeneratedBy": "urn:7564cc1a-4e3d-4126-ba65-335ca4eb7193",
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@@ -795,16 +798,16 @@
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@@ -812,16 +815,16 @@
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@@ -829,16 +832,16 @@
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@@ -846,16 +849,16 @@
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@@ -863,16 +866,16 @@
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@@ -880,7 +883,7 @@
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@@ -888,34 +891,42 @@
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@@ -923,7 +934,7 @@
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@@ -931,7 +942,7 @@
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@@ -939,25 +950,25 @@
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@@ -965,16 +976,16 @@
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@@ -982,16 +993,16 @@
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@@ -999,7 +1010,7 @@
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@@ -1015,16 +1026,16 @@
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@@ -1032,25 +1043,25 @@
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@@ -1058,34 +1069,34 @@
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@@ -1093,25 +1104,25 @@
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@@ -1119,16 +1130,16 @@
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@@ -1136,16 +1147,16 @@
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@@ -1153,7 +1164,7 @@
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@@ -1161,16 +1172,16 @@
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@@ -1178,25 +1189,25 @@
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},
{
- "@id": "urn:772cb077-7825-45a0-8ded-70a44fd2dcf5",
+ "@id": "bids::out.gcor.1D",
"Label": "out.gcor.1D",
"AtLocation": "out.gcor.1D",
"digest": {
@@ -1204,16 +1215,16 @@
}
},
{
- "@id": "urn:596b4850-0e60-4fef-b836-31859e5acfd6",
+ "@id": "urn:uuid:3b75dfdd-46fe-4619-a0d1-046d70b4d127",
"Label": "-",
"AtLocation": "-",
- "GeneratedBy": "urn:d19be31a-0d10-4fd8-bbb9-ecb3b04bb630",
+ "GeneratedBy": "urn:3dtstat-zRHxYgiC",
"digest": {
"sha256": "dac304c9f20899ca1ef5aa403e565345fd0ff4ed80c35f82007c9b03a68292b3"
}
},
{
- "@id": "urn:0a275e5c-c0d9-4118-b74f-803b5bc6cce4",
+ "@id": "bids::rm.errts.unit+tlrc",
"Label": "rm.errts.unit",
"AtLocation": "rm.errts.unit+tlrc",
"digest": {
@@ -1221,16 +1232,16 @@
}
},
{
- "@id": "urn:e26b5930-6e2f-4ec0-9f21-35b13e785b70",
+ "@id": "bids::rm.DP",
"Label": "rm.DP",
"AtLocation": "rm.DP",
- "GeneratedBy": "urn:11763a8d-cb69-4341-906a-023ac7c89975",
+ "GeneratedBy": "urn:3dcalc-yAknuXpJ",
"digest": {
"sha256": "06a0bfbc609c1a06ecf93c479a3288d2911c7f5f3e93cf49c5d26f721c2035ed"
}
},
{
- "@id": "urn:d367e414-b015-406b-a197-efd7feb66c54",
+ "@id": "bids::rm.DP+tlrc",
"Label": "rm.DP",
"AtLocation": "rm.DP+tlrc",
"digest": {
@@ -1238,16 +1249,16 @@
}
},
{
- "@id": "urn:6f94ef41-9565-416d-95a2-f2227bfac3de",
+ "@id": "bids::corr_brain",
"Label": "corr_brain",
"AtLocation": "corr_brain",
- "GeneratedBy": "urn:b63a4d9e-da22-432f-9425-14e1858c050d",
+ "GeneratedBy": "urn:3dtstat-6wWrCL7Q",
"digest": {
"sha256": "74e3aeae0da338b871ab5dc9e8859a4e81fcf1b3c0042cd22fe337eb7baf5eae"
}
},
{
- "@id": "urn:00792443-5789-44db-bbdb-d29db3610079",
+ "@id": "bids::X.nocensor.xmat.1D'[3]'",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D'[3]'",
"digest": {
@@ -1255,16 +1266,16 @@
}
},
{
- "@id": "urn:e783d302-cb95-45c7-9e72-4cd37fece97d",
+ "@id": "bids::ideal_tone_counting.1D",
"Label": "ideal_tone_counting.1D",
"AtLocation": "ideal_tone_counting.1D",
- "GeneratedBy": "urn:5bd73eb4-e099-4f85-8323-c5ac5a30be51",
+ "GeneratedBy": "urn:1dcat-l087IEw3",
"digest": {
"sha256": "9bb1cabac5ce7ca19dffa5cd6336a9bf82d362fea2ce9341978406e421b5333c"
}
},
{
- "@id": "urn:edd5c2c1-889a-4d94-a999-b4070f948200",
+ "@id": "bids::X.nocensor.xmat.1D'[4]'",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D'[4]'",
"digest": {
@@ -1272,16 +1283,16 @@
}
},
{
- "@id": "urn:7a55f318-70f7-435c-a4c3-a4421da5ad45",
+ "@id": "bids::ideal_probe.1D",
"Label": "ideal_probe.1D",
"AtLocation": "ideal_probe.1D",
- "GeneratedBy": "urn:2fb0b489-c714-44c7-b162-eb7700ec8660",
+ "GeneratedBy": "urn:1dcat-LyoM8qes",
"digest": {
"sha256": "705d93afa8b6ded9f4f572db3f967b54e9906942669af51dd8287a9863bb4288"
}
},
{
- "@id": "urn:3088279e-3972-4eba-a902-ec857b348321",
+ "@id": "bids::X.nocensor.xmat.1D%22[$reg_cols]%22",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D\"[$reg_cols]\"",
"digest": {
@@ -1289,52 +1300,52 @@
}
},
{
- "@id": "urn:70831a21-9367-4969-b6d0-7a9333bd935d",
+ "@id": "bids::sum_ideal.1D",
"Label": "sum_ideal.1D",
"AtLocation": "sum_ideal.1D",
- "GeneratedBy": "urn:a09a0349-c9d0-4c79-8d0c-60f7a56c2f33",
+ "GeneratedBy": "urn:3dtstat-zaJyNlVp",
"digest": {
"sha256": "b2dccadcd84b2d26ec9685c4d1846baf2f11b867f31c36a08748d1c85467b01a"
}
},
{
- "@id": "urn:00177879-fe69-465f-b6c1-f0a11477b574",
+ "@id": "bids::X.stim.xmat.1D",
"Label": "X.stim.xmat.1D",
"AtLocation": "X.stim.xmat.1D",
- "GeneratedBy": "urn:512d926c-8516-47af-88d1-07e903350c49",
+ "GeneratedBy": "urn:1dcat-xgxysZLI",
"digest": {
"sha256": "7c61b2f4bbb9eb0cecb19f81faa3a79b94d547b7fb4087ed18e368619e0004e6"
}
},
{
- "@id": "urn:2bcc7a12-cfa9-4e43-8165-2358b7e0fbe4",
+ "@id": "bids::blur.epits.1D",
"Label": "blur.epits.1D",
"AtLocation": "blur.epits.1D",
- "GeneratedBy": "urn:1adc8260-c1e7-4397-a654-b75bf4ea1d73",
+ "GeneratedBy": "urn:3dfwhmx-6mRpHZer",
"digest": {
"sha256": "623e70a42214e56babc1f1dca156e0b11ba09865dbd6ca9549d54ca2fc601515"
}
},
{
- "@id": "urn:44d126c5-0e33-423a-9bc6-0eeb27830d9d",
+ "@id": "bids::blur.errts.1D",
"Label": "blur.errts.1D",
"AtLocation": "blur.errts.1D",
- "GeneratedBy": "urn:21599809-901f-409d-beb8-f9892d2c9091",
+ "GeneratedBy": "urn:3dfwhmx-j8xguQBu",
"digest": {
"sha256": "73969700079b5d3275536ac7eaf0e17571d7e74ec49553b6940f90d5718fc800"
}
},
{
- "@id": "urn:f1939880-f643-4bfb-95ae-feaba72a6d4d",
+ "@id": "bids::ClustSim",
"Label": "ClustSim",
"AtLocation": "ClustSim",
- "GeneratedBy": "urn:2ce72d11-51b1-4fef-82d7-02e62be41cfe",
+ "GeneratedBy": "urn:3dclusts-H3H37Ejv",
"digest": {
"sha256": "2e0cdba2c91902ba12d742a39cb20df66cfd705ba8de767fbf68aae8eb65c6f0"
}
},
{
- "@id": "urn:17ec0eb3-5e3e-4a09-a2f4-84ca5f8b4752",
+ "@id": "bids::pb00.$subj.r*.tcat+orig.HEAD",
"Label": "pb00.$subj.r*.tcat",
"AtLocation": "pb00.$subj.r*.tcat+orig.HEAD",
"digest": {
@@ -1342,10 +1353,10 @@
}
},
{
- "@id": "urn:213f0f36-c90c-4cbe-b10e-70ad5f3efd7d",
+ "@id": "bids::-exit0",
"Label": "-exit0",
"AtLocation": "-exit0",
- "GeneratedBy": "urn:88d4bf46-d31e-433c-a6f6-849d5b08a398",
+ "GeneratedBy": "urn:genssrev-OSEn5lXu",
"digest": {
"sha256": "871a4d3513ed2924cbb10c1c15a196eac4a46a05bdcc248e3bcdb23327b3ad90"
}
diff --git a/examples/from_parsers/afni/afni_thr_clustfwep05_proc.png b/examples/from_parsers/afni/afni_thr_clustfwep05_proc.png
index 73452087f..ebb01e8f2 100644
Binary files a/examples/from_parsers/afni/afni_thr_clustfwep05_proc.png and b/examples/from_parsers/afni/afni_thr_clustfwep05_proc.png differ
diff --git a/examples/from_parsers/afni/afni_thr_clustfwep05_proc_block.jsonld b/examples/from_parsers/afni/afni_thr_clustfwep05_proc_block.jsonld
index 752ae2ca6..3e4102786 100644
--- a/examples/from_parsers/afni/afni_thr_clustfwep05_proc_block.jsonld
+++ b/examples/from_parsers/afni/afni_thr_clustfwep05_proc_block.jsonld
@@ -4,187 +4,189 @@
"Records": {
"Software": [
{
- "@id": "urn:ec7ce89d-a0d6-4e64-8833-d45c6b5f00f4",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:afni-XB2LYpvU",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
- "Version": "afni24"
+ "Version": "afni24",
+ "AltIdentifier": "RRID:SCR_005927"
}
],
"Activities": [
{
- "@id": "urn:5207724d-e906-4471-903b-6cab18cd9c26",
+ "@id": "urn:autobloc-O2EAcJPK",
"Label": "auto block: setup",
- "AssociatedWith": "urn:ec7ce89d-a0d6-4e64-8833-d45c6b5f00f4",
+ "AssociatedWith": "urn:afni-XB2LYpvU",
"Command": "mkdir $output_dir; mkdir $output_dir/stimuli; cp ./afni_clusterwise_fwe/tone_counting_onset_times.txt ./afni_clusterwise_fwe/tone_counting_probe_duration.txt $output_dir/stimuli; 3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w; ",
"Used": [
- "urn:7b140f3d-6abf-41b8-ad5a-22144fa236c2",
- "urn:b0f95d92-523f-4861-bb4b-73d2d24beea0",
- "urn:004588cf-30f4-461b-9397-b1b80f9543cd"
+ "bids::afni_clusterwise_fwe/tone_counting_onset_times.txt",
+ "bids::afni_clusterwise_fwe/tone_counting_probe_duration.txt",
+ "bids::sub-01_T1w.nii.gz"
]
},
{
- "@id": "urn:867c3f3e-61a4-4e15-868f-d6f881110e8b",
+ "@id": "urn:autobloc-K8cP1HXJ",
"Label": "auto block: tcat",
- "AssociatedWith": "urn:ec7ce89d-a0d6-4e64-8833-d45c6b5f00f4",
+ "AssociatedWith": "urn:afni-XB2LYpvU",
"Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ",
"Used": [
- "urn:adc96e19-68de-4e67-a8d8-ff10b9a6ccfd"
+ "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'"
]
},
{
- "@id": "urn:107e60e5-e48c-440a-b943-4a2265ab0c43",
+ "@id": "urn:autobloc-A9ob1Zdf",
"Label": "auto block: outcount",
- "AssociatedWith": "urn:ec7ce89d-a0d6-4e64-8833-d45c6b5f00f4",
+ "AssociatedWith": "urn:afni-XB2LYpvU",
"Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ",
"Used": [
- "urn:d68b18e4-1c77-4350-be64-28f08db7bb70",
- "urn:be821ff6-4e80-48df-9e6b-29d67cfa2267"
+ "bids::pb00.$subj.r$run.tcat+orig",
+ "bids::outcount.r*.1D"
]
},
{
- "@id": "urn:aeac332e-bce4-4c17-b94a-d85ae2953fed",
+ "@id": "urn:tshift-os3rZrwr",
"Label": "tshift",
- "AssociatedWith": "urn:ec7ce89d-a0d6-4e64-8833-d45c6b5f00f4",
+ "AssociatedWith": "urn:afni-XB2LYpvU",
"Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ",
"Used": [
- "urn:d68b18e4-1c77-4350-be64-28f08db7bb70"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:fe6d6a5a-eb3e-4181-805e-a2e2fe4fec50",
+ "@id": "urn:align-YJumoEmQ",
"Label": "align",
- "AssociatedWith": "urn:ec7ce89d-a0d6-4e64-8833-d45c6b5f00f4",
+ "AssociatedWith": "urn:afni-XB2LYpvU",
"Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ",
"Used": [
- "urn:3d7b689f-3ef8-40b2-b094-a6f0e0de5710",
- "urn:3dac42e9-44c5-49f6-8f9b-31610a861698"
+ "bids::pb01.$subj.r01.tshift+orig",
+ "bids::sub-01_T1w+orig"
]
},
{
- "@id": "urn:3e1fcf67-d0c6-41ce-b2d4-494232f1d5fe",
+ "@id": "urn:tlrc-XYGehrKJ",
"Label": "tlrc",
- "AssociatedWith": "urn:ec7ce89d-a0d6-4e64-8833-d45c6b5f00f4",
+ "AssociatedWith": "urn:afni-XB2LYpvU",
"Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ",
"Used": [
- "urn:95a48f5a-4490-43fc-bd15-2f51fcf77876",
- "urn:f0e64142-2ee2-4373-860e-9148861a3561",
- "urn:7b7743c9-a3c9-4e67-af87-66383d6394dd"
+ "bids::TT_N27+tlrc",
+ "bids::sub-01_T1w_ns+orig",
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:6f5054a4-f6c6-4829-b94a-f8b6b8df267a",
+ "@id": "urn:volreg-byFDcmEp",
"Label": "volreg",
- "AssociatedWith": "urn:ec7ce89d-a0d6-4e64-8833-d45c6b5f00f4",
+ "AssociatedWith": "urn:afni-XB2LYpvU",
"Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig; 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1; cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D; 3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run; 3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run; 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc; cat dfile.r*.1D > dfile_rall.1D; 3dcopy rm.epi.min.r01+tlrc mask_epi_extents; 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg; 3dcopy sub-01_T1w_ns+tlrc anat_final.$subj; 3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped; ",
"Used": [
- "urn:bc8fbab4-e820-4f90-9081-1ba940db91d9",
- "urn:bc8fbab4-e820-4f90-9081-1ba940db91d9",
- "urn:7b7743c9-a3c9-4e67-af87-66383d6394dd",
- "urn:3f5a1d1a-02fb-460a-8723-09a384c1d748",
- "urn:bc8fbab4-e820-4f90-9081-1ba940db91d9",
- "urn:3f5a1d1a-02fb-460a-8723-09a384c1d748",
- "urn:defbc177-f0b5-487f-bad3-940bce87dfab",
- "urn:93fac8c7-f8ff-47da-a285-75a5996ee8ea",
- "urn:173c97cf-75fd-46b2-94f8-a66547840fc2",
- "urn:7076137c-82de-4da7-9492-dc2ed26af811",
- "urn:323f4cd3-efa6-4fa6-834a-5e176620c273",
- "urn:6318e784-8873-4577-a8ec-ef187f68f5cd",
- "urn:3f5a1d1a-02fb-460a-8723-09a384c1d748",
- "urn:6c4894c7-3798-4745-a690-665bfb6093a2"
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.epi.all1+orig",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.epi.1.r$run+tlrc",
+ "bids::dfile.r*.1D",
+ "bids::rm.epi.min.r01+tlrc",
+ "bids::mask_epi_extents+tlrc",
+ "bids::rm.epi.nomask.r$run+tlrc",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::anat_final.$subj+tlrc",
+ "bids::warp.anat.Xat.1D"
]
},
{
- "@id": "urn:da70a0c2-17ec-4c1c-9942-adf20b85a387",
+ "@id": "urn:blur-8RPMY4qi",
"Label": "blur",
- "AssociatedWith": "urn:ec7ce89d-a0d6-4e64-8833-d45c6b5f00f4",
+ "AssociatedWith": "urn:afni-XB2LYpvU",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc; ",
"Used": [
- "urn:801d9025-851e-4ae3-88cc-c846408d6be6",
- "urn:968f8eb8-a609-4ea7-b55d-15aa0ec4f553"
+ "bids::pb02.$subj.r$run.volreg+tlrc",
+ "bids::pb03.$subj.r$run.blur"
]
},
{
- "@id": "urn:b5cd528a-7c8f-4f15-ab9f-0bd7bca967ca",
+ "@id": "urn:mask-RISCfneZ",
"Label": "mask",
- "AssociatedWith": "urn:ec7ce89d-a0d6-4e64-8833-d45c6b5f00f4",
+ "AssociatedWith": "urn:afni-XB2LYpvU",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc; 3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj; 3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj; 3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt; 3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt; 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group; ",
"Used": [
- "urn:ae285646-f8c3-4275-ac7c-7b41cab822f8",
- "urn:3f5a1d1a-02fb-460a-8723-09a384c1d748",
- "urn:563fe303-2f17-49bf-8d23-942b7afd445c",
- "urn:6f437b9f-b660-4ffa-a0e6-089fd8e50b9a",
- "urn:4cce67b5-2b9a-4121-b733-9d5228c677c5",
- "urn:de11a3ef-48eb-49af-8f70-74c35c37293a",
- "urn:4cce67b5-2b9a-4121-b733-9d5228c677c5",
- "urn:de11a3ef-48eb-49af-8f70-74c35c37293a",
- "urn:563fe303-2f17-49bf-8d23-942b7afd445c",
- "urn:fb6b7ab0-3879-487e-a6e6-40d5ca92c3f9",
- "urn:00950c27-cd02-4bcf-a2f6-971b963c5868"
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.resam.anat+tlrc",
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee",
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee",
+ "bids::/Users/u1591557/abin/TT_N27+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.resam.group+tlrc"
]
},
{
- "@id": "urn:521a1422-bf72-4868-a196-36ea32e32333",
+ "@id": "urn:scale-TtlMGQiE",
"Label": "scale",
- "AssociatedWith": "urn:ec7ce89d-a0d6-4e64-8833-d45c6b5f00f4",
+ "AssociatedWith": "urn:afni-XB2LYpvU",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc; 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale; ",
"Used": [
- "urn:ae285646-f8c3-4275-ac7c-7b41cab822f8",
- "urn:6318e784-8873-4577-a8ec-ef187f68f5cd",
- "urn:ae285646-f8c3-4275-ac7c-7b41cab822f8",
- "urn:cbf092fe-95f6-4477-a6d8-4ba609793da0"
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::mask_epi_extents+tlrc",
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::rm.mean_r$run+tlrc"
]
},
{
- "@id": "urn:abf58822-094d-478e-8a84-f7519450b542",
+ "@id": "urn:regress-SE5Q0bej",
"Label": "regress",
- "AssociatedWith": "urn:ec7ce89d-a0d6-4e64-8833-d45c6b5f00f4",
+ "AssociatedWith": "urn:afni-XB2LYpvU",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}; 3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj; 1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt; 3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD; 3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"; 3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"; 3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj; 3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc; 3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D; 3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D; 3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP; 3dTstat -sum -prefix corr_brain rm.DP+tlrc; 1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D; 1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D; 3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"; 1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D; ",
"Used": [
- "urn:23473f19-2887-4f4e-88e3-ccfa739597f3",
- "urn:23473f19-2887-4f4e-88e3-ccfa739597f3",
- "urn:23473f19-2887-4f4e-88e3-ccfa739597f3",
- "urn:0f953e19-1447-4b9a-9e28-41be969a521e",
- "urn:0f953e19-1447-4b9a-9e28-41be969a521e",
- "urn:857e8e51-3c15-4221-9d57-2b50496bd630",
- "urn:ac6fc9f2-1d1f-4612-ad97-fb964bfe01e8",
- "urn:563fe303-2f17-49bf-8d23-942b7afd445c",
- "urn:680f5096-e37f-4ec7-b010-2dae5b5a44fd",
- "urn:df0f3c2c-5569-4f68-b81d-0a334275b3d2",
- "urn:16bf4939-3694-4686-af30-f2acf3976d7b",
- "urn:426ecd4c-c844-4216-95ee-fdea203c4ac7",
- "urn:4c94d596-d066-4fae-b4ac-31bd8a4eb431",
- "urn:cf039742-a7cf-4661-8c5a-8028ee16f56b",
- "urn:a6816927-efa4-41b8-9288-3137c8b366a0",
- "urn:f76d19e5-b0b5-45bc-a574-b35b52c5604a",
- "urn:2b13402b-a51c-4043-8706-ad2728b1668d",
- "urn:2b13402b-a51c-4043-8706-ad2728b1668d"
+ "bids::dfile_rall.1D",
+ "bids::dfile_rall.1D",
+ "bids::dfile_rall.1D",
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD",
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD",
+ "bids::all_runs.$subj+tlrc%22[$ktrs]%22",
+ "bids::errts.$%7Bsubj%7D+tlrc%22[$ktrs]%22",
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.noise.all+tlrc",
+ "bids::rm.signal.all+tlrc",
+ "bids::errts.$%7Bsubj%7D+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::out.gcor.1D",
+ "bids::rm.errts.unit+tlrc",
+ "bids::rm.DP+tlrc",
+ "bids::X.nocensor.xmat.1D'[3]'",
+ "bids::X.nocensor.xmat.1D'[4]'",
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22",
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:209a7ec7-d866-4295-a415-a6b5798cc3de",
+ "@id": "urn:bluresti-LQzLcXWZ",
"Label": "blur estimation",
- "AssociatedWith": "urn:ec7ce89d-a0d6-4e64-8833-d45c6b5f00f4",
+ "AssociatedWith": "urn:afni-XB2LYpvU",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D; 3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D; 3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim; ",
"Used": [
- "urn:563fe303-2f17-49bf-8d23-942b7afd445c",
- "urn:563fe303-2f17-49bf-8d23-942b7afd445c",
- "urn:563fe303-2f17-49bf-8d23-942b7afd445c"
+ "bids::full_mask.$subj+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:7f47301c-e203-4fac-b2bd-efb02325b318",
+ "@id": "urn:autobloc-Wk5QBdUZ",
"Label": "auto block: generate review scripts",
- "AssociatedWith": "urn:ec7ce89d-a0d6-4e64-8833-d45c6b5f00f4",
+ "AssociatedWith": "urn:afni-XB2LYpvU",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD; gen_ss_review_scripts.py -mot_limit 0.3 -exit0; ",
"Used": [
- "urn:21d86d5a-4768-45a5-90d2-055e94a0aa9b"
+ "bids::pb00.$subj.r*.tcat+orig.HEAD"
]
}
],
"Entities": [
{
- "@id": "urn:7b140f3d-6abf-41b8-ad5a-22144fa236c2",
+ "@id": "bids::afni_clusterwise_fwe/tone_counting_onset_times.txt",
"Label": "tone_counting_onset_times.txt",
"AtLocation": "./afni_clusterwise_fwe/tone_counting_onset_times.txt",
"digest": {
@@ -192,7 +194,7 @@
}
},
{
- "@id": "urn:b0f95d92-523f-4861-bb4b-73d2d24beea0",
+ "@id": "bids::afni_clusterwise_fwe/tone_counting_probe_duration.txt",
"Label": "tone_counting_probe_duration.txt",
"AtLocation": "./afni_clusterwise_fwe/tone_counting_probe_duration.txt",
"digest": {
@@ -200,7 +202,7 @@
}
},
{
- "@id": "urn:004588cf-30f4-461b-9397-b1b80f9543cd",
+ "@id": "bids::sub-01_T1w.nii.gz",
"Label": "sub-01_T1w.nii.gz",
"AtLocation": "sub-01_T1w.nii.gz",
"digest": {
@@ -208,34 +210,34 @@
}
},
{
- "@id": "urn:4bfb75c7-997a-4f9f-b33a-af1843939f5b",
+ "@id": "bids::$output_dir",
"Label": "$output_dir",
"AtLocation": "$output_dir",
- "GeneratedBy": "urn:5207724d-e906-4471-903b-6cab18cd9c26",
+ "GeneratedBy": "urn:autobloc-O2EAcJPK",
"digest": {
"sha256": "9fa4c635e6533ddf2fed54295920052818d948c3ffe97bc753bd7336b453f8cb"
}
},
{
- "@id": "urn:e5d05490-30b3-495e-a514-6e8d545b6c71",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:5207724d-e906-4471-903b-6cab18cd9c26"
+ "GeneratedBy": "urn:autobloc-O2EAcJPK"
},
{
- "@id": "urn:fd68f623-a09b-4e5b-aa19-e745c7e03a62",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:5207724d-e906-4471-903b-6cab18cd9c26"
+ "GeneratedBy": "urn:autobloc-O2EAcJPK"
},
{
- "@id": "urn:e0a8e579-f99e-458f-821d-5acd22c4a3ba",
+ "@id": "bids::$output_dir/sub-01_T1w",
"Label": "sub-01_T1w",
"AtLocation": "$output_dir/sub-01_T1w",
- "GeneratedBy": "urn:5207724d-e906-4471-903b-6cab18cd9c26"
+ "GeneratedBy": "urn:autobloc-O2EAcJPK"
},
{
- "@id": "urn:adc96e19-68de-4e67-a8d8-ff10b9a6ccfd",
+ "@id": "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Label": "sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"digest": {
@@ -243,13 +245,13 @@
}
},
{
- "@id": "urn:033237d4-454f-4b72-a451-b233c06dfbbc",
+ "@id": "bids::$output_dir/pb00.$subj.r01.tcat",
"Label": "pb00.$subj.r01.tcat",
"AtLocation": "$output_dir/pb00.$subj.r01.tcat",
- "GeneratedBy": "urn:867c3f3e-61a4-4e15-868f-d6f881110e8b"
+ "GeneratedBy": "urn:autobloc-K8cP1HXJ"
},
{
- "@id": "urn:d68b18e4-1c77-4350-be64-28f08db7bb70",
+ "@id": "bids::pb00.$subj.r$run.tcat+orig",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -257,7 +259,7 @@
}
},
{
- "@id": "urn:be821ff6-4e80-48df-9e6b-29d67cfa2267",
+ "@id": "bids::outcount.r*.1D",
"Label": "outcount.r*.1D",
"AtLocation": "outcount.r*.1D",
"digest": {
@@ -265,25 +267,25 @@
}
},
{
- "@id": "urn:de94b5e5-8f36-4088-98ad-e974638117af",
+ "@id": "bids::outcount.r$run.1D",
"Label": "outcount.r$run.1D",
"AtLocation": "outcount.r$run.1D",
- "GeneratedBy": "urn:107e60e5-e48c-440a-b943-4a2265ab0c43",
+ "GeneratedBy": "urn:autobloc-A9ob1Zdf",
"digest": {
"sha256": "63d9f539e5470badc625d557109f68bc4eecbb02ca2667483739d52f95e5d0dd"
}
},
{
- "@id": "urn:78eb9655-2615-48cb-8175-bdc58d75afa9",
+ "@id": "bids::outcount_rall.1D",
"Label": "outcount_rall.1D",
"AtLocation": "outcount_rall.1D",
- "GeneratedBy": "urn:107e60e5-e48c-440a-b943-4a2265ab0c43",
+ "GeneratedBy": "urn:autobloc-A9ob1Zdf",
"digest": {
"sha256": "cb887fd5e4d5e9acb3a24820d0f7a62ed38a5ffb0fdedd373440ac0219fb186a"
}
},
{
- "@id": "urn:d68b18e4-1c77-4350-be64-28f08db7bb70",
+ "@id": "bids::pb00.$subj.r$run.tcat+orig",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -291,16 +293,16 @@
}
},
{
- "@id": "urn:7aa980a3-a715-4b02-9615-8bff400a4ae8",
+ "@id": "bids::pb01.$subj.r$run.tshift",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift",
- "GeneratedBy": "urn:aeac332e-bce4-4c17-b94a-d85ae2953fed",
+ "GeneratedBy": "urn:tshift-os3rZrwr",
"digest": {
"sha256": "c6bf01cea8d2eac1d7a866f80b865c6e7d4b4e012dbb63d480ac9a8551162d72"
}
},
{
- "@id": "urn:3dac42e9-44c5-49f6-8f9b-31610a861698",
+ "@id": "bids::sub-01_T1w+orig",
"Label": "sub-01_T1w",
"AtLocation": "sub-01_T1w+orig",
"digest": {
@@ -308,7 +310,7 @@
}
},
{
- "@id": "urn:3d7b689f-3ef8-40b2-b094-a6f0e0de5710",
+ "@id": "bids::pb01.$subj.r01.tshift+orig",
"Label": "pb01.$subj.r01.tshift",
"AtLocation": "pb01.$subj.r01.tshift+orig",
"digest": {
@@ -316,16 +318,16 @@
}
},
{
- "@id": "urn:748e083f-795d-442f-b1cf-3021e2192314",
+ "@id": "bids::_al_junk",
"Label": "_al_junk",
"AtLocation": "_al_junk",
- "GeneratedBy": "urn:fe6d6a5a-eb3e-4181-805e-a2e2fe4fec50",
+ "GeneratedBy": "urn:align-YJumoEmQ",
"digest": {
"sha256": "bd785a075a4c6446e1e54de9e628913f7f1c814e86b69a9fbfe933209e6d37b5"
}
},
{
- "@id": "urn:f0e64142-2ee2-4373-860e-9148861a3561",
+ "@id": "bids::TT_N27+tlrc",
"Label": "TT_N27",
"AtLocation": "TT_N27+tlrc",
"digest": {
@@ -333,7 +335,7 @@
}
},
{
- "@id": "urn:95a48f5a-4490-43fc-bd15-2f51fcf77876",
+ "@id": "bids::sub-01_T1w_ns+orig",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+orig",
"digest": {
@@ -341,7 +343,7 @@
}
},
{
- "@id": "urn:7b7743c9-a3c9-4e67-af87-66383d6394dd",
+ "@id": "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc::WARP_DATA",
"digest": {
@@ -349,16 +351,16 @@
}
},
{
- "@id": "urn:6c4894c7-3798-4745-a690-665bfb6093a2",
+ "@id": "bids::warp.anat.Xat.1D",
"Label": "warp.anat.Xat.1D",
"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:3e1fcf67-d0c6-41ce-b2d4-494232f1d5fe",
+ "GeneratedBy": "urn:tlrc-XYGehrKJ",
"digest": {
"sha256": "800633fb5b4e9be64078bc181c4d5510ffb73fc5cccaf364c7fb6a294aa06728"
}
},
{
- "@id": "urn:7b7743c9-a3c9-4e67-af87-66383d6394dd",
+ "@id": "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc::WARP_DATA",
"digest": {
@@ -366,16 +368,16 @@
}
},
{
- "@id": "urn:6c4894c7-3798-4745-a690-665bfb6093a2",
+ "@id": "bids::warp.anat.Xat.1D",
"Label": "warp.anat.Xat.1D",
"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:3e1fcf67-d0c6-41ce-b2d4-494232f1d5fe",
+ "GeneratedBy": "urn:tlrc-XYGehrKJ",
"digest": {
"sha256": "800633fb5b4e9be64078bc181c4d5510ffb73fc5cccaf364c7fb6a294aa06728"
}
},
{
- "@id": "urn:bc8fbab4-e820-4f90-9081-1ba940db91d9",
+ "@id": "bids::pb01.$subj.r$run.tshift+orig",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift+orig",
"digest": {
@@ -383,7 +385,7 @@
}
},
{
- "@id": "urn:3f5a1d1a-02fb-460a-8723-09a384c1d748",
+ "@id": "bids::sub-01_T1w_ns+tlrc",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc",
"digest": {
@@ -391,7 +393,7 @@
}
},
{
- "@id": "urn:defbc177-f0b5-487f-bad3-940bce87dfab",
+ "@id": "bids::rm.epi.all1+orig",
"Label": "rm.epi.all1",
"AtLocation": "rm.epi.all1+orig",
"digest": {
@@ -399,7 +401,7 @@
}
},
{
- "@id": "urn:93fac8c7-f8ff-47da-a285-75a5996ee8ea",
+ "@id": "bids::rm.epi.1.r$run+tlrc",
"Label": "rm.epi.1.r$run",
"AtLocation": "rm.epi.1.r$run+tlrc",
"digest": {
@@ -407,7 +409,7 @@
}
},
{
- "@id": "urn:173c97cf-75fd-46b2-94f8-a66547840fc2",
+ "@id": "bids::dfile.r*.1D",
"Label": "dfile.r*.1D",
"AtLocation": "dfile.r*.1D",
"digest": {
@@ -415,7 +417,7 @@
}
},
{
- "@id": "urn:7076137c-82de-4da7-9492-dc2ed26af811",
+ "@id": "bids::rm.epi.min.r01+tlrc",
"Label": "rm.epi.min.r01",
"AtLocation": "rm.epi.min.r01+tlrc",
"digest": {
@@ -423,7 +425,7 @@
}
},
{
- "@id": "urn:323f4cd3-efa6-4fa6-834a-5e176620c273",
+ "@id": "bids::rm.epi.nomask.r$run+tlrc",
"Label": "rm.epi.nomask.r$run",
"AtLocation": "rm.epi.nomask.r$run+tlrc",
"digest": {
@@ -431,7 +433,7 @@
}
},
{
- "@id": "urn:6318e784-8873-4577-a8ec-ef187f68f5cd",
+ "@id": "bids::mask_epi_extents+tlrc",
"Label": "mask_epi_extents",
"AtLocation": "mask_epi_extents+tlrc",
"digest": {
@@ -439,97 +441,105 @@
}
},
{
- "@id": "urn:548fb52c-9c65-4932-ae44-f69ae07b3515",
+ "@id": "bids::anat_final.$subj+tlrc",
+ "Label": "anat_final.$subj",
+ "AtLocation": "anat_final.$subj+tlrc",
+ "digest": {
+ "sha256": "94eb1853614cc085b22772c011f119f6a0ad7ec06cba2850587762e7f1a6eae6"
+ }
+ },
+ {
+ "@id": "bids::mat.r$run.vr.aff12.1D",
"Label": "mat.r$run.vr.aff12.1D",
"AtLocation": "mat.r$run.vr.aff12.1D",
- "GeneratedBy": "urn:6f5054a4-f6c6-4829-b94a-f8b6b8df267a",
+ "GeneratedBy": "urn:volreg-byFDcmEp",
"digest": {
"sha256": "2e6e6c2ce8089cfa3c6e11dc72fca0cc8497f7a55faae2ced402de4867466c91"
}
},
{
- "@id": "urn:8dd10906-ab30-45b6-b7bd-b140ffc50ba3",
+ "@id": "bids::rm.epi.all1",
"Label": "rm.epi.all1",
"AtLocation": "rm.epi.all1",
- "GeneratedBy": "urn:6f5054a4-f6c6-4829-b94a-f8b6b8df267a",
+ "GeneratedBy": "urn:volreg-byFDcmEp",
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@@ -537,7 +547,7 @@
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@@ -545,7 +555,7 @@
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@@ -553,7 +563,7 @@
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@@ -561,7 +571,7 @@
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@@ -569,7 +579,7 @@
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@@ -577,7 +587,7 @@
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@@ -585,7 +595,7 @@
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@@ -593,7 +603,7 @@
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@@ -601,7 +611,7 @@
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@@ -609,61 +619,61 @@
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@@ -671,7 +681,7 @@
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@@ -679,7 +689,7 @@
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@@ -687,34 +697,34 @@
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@@ -722,7 +732,7 @@
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@@ -730,7 +740,7 @@
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@@ -738,7 +748,7 @@
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@@ -746,7 +756,7 @@
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@@ -754,7 +764,7 @@
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@@ -762,7 +772,7 @@
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@@ -770,7 +780,7 @@
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@@ -778,7 +788,7 @@
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@@ -786,7 +796,7 @@
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@@ -794,7 +804,7 @@
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@@ -802,7 +812,7 @@
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@@ -810,7 +820,7 @@
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@@ -818,133 +828,133 @@
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"AtLocation": "rm.DP",
- "GeneratedBy": "urn:abf58822-094d-478e-8a84-f7519450b542",
+ "GeneratedBy": "urn:regress-SE5Q0bej",
"digest": {
"sha256": "06a0bfbc609c1a06ecf93c479a3288d2911c7f5f3e93cf49c5d26f721c2035ed"
}
},
{
- "@id": "urn:8b7d7bf5-ff2c-4b73-991f-6067e1e2d1b9",
+ "@id": "bids::corr_brain",
"Label": "corr_brain",
"AtLocation": "corr_brain",
- "GeneratedBy": "urn:abf58822-094d-478e-8a84-f7519450b542",
+ "GeneratedBy": "urn:regress-SE5Q0bej",
"digest": {
"sha256": "74e3aeae0da338b871ab5dc9e8859a4e81fcf1b3c0042cd22fe337eb7baf5eae"
}
},
{
- "@id": "urn:66c6f4a5-e5db-46b2-b07c-e741461d17cd",
+ "@id": "bids::ideal_tone_counting.1D",
"Label": "ideal_tone_counting.1D",
"AtLocation": "ideal_tone_counting.1D",
- "GeneratedBy": "urn:abf58822-094d-478e-8a84-f7519450b542",
+ "GeneratedBy": "urn:regress-SE5Q0bej",
"digest": {
"sha256": "9bb1cabac5ce7ca19dffa5cd6336a9bf82d362fea2ce9341978406e421b5333c"
}
},
{
- "@id": "urn:47364376-8009-46b5-9c2c-50f39f9aa7b7",
+ "@id": "bids::ideal_probe.1D",
"Label": "ideal_probe.1D",
"AtLocation": "ideal_probe.1D",
- "GeneratedBy": "urn:abf58822-094d-478e-8a84-f7519450b542",
+ "GeneratedBy": "urn:regress-SE5Q0bej",
"digest": {
"sha256": "705d93afa8b6ded9f4f572db3f967b54e9906942669af51dd8287a9863bb4288"
}
},
{
- "@id": "urn:1bccfb06-3514-411e-bc4d-7d5021d773b8",
+ "@id": "bids::sum_ideal.1D",
"Label": "sum_ideal.1D",
"AtLocation": "sum_ideal.1D",
- "GeneratedBy": "urn:abf58822-094d-478e-8a84-f7519450b542",
+ "GeneratedBy": "urn:regress-SE5Q0bej",
"digest": {
"sha256": "b2dccadcd84b2d26ec9685c4d1846baf2f11b867f31c36a08748d1c85467b01a"
}
},
{
- "@id": "urn:816045b3-2730-4afa-9cce-255578e9966f",
+ "@id": "bids::X.stim.xmat.1D",
"Label": "X.stim.xmat.1D",
"AtLocation": "X.stim.xmat.1D",
- "GeneratedBy": "urn:abf58822-094d-478e-8a84-f7519450b542",
+ "GeneratedBy": "urn:regress-SE5Q0bej",
"digest": {
"sha256": "7c61b2f4bbb9eb0cecb19f81faa3a79b94d547b7fb4087ed18e368619e0004e6"
}
},
{
- "@id": "urn:563fe303-2f17-49bf-8d23-942b7afd445c",
+ "@id": "bids::full_mask.$subj+tlrc",
"Label": "full_mask.$subj",
"AtLocation": "full_mask.$subj+tlrc",
"digest": {
@@ -952,34 +962,34 @@
}
},
{
- "@id": "urn:a1b2679b-c5c0-441b-a89d-c14f0248f813",
+ "@id": "bids::blur.epits.1D",
"Label": "blur.epits.1D",
"AtLocation": "blur.epits.1D",
- "GeneratedBy": "urn:209a7ec7-d866-4295-a415-a6b5798cc3de",
+ "GeneratedBy": "urn:bluresti-LQzLcXWZ",
"digest": {
"sha256": "623e70a42214e56babc1f1dca156e0b11ba09865dbd6ca9549d54ca2fc601515"
}
},
{
- "@id": "urn:18a3d038-b80d-44fc-9706-301753499bc1",
+ "@id": "bids::blur.errts.1D",
"Label": "blur.errts.1D",
"AtLocation": "blur.errts.1D",
- "GeneratedBy": "urn:209a7ec7-d866-4295-a415-a6b5798cc3de",
+ "GeneratedBy": "urn:bluresti-LQzLcXWZ",
"digest": {
"sha256": "73969700079b5d3275536ac7eaf0e17571d7e74ec49553b6940f90d5718fc800"
}
},
{
- "@id": "urn:db266899-a1e3-4ced-ac54-5e9fc8e925ff",
+ "@id": "bids::ClustSim",
"Label": "ClustSim",
"AtLocation": "ClustSim",
- "GeneratedBy": "urn:209a7ec7-d866-4295-a415-a6b5798cc3de",
+ "GeneratedBy": "urn:bluresti-LQzLcXWZ",
"digest": {
"sha256": "2e0cdba2c91902ba12d742a39cb20df66cfd705ba8de767fbf68aae8eb65c6f0"
}
},
{
- "@id": "urn:21d86d5a-4768-45a5-90d2-055e94a0aa9b",
+ "@id": "bids::pb00.$subj.r*.tcat+orig.HEAD",
"Label": "pb00.$subj.r*.tcat",
"AtLocation": "pb00.$subj.r*.tcat+orig.HEAD",
"digest": {
@@ -987,10 +997,10 @@
}
},
{
- "@id": "urn:9c79005b-4a9a-49e5-9b9e-e8bfd5752c8e",
+ "@id": "bids::-exit0",
"Label": "-exit0",
"AtLocation": "-exit0",
- "GeneratedBy": "urn:7f47301c-e203-4fac-b2bd-efb02325b318",
+ "GeneratedBy": "urn:autobloc-Wk5QBdUZ",
"digest": {
"sha256": "871a4d3513ed2924cbb10c1c15a196eac4a46a05bdcc248e3bcdb23327b3ad90"
}
diff --git a/examples/from_parsers/afni/afni_thr_clustfwep05_proc_block.png b/examples/from_parsers/afni/afni_thr_clustfwep05_proc_block.png
index 980dad64b..6db69fc97 100644
Binary files a/examples/from_parsers/afni/afni_thr_clustfwep05_proc_block.png and b/examples/from_parsers/afni/afni_thr_clustfwep05_proc_block.png differ
diff --git a/examples/from_parsers/afni/afni_thr_clustunck10_proc.jsonld b/examples/from_parsers/afni/afni_thr_clustunck10_proc.jsonld
index 56a703339..5cee27465 100644
--- a/examples/from_parsers/afni/afni_thr_clustunck10_proc.jsonld
+++ b/examples/from_parsers/afni/afni_thr_clustunck10_proc.jsonld
@@ -4,578 +4,581 @@
"Records": {
"Software": [
{
- "@id": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:afni-hJIahMsr",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
- "Version": "afni24"
+ "Version": "afni24",
+ "AltIdentifier": "RRID:SCR_005927"
}
],
"Activities": [
{
- "@id": "urn:23e29248-772c-45f4-8176-869d5bb08030",
+ "@id": "urn:makedire-OY6SE0Gy",
"Label": "Make directory",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "mkdir $output_dir",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:2e2b5804-370a-4157-afe6-5eec67dc99bc",
+ "@id": "urn:makedire-VjI1qbRf",
"Label": "Make directory",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "mkdir $output_dir/stimuli",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:007fea83-88d4-4476-9ebe-a068d8f273a9",
+ "@id": "urn:cp-JaVdQoMW",
"Label": "cp",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "cp ./afni_cluster_k10/tone_counting_onset_times.txt ./afni_cluster_k10/tone_counting_probe_duration.txt $output_dir/stimuli",
"Parameters": {},
"Used": [
- "urn:b1ef0ad0-b2b0-44dd-9931-2539fcf6b38f",
- "urn:e8a448c0-04d3-4137-bc5d-41cee7d54402"
+ "bids::afni_cluster_k10/tone_counting_onset_times.txt",
+ "bids::afni_cluster_k10/tone_counting_probe_duration.txt"
]
},
{
- "@id": "urn:adfb00cf-7b00-42d8-98e9-8e3a0f472bf9",
+ "@id": "urn:3dcopy-xF0uDGm7",
"Label": "3dcopy",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w",
"Parameters": {},
"Used": [
- "urn:707144f1-53d3-42ec-ba6f-542f54333737"
+ "bids::sub-01_T1w.nii.gz"
]
},
{
- "@id": "urn:3949d23a-4ffc-49cf-90b3-b9af6d0ecad5",
+ "@id": "urn:3dtcat-xQIY5D9z",
"Label": "3dTcat",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Parameters": {},
"Used": [
- "urn:3d2b1791-0c11-4d49-a9c6-abd1f5374040"
+ "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'"
]
},
{
- "@id": "urn:58c948bc-0362-4182-8931-a893b5bbd077",
+ "@id": "urn:3dtoutco-3pmrFtyf",
"Label": "3dToutcount",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D",
"Parameters": {},
"Used": [
- "urn:8552e2e6-e17e-4c59-a484-215e804f9bc9"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:c2144b4f-8b0f-4584-863a-cb9f06b98711",
+ "@id": "urn:cat-SMezXh8B",
"Label": "cat",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "cat outcount.r*.1D > outcount_rall.1D",
"Parameters": {},
"Used": [
- "urn:993a79b8-7882-4321-8efe-8cd8a183e117"
+ "bids::outcount.r*.1D"
]
},
{
- "@id": "urn:56bfa84e-6649-4581-80e0-37102dd5b138",
+ "@id": "urn:3dtshift-iXx5fsUq",
"Label": "3dTshift",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig",
"Parameters": {},
"Used": [
- "urn:8552e2e6-e17e-4c59-a484-215e804f9bc9"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:67375711-0a1c-4a22-8890-066992754f34",
+ "@id": "urn:alignepi-b6S1htVH",
"Label": "align_epi_anat.py",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off",
"Parameters": {},
"Used": [
- "urn:1d0b4ab1-9c00-460b-a339-d7f4602a8644",
- "urn:8d8b1a81-efd4-4ec8-9f8c-f8bd29768886"
+ "bids::pb01.$subj.r01.tshift+orig",
+ "bids::sub-01_T1w+orig"
]
},
{
- "@id": "urn:5b079aab-bbe2-4c2c-bf2a-b67914b572b1",
+ "@id": "urn:autotlrc-A74FNMle",
"Label": "@auto_tlrc",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss",
"Parameters": {},
"Used": [
- "urn:2c6ed95e-eb33-4067-b5f8-cc3f3a766674",
- "urn:5e822140-db59-4c75-9aa9-366cb3b7ce0b"
+ "bids::TT_N27+tlrc",
+ "bids::sub-01_T1w_ns+orig"
]
},
{
- "@id": "urn:f82eb87b-862d-408e-b96c-a142427057ff",
+ "@id": "urn:catmatve-GL1r7ATk",
"Label": "cat_matvec",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D",
"Parameters": {},
"Used": [
- "urn:4a586b50-9b84-4d1c-ae6a-04112b3056b3"
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:23222b56-9dab-492e-a52d-bc03428a978d",
+ "@id": "urn:3dvolreg-NBrMfK1y",
"Label": "3dvolreg",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig",
"Parameters": {},
"Used": [
- "urn:f5ff2181-2e0f-41da-93d1-7d37e905c7d1"
+ "bids::pb01.$subj.r$run.tshift+orig"
]
},
{
- "@id": "urn:17aaefab-df5e-46d1-b244-9cd0910ac1f3",
+ "@id": "urn:3dcalc-bycui7e4",
"Label": "3dcalc",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1",
"Parameters": {},
"Used": [
- "urn:f5ff2181-2e0f-41da-93d1-7d37e905c7d1"
+ "bids::pb01.$subj.r$run.tshift+orig"
]
},
{
- "@id": "urn:ea4a8cca-b7ce-4a88-b4c9-61ed7f6a36b5",
+ "@id": "urn:catmatve-bmNwpYtV",
"Label": "cat_matvec",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D",
"Parameters": {},
"Used": [
- "urn:4a586b50-9b84-4d1c-ae6a-04112b3056b3"
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:73dc9b49-8e2c-44bc-a868-f4864e9d45bd",
+ "@id": "urn:3dalline-1xNOZt2X",
"Label": "3dAllineate",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run",
"Parameters": {},
"Used": [
- "urn:43108f9f-e538-4064-bc43-7b0bbec78ff2",
- "urn:8ffaad12-2674-47c2-b699-94f587264526",
- "urn:f5ff2181-2e0f-41da-93d1-7d37e905c7d1"
+ "bids::mat.r$run.warp.aff12.1D",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:6881a5cc-9595-41df-aa57-9282e12aff08",
+ "@id": "urn:3dalline-lTu4iPLW",
"Label": "3dAllineate",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run",
"Parameters": {},
"Used": [
- "urn:43108f9f-e538-4064-bc43-7b0bbec78ff2",
- "urn:8ffaad12-2674-47c2-b699-94f587264526",
- "urn:905ff829-f251-4ceb-a3a9-68cfc3bca833"
+ "bids::mat.r$run.warp.aff12.1D",
+ "bids::rm.epi.all1+orig",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:2547b3a8-a472-485f-8c9d-286bf6141ad9",
+ "@id": "urn:3dtstat-zffgHJ5p",
"Label": "3dTstat",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc",
"Parameters": {},
"Used": [
- "urn:5f30236b-7177-4396-8dc1-f5273c7647d9"
+ "bids::rm.epi.1.r$run+tlrc"
]
},
{
- "@id": "urn:9e33b686-c0c9-443c-b09a-e260a466da80",
+ "@id": "urn:cat-e3C1aNZg",
"Label": "cat",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "cat dfile.r*.1D > dfile_rall.1D",
"Parameters": {},
"Used": [
- "urn:22577639-ce6b-4c30-91e9-2c95f8eab904"
+ "bids::dfile.r*.1D"
]
},
{
- "@id": "urn:ca3ac5a5-7b11-4707-8113-dddff04409ce",
+ "@id": "urn:3dcopy-vvTaRlWw",
"Label": "3dcopy",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents",
"Parameters": {},
"Used": [
- "urn:32cbe895-a1a0-47d4-a58b-7ec37bc724b9"
+ "bids::rm.epi.min.r01+tlrc"
]
},
{
- "@id": "urn:036f2b82-0e8d-46c3-bc57-1f2f0456e364",
+ "@id": "urn:3dcalc-uVIWlPiD",
"Label": "3dcalc",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg",
"Parameters": {},
"Used": [
- "urn:517a16eb-aa7f-4d32-8cd0-19db3ce2d355",
- "urn:ec085929-3a73-462c-837f-7b8ada04bdf4"
+ "bids::mask_epi_extents+tlrc",
+ "bids::rm.epi.nomask.r$run+tlrc"
]
},
{
- "@id": "urn:a00d33e9-976c-4da2-bfd5-c323f5de4e6d",
+ "@id": "urn:3dcopy-Dzjz2HnL",
"Label": "3dcopy",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj",
"Parameters": {},
"Used": [
- "urn:43108f9f-e538-4064-bc43-7b0bbec78ff2"
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:9a8c6a5d-e331-49ee-9cbf-7aae85f6c449",
+ "@id": "urn:3dalline-k1TXBknG",
"Label": "3dAllineate",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped",
"Parameters": {},
"Used": [
- "urn:00f3a18e-2b92-41d7-9916-5c12aee8b210"
+ "bids::anat_final.$subj+tlrc",
+ "bids::warp.anat.Xat.1D"
]
},
{
- "@id": "urn:1e1b8b6a-4f33-4ce5-b008-9056f9eade30",
+ "@id": "urn:3dmerge-NNfu6hxa",
"Label": "3dmerge",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc",
"Parameters": {},
"Used": [
- "urn:5174fcd8-825d-46ed-a9f2-6b364163d866",
- "urn:b0783160-cc25-4f90-87b0-62ea91dd364e"
+ "bids::pb02.$subj.r$run.volreg+tlrc",
+ "bids::pb03.$subj.r$run.blur"
]
},
{
- "@id": "urn:fffdce39-1022-4364-aa1b-182e4f764878",
+ "@id": "urn:3dautoma-Dlp8THpI",
"Label": "3dAutomask",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:6918cf06-5b73-4345-8163-3633a24242b4"
+ "bids::pb03.$subj.r$run.blur+tlrc"
]
},
{
- "@id": "urn:a4a72b44-266e-4cf8-843b-40c5956df505",
+ "@id": "urn:3dmaskto-IeXPRJi8",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:3318f2f4-021e-4945-ac68-a79194eece86",
+ "@id": "urn:3dresamp-24JIQmw1",
"Label": "3dresample",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat",
"Parameters": {},
"Used": [
- "urn:43108f9f-e538-4064-bc43-7b0bbec78ff2",
- "urn:96b92e44-3256-4d88-85cd-4eed25cd88cd"
+ "bids::full_mask.$subj+tlrc",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:0cc3f639-004a-4d2d-af86-b5c8d36f74bf",
+ "@id": "urn:3dmaskto-QPPysgL0",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj",
"Parameters": {},
"Used": [
- "urn:1aa7103f-ebf2-4568-be03-f2d1e223af21"
+ "bids::rm.resam.anat+tlrc"
]
},
{
- "@id": "urn:cd671150-53fa-415a-ad4f-d28f69a46244",
+ "@id": "urn:3dabover-4tTtcN3O",
"Label": "3dABoverlap",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt",
"Parameters": {},
"Used": [
- "urn:1459fb22-3e8e-4f90-898a-d1defbf3be77",
- "urn:d14b7740-d4ad-41e7-8204-c7cb9f0d331a"
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee"
]
},
{
- "@id": "urn:4dde7fde-d83c-4871-9581-a2f80c237204",
+ "@id": "urn:3ddot-U2YcbixB",
"Label": "3ddot",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt",
"Parameters": {},
"Used": [
- "urn:1459fb22-3e8e-4f90-898a-d1defbf3be77",
- "urn:d14b7740-d4ad-41e7-8204-c7cb9f0d331a"
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee"
]
},
{
- "@id": "urn:66c4a64b-24fb-4355-b6f0-745d29806e79",
+ "@id": "urn:3dresamp-uVnI1DWZ",
"Label": "3dresample",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc",
"Parameters": {},
"Used": [
- "urn:71135527-0811-46d0-887d-1b56a42edc2e",
- "urn:96b92e44-3256-4d88-85cd-4eed25cd88cd"
+ "bids::/Users/u1591557/abin/TT_N27+tlrc",
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:2159c5ee-3437-45f6-ba8e-e352b535e409",
+ "@id": "urn:3dmaskto-xd2PfRzE",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group",
"Parameters": {},
"Used": [
- "urn:d26df013-060e-48ab-9186-368004271dd6"
+ "bids::rm.resam.group+tlrc"
]
},
{
- "@id": "urn:b8e6f38b-bdf3-4d81-9788-8890b5877ee1",
+ "@id": "urn:3dtstat-17thIIuc",
"Label": "3dTstat",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:6918cf06-5b73-4345-8163-3633a24242b4"
+ "bids::pb03.$subj.r$run.blur+tlrc"
]
},
{
- "@id": "urn:63a6fef4-fa62-4df6-8328-87f0bddf63b2",
+ "@id": "urn:3dcalc-zTQ3B910",
"Label": "3dcalc",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale",
"Parameters": {},
"Used": [
- "urn:6918cf06-5b73-4345-8163-3633a24242b4",
- "urn:a4807546-b85f-4467-b4e1-5302e8f0d87c",
- "urn:ec085929-3a73-462c-837f-7b8ada04bdf4"
+ "bids::mask_epi_extents+tlrc",
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::rm.mean_r$run+tlrc"
]
},
{
- "@id": "urn:53043b2a-cb9b-43cc-8521-29127997d9dc",
+ "@id": "urn:1dtoolpy-J7rvb59O",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D",
"Parameters": {},
"Used": [
- "urn:0190bd90-1ced-4bde-bb32-dc91ffd47ebf"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:ecd29557-0d0a-4e07-b160-323fcdaf374d",
+ "@id": "urn:1dtoolpy-povM5av3",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D",
"Parameters": {},
"Used": [
- "urn:0190bd90-1ced-4bde-bb32-dc91ffd47ebf"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:c376d8f1-2b0b-4703-a53b-c66fbc30b7ab",
+ "@id": "urn:1dtoolpy-ssHLOGUR",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}",
"Parameters": {},
"Used": [
- "urn:0190bd90-1ced-4bde-bb32-dc91ffd47ebf"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:fea42141-8ffc-435c-bab7-a16e244425dc",
+ "@id": "urn:3ddeconv-fML2IpFp",
"Label": "3dDeconvolve",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj",
"Parameters": {},
"Used": [
- "urn:cd14b883-d42f-4539-a28d-9c0afc94d394"
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD"
]
},
{
- "@id": "urn:11a44ba1-105e-4ecd-ad59-a75e07367e7d",
+ "@id": "urn:1dtoolpy-eMfyeIYj",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt",
"Parameters": {},
"Used": [
- "urn:5931aa32-07bf-4032-a21d-cf78b7684d58"
+ "bids::X.xmat.1D"
]
},
{
- "@id": "urn:128c7da5-ae5e-4ea1-85ff-004497f4cfd6",
+ "@id": "urn:3dtcat-DQwVr0Uo",
"Label": "3dTcat",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD",
"Parameters": {},
"Used": [
- "urn:cd14b883-d42f-4539-a28d-9c0afc94d394"
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD"
]
},
{
- "@id": "urn:9a8178c0-e37c-46d4-97cf-dcb710a6c585",
+ "@id": "urn:3dtstat-uDZRncVM",
"Label": "3dTstat",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:a6a6203b-3d06-41b5-b2e1-748bf1798d90"
+ "bids::all_runs.$subj+tlrc%22[$ktrs]%22"
]
},
{
- "@id": "urn:44507117-d812-483e-8273-42bee72dae49",
+ "@id": "urn:3dtstat-r7lNHPYE",
"Label": "3dTstat",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:e23efce6-e63a-4362-b5a0-1a7040a484cf"
+ "bids::errts.$%7Bsubj%7D+tlrc%22[$ktrs]%22"
]
},
{
- "@id": "urn:41107f04-1af4-41a4-81c7-4e597cd0c7d7",
+ "@id": "urn:3dcalc-Y84nz2OI",
"Label": "3dcalc",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj",
"Parameters": {},
"Used": [
- "urn:93400375-d710-4879-8f2b-74ac3a72470d",
- "urn:96b92e44-3256-4d88-85cd-4eed25cd88cd",
- "urn:cacb4e68-b84c-40a7-8f92-26fd5ff055a9"
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.noise.all+tlrc",
+ "bids::rm.signal.all+tlrc"
]
},
{
- "@id": "urn:1a587f9b-fc4a-4277-9fb0-9f79e2d2db5d",
+ "@id": "urn:3dtnorm-N3ej7CkG",
"Label": "3dTnorm",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc",
"Parameters": {},
"Used": [
- "urn:2651517a-d223-43a6-8156-df647cf71859"
+ "bids::errts.$%7Bsubj%7D+tlrc"
]
},
{
- "@id": "urn:c3c6543b-54bc-42b7-9412-951ebc52f6b4",
+ "@id": "urn:3dmaskav-TMgsSY8d",
"Label": "3dmaskave",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D",
"Parameters": {},
- "Used": []
+ "Used": [
+ "bids::full_mask.$subj+tlrc"
+ ]
},
{
- "@id": "urn:731707e8-ab6e-4f05-ad4b-e7145f2957bb",
+ "@id": "urn:3dtstat-r4WfRcQO",
"Label": "3dTstat",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D",
"Parameters": {},
"Used": [
- "urn:a4f766bd-98cb-4832-965d-0fcc6ad8cb7e"
+ "bids::out.gcor.1D"
]
},
{
- "@id": "urn:c3d81b35-0bb9-41de-9ab5-8b111d19f41a",
+ "@id": "urn:3dcalc-Diz78Vi7",
"Label": "3dcalc",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP",
"Parameters": {},
"Used": [
- "urn:5429a21c-8c73-4605-bb15-755f447b9ae6",
- "urn:f0039bc0-40e7-4b50-bf95-40e5d7fa3bb4"
+ "bids::gmean.errts.unit.1D",
+ "bids::rm.errts.unit+tlrc"
]
},
{
- "@id": "urn:5588370f-b147-4f11-beff-a8afc6bc1744",
+ "@id": "urn:3dtstat-YBxYvXSr",
"Label": "3dTstat",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc",
"Parameters": {},
"Used": [
- "urn:1e0b2ec0-5b80-47ba-ad3c-5b8cd6caa41c"
+ "bids::rm.DP+tlrc"
]
},
{
- "@id": "urn:b3504581-2806-4e1d-814e-0f0ba71c883e",
+ "@id": "urn:1dcat-mKOV8OBk",
"Label": "1dcat",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D",
"Parameters": {},
"Used": [
- "urn:16e56703-dac3-4c6f-b5bb-6421103ed9de"
+ "bids::X.nocensor.xmat.1D'[3]'"
]
},
{
- "@id": "urn:167b3a0d-1009-48d6-9d79-508f4f330c29",
+ "@id": "urn:1dcat-ik7pWJJu",
"Label": "1dcat",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D",
"Parameters": {},
"Used": [
- "urn:1f2447f7-73a4-4261-90bd-3f92589a700f"
+ "bids::X.nocensor.xmat.1D'[4]'"
]
},
{
- "@id": "urn:bfddd750-a372-43d1-ae2a-a023348e8b54",
+ "@id": "urn:3dtstat-KMyBshB8",
"Label": "3dTstat",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"",
"Parameters": {},
"Used": [
- "urn:0d2391fb-541e-4ca4-9322-d7ead2a3faba"
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:2ff95f50-a969-489e-a40e-e7790f83f572",
+ "@id": "urn:1dcat-BYaIlWxZ",
"Label": "1dcat",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D",
"Parameters": {},
"Used": [
- "urn:0d2391fb-541e-4ca4-9322-d7ead2a3faba"
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:fd15a9b8-4e08-4138-bc21-ad000cf37cb5",
+ "@id": "urn:3dfwhmx-Ud3U0uO1",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D",
"Parameters": {},
"Used": [
- "urn:96b92e44-3256-4d88-85cd-4eed25cd88cd"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:3ccddd9f-ea57-4ce6-9092-ca4b5a77eac7",
+ "@id": "urn:3dfwhmx-5rR4o8zi",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D",
"Parameters": {},
"Used": [
- "urn:96b92e44-3256-4d88-85cd-4eed25cd88cd"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:a8f3bb8f-3e44-47c6-ace2-cf65386c4b34",
+ "@id": "urn:3dclusts-yn5oKahn",
"Label": "3dClustSim",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim",
"Parameters": {},
"Used": [
- "urn:96b92e44-3256-4d88-85cd-4eed25cd88cd"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:3854bb96-45ee-42d9-bdf9-bbdbef7bd919",
+ "@id": "urn:genepire-EZvDz1cD",
"Label": "gen_epi_review.py",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD",
"Parameters": {},
"Used": [
- "urn:779bba0c-3ae9-48cb-acab-b1e42ff2ac39"
+ "bids::pb00.$subj.r*.tcat+orig.HEAD"
]
},
{
- "@id": "urn:2c85290f-b3f2-431b-91c4-402a54caa3b8",
+ "@id": "urn:genssrev-F0b9dXGV",
"Label": "gen_ss_review_scripts.py",
- "AssociatedWith": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "AssociatedWith": "urn:afni-hJIahMsr",
"Command": "gen_ss_review_scripts.py -mot_limit 0.3 -exit0",
"Parameters": {
"-mot_limit": "0.3",
@@ -586,22 +589,22 @@
],
"Entities": [
{
- "@id": "urn:b7e9d248-a3aa-4de7-bd2a-0c2db25f4d01",
+ "@id": "bids::$output_dir",
"Label": "$output_dir",
"AtLocation": "$output_dir",
- "GeneratedBy": "urn:23e29248-772c-45f4-8176-869d5bb08030",
+ "GeneratedBy": "urn:makedire-OY6SE0Gy",
"digest": {
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}
},
{
- "@id": "urn:4dd0b74d-0f56-46f4-a431-38c65782ceb7",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:2e2b5804-370a-4157-afe6-5eec67dc99bc"
+ "GeneratedBy": "urn:makedire-VjI1qbRf"
},
{
- "@id": "urn:b1ef0ad0-b2b0-44dd-9931-2539fcf6b38f",
+ "@id": "bids::afni_cluster_k10/tone_counting_onset_times.txt",
"Label": "tone_counting_onset_times.txt",
"AtLocation": "./afni_cluster_k10/tone_counting_onset_times.txt",
"digest": {
@@ -609,7 +612,7 @@
}
},
{
- "@id": "urn:e8a448c0-04d3-4137-bc5d-41cee7d54402",
+ "@id": "bids::afni_cluster_k10/tone_counting_probe_duration.txt",
"Label": "tone_counting_probe_duration.txt",
"AtLocation": "./afni_cluster_k10/tone_counting_probe_duration.txt",
"digest": {
@@ -617,13 +620,13 @@
}
},
{
- "@id": "urn:e260306a-0d19-4ee0-9fc1-08f7c3aa2ec3",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:007fea83-88d4-4476-9ebe-a068d8f273a9"
+ "GeneratedBy": "urn:cp-JaVdQoMW"
},
{
- "@id": "urn:707144f1-53d3-42ec-ba6f-542f54333737",
+ "@id": "bids::sub-01_T1w.nii.gz",
"Label": "sub-01_T1w.nii.gz",
"AtLocation": "sub-01_T1w.nii.gz",
"digest": {
@@ -631,13 +634,13 @@
}
},
{
- "@id": "urn:f8fccd8c-a469-43b6-a102-7923558cdb83",
+ "@id": "bids::$output_dir/sub-01_T1w",
"Label": "sub-01_T1w",
"AtLocation": "$output_dir/sub-01_T1w",
- "GeneratedBy": "urn:adfb00cf-7b00-42d8-98e9-8e3a0f472bf9"
+ "GeneratedBy": "urn:3dcopy-xF0uDGm7"
},
{
- "@id": "urn:3d2b1791-0c11-4d49-a9c6-abd1f5374040",
+ "@id": "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Label": "sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"digest": {
@@ -645,13 +648,13 @@
}
},
{
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+ "@id": "bids::$output_dir/pb00.$subj.r01.tcat",
"Label": "pb00.$subj.r01.tcat",
"AtLocation": "$output_dir/pb00.$subj.r01.tcat",
- "GeneratedBy": "urn:3949d23a-4ffc-49cf-90b3-b9af6d0ecad5"
+ "GeneratedBy": "urn:3dtcat-xQIY5D9z"
},
{
- "@id": "urn:8552e2e6-e17e-4c59-a484-215e804f9bc9",
+ "@id": "bids::pb00.$subj.r$run.tcat+orig",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -659,16 +662,16 @@
}
},
{
- "@id": "urn:e5c4f37c-5ede-4554-b781-b5e04d9ac5ba",
+ "@id": "bids::outcount.r$run.1D",
"Label": "outcount.r$run.1D",
"AtLocation": "outcount.r$run.1D",
- "GeneratedBy": "urn:58c948bc-0362-4182-8931-a893b5bbd077",
+ "GeneratedBy": "urn:3dtoutco-3pmrFtyf",
"digest": {
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}
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{
- "@id": "urn:993a79b8-7882-4321-8efe-8cd8a183e117",
+ "@id": "bids::outcount.r*.1D",
"Label": "outcount.r*.1D",
"AtLocation": "outcount.r*.1D",
"digest": {
@@ -676,25 +679,25 @@
}
},
{
- "@id": "urn:3c0180cc-d6d3-4ccc-8f38-fe8174ca9257",
+ "@id": "bids::outcount_rall.1D",
"Label": "outcount_rall.1D",
"AtLocation": "outcount_rall.1D",
- "GeneratedBy": "urn:c2144b4f-8b0f-4584-863a-cb9f06b98711",
+ "GeneratedBy": "urn:cat-SMezXh8B",
"digest": {
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}
},
{
- "@id": "urn:fe43eb18-b0fc-4dfc-9d79-e154b0bf1b40",
+ "@id": "bids::pb01.$subj.r$run.tshift",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift",
- "GeneratedBy": "urn:56bfa84e-6649-4581-80e0-37102dd5b138",
+ "GeneratedBy": "urn:3dtshift-iXx5fsUq",
"digest": {
"sha256": "c6bf01cea8d2eac1d7a866f80b865c6e7d4b4e012dbb63d480ac9a8551162d72"
}
},
{
- "@id": "urn:8d8b1a81-efd4-4ec8-9f8c-f8bd29768886",
+ "@id": "bids::sub-01_T1w+orig",
"Label": "sub-01_T1w",
"AtLocation": "sub-01_T1w+orig",
"digest": {
@@ -702,7 +705,7 @@
}
},
{
- "@id": "urn:1d0b4ab1-9c00-460b-a339-d7f4602a8644",
+ "@id": "bids::pb01.$subj.r01.tshift+orig",
"Label": "pb01.$subj.r01.tshift",
"AtLocation": "pb01.$subj.r01.tshift+orig",
"digest": {
@@ -710,16 +713,16 @@
}
},
{
- "@id": "urn:f96391da-8ad6-4968-90fc-e3e5e9d1f810",
+ "@id": "bids::_al_junk",
"Label": "_al_junk",
"AtLocation": "_al_junk",
- "GeneratedBy": "urn:67375711-0a1c-4a22-8890-066992754f34",
+ "GeneratedBy": "urn:alignepi-b6S1htVH",
"digest": {
"sha256": "bd785a075a4c6446e1e54de9e628913f7f1c814e86b69a9fbfe933209e6d37b5"
}
},
{
- "@id": "urn:5e822140-db59-4c75-9aa9-366cb3b7ce0b",
+ "@id": "bids::TT_N27+tlrc",
"Label": "TT_N27",
"AtLocation": "TT_N27+tlrc",
"digest": {
@@ -727,7 +730,7 @@
}
},
{
- "@id": "urn:2c6ed95e-eb33-4067-b5f8-cc3f3a766674",
+ "@id": "bids::sub-01_T1w_ns+orig",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+orig",
"digest": {
@@ -735,7 +738,7 @@
}
},
{
- "@id": "urn:4a586b50-9b84-4d1c-ae6a-04112b3056b3",
+ "@id": "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc::WARP_DATA",
"digest": {
@@ -743,16 +746,16 @@
}
},
{
- "@id": "urn:00f3a18e-2b92-41d7-9916-5c12aee8b210",
+ "@id": "bids::warp.anat.Xat.1D",
"Label": "warp.anat.Xat.1D",
"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:f82eb87b-862d-408e-b96c-a142427057ff",
+ "GeneratedBy": "urn:catmatve-GL1r7ATk",
"digest": {
"sha256": "800633fb5b4e9be64078bc181c4d5510ffb73fc5cccaf364c7fb6a294aa06728"
}
},
{
- "@id": "urn:f5ff2181-2e0f-41da-93d1-7d37e905c7d1",
+ "@id": "bids::pb01.$subj.r$run.tshift+orig",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift+orig",
"digest": {
@@ -760,34 +763,34 @@
}
},
{
- "@id": "urn:99a72a05-324e-47a9-a72f-17d952a1b355",
+ "@id": "bids::mat.r$run.vr.aff12.1D",
"Label": "mat.r$run.vr.aff12.1D",
"AtLocation": "mat.r$run.vr.aff12.1D",
- "GeneratedBy": "urn:23222b56-9dab-492e-a52d-bc03428a978d",
+ "GeneratedBy": "urn:3dvolreg-NBrMfK1y",
"digest": {
"sha256": "2e6e6c2ce8089cfa3c6e11dc72fca0cc8497f7a55faae2ced402de4867466c91"
}
},
{
- "@id": "urn:ad457a1a-305f-48e0-944c-307688941533",
+ "@id": "bids::rm.epi.all1",
"Label": "rm.epi.all1",
"AtLocation": "rm.epi.all1",
- "GeneratedBy": "urn:17aaefab-df5e-46d1-b244-9cd0910ac1f3",
+ "GeneratedBy": "urn:3dcalc-bycui7e4",
"digest": {
"sha256": "1023e3c16cecdbdc73ea456bcf33c2e5bb4f1e07094b73d29022d651e5fa3f85"
}
},
{
- "@id": "urn:8ffaad12-2674-47c2-b699-94f587264526",
+ "@id": "bids::mat.r$run.warp.aff12.1D",
"Label": "mat.r$run.warp.aff12.1D",
"AtLocation": "mat.r$run.warp.aff12.1D",
- "GeneratedBy": "urn:ea4a8cca-b7ce-4a88-b4c9-61ed7f6a36b5",
+ "GeneratedBy": "urn:catmatve-bmNwpYtV",
"digest": {
"sha256": "7c536b6f582a067c718f9e5ea2566cb535c73b43b4e15116c4c46045734d6eee"
}
},
{
- "@id": "urn:43108f9f-e538-4064-bc43-7b0bbec78ff2",
+ "@id": "bids::sub-01_T1w_ns+tlrc",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc",
"digest": {
@@ -795,16 +798,16 @@
}
},
{
- "@id": "urn:95ccaf05-817e-4a81-834c-2318041fff1c",
+ "@id": "bids::rm.epi.nomask.r$run",
"Label": "rm.epi.nomask.r$run",
"AtLocation": "rm.epi.nomask.r$run",
- "GeneratedBy": "urn:73dc9b49-8e2c-44bc-a868-f4864e9d45bd",
+ "GeneratedBy": "urn:3dalline-1xNOZt2X",
"digest": {
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}
},
{
- "@id": "urn:905ff829-f251-4ceb-a3a9-68cfc3bca833",
+ "@id": "bids::rm.epi.all1+orig",
"Label": "rm.epi.all1",
"AtLocation": "rm.epi.all1+orig",
"digest": {
@@ -812,16 +815,16 @@
}
},
{
- "@id": "urn:b6f3d426-8b9e-4890-bdfe-fd4ff7add62d",
+ "@id": "bids::rm.epi.1.r$run",
"Label": "rm.epi.1.r$run",
"AtLocation": "rm.epi.1.r$run",
- "GeneratedBy": "urn:6881a5cc-9595-41df-aa57-9282e12aff08",
+ "GeneratedBy": "urn:3dalline-lTu4iPLW",
"digest": {
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}
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{
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+ "@id": "bids::rm.epi.1.r$run+tlrc",
"Label": "rm.epi.1.r$run",
"AtLocation": "rm.epi.1.r$run+tlrc",
"digest": {
@@ -829,16 +832,16 @@
}
},
{
- "@id": "urn:7f7e32bd-8c96-4db8-a1c2-6dce6a2dd739",
+ "@id": "bids::rm.epi.min.r$run",
"Label": "rm.epi.min.r$run",
"AtLocation": "rm.epi.min.r$run",
- "GeneratedBy": "urn:2547b3a8-a472-485f-8c9d-286bf6141ad9",
+ "GeneratedBy": "urn:3dtstat-zffgHJ5p",
"digest": {
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}
},
{
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+ "@id": "bids::dfile.r*.1D",
"Label": "dfile.r*.1D",
"AtLocation": "dfile.r*.1D",
"digest": {
@@ -846,16 +849,16 @@
}
},
{
- "@id": "urn:0190bd90-1ced-4bde-bb32-dc91ffd47ebf",
+ "@id": "bids::dfile_rall.1D",
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"AtLocation": "dfile_rall.1D",
- "GeneratedBy": "urn:9e33b686-c0c9-443c-b09a-e260a466da80",
+ "GeneratedBy": "urn:cat-e3C1aNZg",
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}
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{
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+ "@id": "bids::rm.epi.min.r01+tlrc",
"Label": "rm.epi.min.r01",
"AtLocation": "rm.epi.min.r01+tlrc",
"digest": {
@@ -863,16 +866,16 @@
}
},
{
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+ "@id": "bids::mask_epi_extents",
"Label": "mask_epi_extents",
"AtLocation": "mask_epi_extents",
- "GeneratedBy": "urn:ca3ac5a5-7b11-4707-8113-dddff04409ce",
+ "GeneratedBy": "urn:3dcopy-vvTaRlWw",
"digest": {
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{
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+ "@id": "bids::rm.epi.nomask.r$run+tlrc",
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"AtLocation": "rm.epi.nomask.r$run+tlrc",
"digest": {
@@ -880,7 +883,7 @@
}
},
{
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+ "@id": "bids::mask_epi_extents+tlrc",
"Label": "mask_epi_extents",
"AtLocation": "mask_epi_extents+tlrc",
"digest": {
@@ -888,34 +891,42 @@
}
},
{
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+ "@id": "bids::pb02.$subj.r$run.volreg",
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"AtLocation": "pb02.$subj.r$run.volreg",
- "GeneratedBy": "urn:036f2b82-0e8d-46c3-bc57-1f2f0456e364",
+ "GeneratedBy": "urn:3dcalc-uVIWlPiD",
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}
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{
- "@id": "urn:58eb8130-38d3-46cc-8a21-e4b5ff740ae4",
+ "@id": "bids::anat_final.$subj",
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"AtLocation": "anat_final.$subj",
- "GeneratedBy": "urn:a00d33e9-976c-4da2-bfd5-c323f5de4e6d",
+ "GeneratedBy": "urn:3dcopy-Dzjz2HnL",
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{
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+ "@id": "bids::anat_final.$subj+tlrc",
+ "Label": "anat_final.$subj",
+ "AtLocation": "anat_final.$subj+tlrc",
+ "digest": {
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+ }
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+ {
+ "@id": "bids::anat_w_skull_warped",
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"AtLocation": "anat_w_skull_warped",
- "GeneratedBy": "urn:9a8c6a5d-e331-49ee-9cbf-7aae85f6c449",
+ "GeneratedBy": "urn:3dalline-k1TXBknG",
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{
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+ "@id": "bids::pb03.$subj.r$run.blur",
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"digest": {
@@ -923,7 +934,7 @@
}
},
{
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"digest": {
@@ -931,7 +942,7 @@
}
},
{
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+ "@id": "bids::pb03.$subj.r$run.blur+tlrc",
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"AtLocation": "pb03.$subj.r$run.blur+tlrc",
"digest": {
@@ -939,25 +950,25 @@
}
},
{
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"AtLocation": "rm.mask_r$run",
- "GeneratedBy": "urn:fffdce39-1022-4364-aa1b-182e4f764878",
+ "GeneratedBy": "urn:3dautoma-Dlp8THpI",
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{
- "@id": "urn:2eace7c1-48d7-42d0-8a53-9cd10b219f30",
+ "@id": "bids::full_mask.$subj",
"Label": "full_mask.$subj",
"AtLocation": "full_mask.$subj",
- "GeneratedBy": "urn:a4a72b44-266e-4cf8-843b-40c5956df505",
+ "GeneratedBy": "urn:3dmaskto-IeXPRJi8",
"digest": {
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},
{
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+ "@id": "bids::full_mask.$subj+tlrc",
"Label": "full_mask.$subj",
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"digest": {
@@ -965,16 +976,16 @@
}
},
{
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+ "@id": "bids::rm.resam.anat",
"Label": "rm.resam.anat",
"AtLocation": "rm.resam.anat",
- "GeneratedBy": "urn:3318f2f4-021e-4945-ac68-a79194eece86",
+ "GeneratedBy": "urn:3dresamp-24JIQmw1",
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}
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{
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"digest": {
@@ -982,16 +993,16 @@
}
},
{
- "@id": "urn:9c84233e-4c3f-40e2-8828-b10d5fc0b1ef",
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- "GeneratedBy": "urn:0cc3f639-004a-4d2d-af86-b5c8d36f74bf",
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}
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{
- "@id": "urn:1459fb22-3e8e-4f90-898a-d1defbf3be77",
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@@ -999,7 +1010,7 @@
}
},
{
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+ "@id": "bids::tee",
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"digest": {
@@ -1007,7 +1018,7 @@
}
},
{
- "@id": "urn:71135527-0811-46d0-887d-1b56a42edc2e",
+ "@id": "bids::/Users/u1591557/abin/TT_N27+tlrc",
"Label": "TT_N27",
"AtLocation": "/Users/u1591557/abin/TT_N27+tlrc",
"digest": {
@@ -1015,16 +1026,16 @@
}
},
{
- "@id": "urn:f9294378-917d-4969-b1ea-e82eef53f208",
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"AtLocation": "./rm.resam.group",
- "GeneratedBy": "urn:66c4a64b-24fb-4355-b6f0-745d29806e79",
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}
},
{
- "@id": "urn:d26df013-060e-48ab-9186-368004271dd6",
+ "@id": "bids::rm.resam.group+tlrc",
"Label": "rm.resam.group",
"AtLocation": "rm.resam.group+tlrc",
"digest": {
@@ -1032,25 +1043,25 @@
}
},
{
- "@id": "urn:60f84ff1-e701-4e52-8dbe-dca9e99a1c2f",
+ "@id": "bids::mask_group",
"Label": "mask_group",
"AtLocation": "mask_group",
- "GeneratedBy": "urn:2159c5ee-3437-45f6-ba8e-e352b535e409",
+ "GeneratedBy": "urn:3dmaskto-xd2PfRzE",
"digest": {
"sha256": "d7093b26470ded8d7e939359017b18d28a2da4c6bb702c1183df20bca614f949"
}
},
{
- "@id": "urn:e502668a-42ab-4093-9bf5-a7a57645e2ad",
+ "@id": "bids::rm.mean_r$run",
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"AtLocation": "rm.mean_r$run",
- "GeneratedBy": "urn:b8e6f38b-bdf3-4d81-9788-8890b5877ee1",
+ "GeneratedBy": "urn:3dtstat-17thIIuc",
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}
},
{
- "@id": "urn:a4807546-b85f-4467-b4e1-5302e8f0d87c",
+ "@id": "bids::rm.mean_r$run+tlrc",
"Label": "rm.mean_r$run",
"AtLocation": "rm.mean_r$run+tlrc",
"digest": {
@@ -1058,34 +1069,34 @@
}
},
{
- "@id": "urn:29409d41-a531-4b0b-a6ff-7d8bb83a2d57",
+ "@id": "bids::pb04.$subj.r$run.scale",
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"AtLocation": "pb04.$subj.r$run.scale",
- "GeneratedBy": "urn:63a6fef4-fa62-4df6-8328-87f0bddf63b2",
+ "GeneratedBy": "urn:3dcalc-zTQ3B910",
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}
},
{
- "@id": "urn:2eb30742-cf34-4fe0-8ac9-40a44a229224",
+ "@id": "bids::motion_demean.1D",
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"AtLocation": "motion_demean.1D",
- "GeneratedBy": "urn:53043b2a-cb9b-43cc-8521-29127997d9dc",
+ "GeneratedBy": "urn:1dtoolpy-J7rvb59O",
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}
},
{
- "@id": "urn:6418fb3a-4697-42cb-844f-98221898c9a4",
+ "@id": "bids::motion_deriv.1D",
"Label": "motion_deriv.1D",
"AtLocation": "motion_deriv.1D",
- "GeneratedBy": "urn:ecd29557-0d0a-4e07-b160-323fcdaf374d",
+ "GeneratedBy": "urn:1dtoolpy-povM5av3",
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}
},
{
- "@id": "urn:cd14b883-d42f-4539-a28d-9c0afc94d394",
+ "@id": "bids::pb04.$subj.r*.scale+tlrc.HEAD",
"Label": "pb04.$subj.r*.scale",
"AtLocation": "pb04.$subj.r*.scale+tlrc.HEAD",
"digest": {
@@ -1093,25 +1104,25 @@
}
},
{
- "@id": "urn:5931aa32-07bf-4032-a21d-cf78b7684d58",
+ "@id": "bids::X.xmat.1D",
"Label": "X.xmat.1D",
"AtLocation": "X.xmat.1D",
- "GeneratedBy": "urn:fea42141-8ffc-435c-bab7-a16e244425dc",
+ "GeneratedBy": "urn:3ddeconv-fML2IpFp",
"digest": {
"sha256": "cdbd4f4edf6fa02a9d7fcf9a3e593893438e9279c9523fbb6993630a83ad5162"
}
},
{
- "@id": "urn:d1982c0f-816a-4e2d-8d0d-c5a1c170463f",
+ "@id": "bids::all_runs.$subj",
"Label": "all_runs.$subj",
"AtLocation": "all_runs.$subj",
- "GeneratedBy": "urn:128c7da5-ae5e-4ea1-85ff-004497f4cfd6",
+ "GeneratedBy": "urn:3dtcat-DQwVr0Uo",
"digest": {
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}
},
{
- "@id": "urn:a6a6203b-3d06-41b5-b2e1-748bf1798d90",
+ "@id": "bids::all_runs.$subj+tlrc%22[$ktrs]%22",
"Label": "all_runs.$subj",
"AtLocation": "all_runs.$subj+tlrc\"[$ktrs]\"",
"digest": {
@@ -1119,16 +1130,16 @@
}
},
{
- "@id": "urn:3fd2d4d5-677d-469b-bae5-9d764bd9e696",
+ "@id": "bids::rm.signal.all",
"Label": "rm.signal.all",
"AtLocation": "rm.signal.all",
- "GeneratedBy": "urn:9a8178c0-e37c-46d4-97cf-dcb710a6c585",
+ "GeneratedBy": "urn:3dtstat-uDZRncVM",
"digest": {
"sha256": "bda68a16c0afd5e55d4d7415c8c959e61a9aad7898dd456b0f3bb597363dde31"
}
},
{
- "@id": "urn:e23efce6-e63a-4362-b5a0-1a7040a484cf",
+ "@id": "bids::errts.$%7Bsubj%7D+tlrc%22[$ktrs]%22",
"Label": "errts.${subj}",
"AtLocation": "errts.${subj}+tlrc\"[$ktrs]\"",
"digest": {
@@ -1136,16 +1147,16 @@
}
},
{
- "@id": "urn:75b7b742-134c-4743-b2c6-7783513975e0",
+ "@id": "bids::rm.noise.all",
"Label": "rm.noise.all",
"AtLocation": "rm.noise.all",
- "GeneratedBy": "urn:44507117-d812-483e-8273-42bee72dae49",
+ "GeneratedBy": "urn:3dtstat-r7lNHPYE",
"digest": {
"sha256": "431314eb75d086ce08373b3a374427969e89414c4a2d607e449c1f6485c547af"
}
},
{
- "@id": "urn:93400375-d710-4879-8f2b-74ac3a72470d",
+ "@id": "bids::rm.signal.all+tlrc",
"Label": "rm.signal.all",
"AtLocation": "rm.signal.all+tlrc",
"digest": {
@@ -1153,7 +1164,7 @@
}
},
{
- "@id": "urn:cacb4e68-b84c-40a7-8f92-26fd5ff055a9",
+ "@id": "bids::rm.noise.all+tlrc",
"Label": "rm.noise.all",
"AtLocation": "rm.noise.all+tlrc",
"digest": {
@@ -1161,16 +1172,16 @@
}
},
{
- "@id": "urn:7328ba94-9c2f-4c40-ac01-9f1f0a322c34",
+ "@id": "bids::TSNR.$subj",
"Label": "TSNR.$subj",
"AtLocation": "TSNR.$subj",
- "GeneratedBy": "urn:41107f04-1af4-41a4-81c7-4e597cd0c7d7",
+ "GeneratedBy": "urn:3dcalc-Y84nz2OI",
"digest": {
"sha256": "303f183145a1e295686c08335d3b70753777cf0fa0b3f9628cf8de5471359a00"
}
},
{
- "@id": "urn:2651517a-d223-43a6-8156-df647cf71859",
+ "@id": "bids::errts.$%7Bsubj%7D+tlrc",
"Label": "errts.${subj}",
"AtLocation": "errts.${subj}+tlrc",
"digest": {
@@ -1178,25 +1189,25 @@
}
},
{
- "@id": "urn:7a2052c8-bcaa-4303-b9be-aa9d0ef702c7",
+ "@id": "bids::rm.errts.unit",
"Label": "rm.errts.unit",
"AtLocation": "rm.errts.unit",
- "GeneratedBy": "urn:1a587f9b-fc4a-4277-9fb0-9f79e2d2db5d",
+ "GeneratedBy": "urn:3dtnorm-N3ej7CkG",
"digest": {
"sha256": "03b570ad773a00f51ab7e6cdedfebdeca45f5356de0c25f9e3be44d7bf2c7151"
}
},
{
- "@id": "urn:f0039bc0-40e7-4b50-bf95-40e5d7fa3bb4",
+ "@id": "bids::gmean.errts.unit.1D",
"Label": "gmean.errts.unit.1D",
"AtLocation": "gmean.errts.unit.1D",
- "GeneratedBy": "urn:c3c6543b-54bc-42b7-9412-951ebc52f6b4",
+ "GeneratedBy": "urn:3dmaskav-TMgsSY8d",
"digest": {
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}
},
{
- "@id": "urn:a4f766bd-98cb-4832-965d-0fcc6ad8cb7e",
+ "@id": "bids::out.gcor.1D",
"Label": "out.gcor.1D",
"AtLocation": "out.gcor.1D",
"digest": {
@@ -1204,16 +1215,16 @@
}
},
{
- "@id": "urn:7b0e85df-6682-4dd4-b97d-04aadce54c0d",
+ "@id": "urn:uuid:6025627a-83a3-456d-8132-1ccb33c06fd5",
"Label": "-",
"AtLocation": "-",
- "GeneratedBy": "urn:731707e8-ab6e-4f05-ad4b-e7145f2957bb",
+ "GeneratedBy": "urn:3dtstat-r4WfRcQO",
"digest": {
"sha256": "dac304c9f20899ca1ef5aa403e565345fd0ff4ed80c35f82007c9b03a68292b3"
}
},
{
- "@id": "urn:5429a21c-8c73-4605-bb15-755f447b9ae6",
+ "@id": "bids::rm.errts.unit+tlrc",
"Label": "rm.errts.unit",
"AtLocation": "rm.errts.unit+tlrc",
"digest": {
@@ -1221,16 +1232,16 @@
}
},
{
- "@id": "urn:b4433074-6ca1-4071-9831-979ee1865166",
+ "@id": "bids::rm.DP",
"Label": "rm.DP",
"AtLocation": "rm.DP",
- "GeneratedBy": "urn:c3d81b35-0bb9-41de-9ab5-8b111d19f41a",
+ "GeneratedBy": "urn:3dcalc-Diz78Vi7",
"digest": {
"sha256": "06a0bfbc609c1a06ecf93c479a3288d2911c7f5f3e93cf49c5d26f721c2035ed"
}
},
{
- "@id": "urn:1e0b2ec0-5b80-47ba-ad3c-5b8cd6caa41c",
+ "@id": "bids::rm.DP+tlrc",
"Label": "rm.DP",
"AtLocation": "rm.DP+tlrc",
"digest": {
@@ -1238,16 +1249,16 @@
}
},
{
- "@id": "urn:4f23fee2-dbc5-4548-8c36-f9da7b4b6e9a",
+ "@id": "bids::corr_brain",
"Label": "corr_brain",
"AtLocation": "corr_brain",
- "GeneratedBy": "urn:5588370f-b147-4f11-beff-a8afc6bc1744",
+ "GeneratedBy": "urn:3dtstat-YBxYvXSr",
"digest": {
"sha256": "74e3aeae0da338b871ab5dc9e8859a4e81fcf1b3c0042cd22fe337eb7baf5eae"
}
},
{
- "@id": "urn:16e56703-dac3-4c6f-b5bb-6421103ed9de",
+ "@id": "bids::X.nocensor.xmat.1D'[3]'",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D'[3]'",
"digest": {
@@ -1255,16 +1266,16 @@
}
},
{
- "@id": "urn:838961dc-199d-4121-88e2-2675adb60b37",
+ "@id": "bids::ideal_tone_counting.1D",
"Label": "ideal_tone_counting.1D",
"AtLocation": "ideal_tone_counting.1D",
- "GeneratedBy": "urn:b3504581-2806-4e1d-814e-0f0ba71c883e",
+ "GeneratedBy": "urn:1dcat-mKOV8OBk",
"digest": {
"sha256": "9bb1cabac5ce7ca19dffa5cd6336a9bf82d362fea2ce9341978406e421b5333c"
}
},
{
- "@id": "urn:1f2447f7-73a4-4261-90bd-3f92589a700f",
+ "@id": "bids::X.nocensor.xmat.1D'[4]'",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D'[4]'",
"digest": {
@@ -1272,16 +1283,16 @@
}
},
{
- "@id": "urn:0bda345e-cc65-4137-9486-069f0222536f",
+ "@id": "bids::ideal_probe.1D",
"Label": "ideal_probe.1D",
"AtLocation": "ideal_probe.1D",
- "GeneratedBy": "urn:167b3a0d-1009-48d6-9d79-508f4f330c29",
+ "GeneratedBy": "urn:1dcat-ik7pWJJu",
"digest": {
"sha256": "705d93afa8b6ded9f4f572db3f967b54e9906942669af51dd8287a9863bb4288"
}
},
{
- "@id": "urn:0d2391fb-541e-4ca4-9322-d7ead2a3faba",
+ "@id": "bids::X.nocensor.xmat.1D%22[$reg_cols]%22",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D\"[$reg_cols]\"",
"digest": {
@@ -1289,52 +1300,52 @@
}
},
{
- "@id": "urn:dbd3b92d-80ca-4cdb-9a6a-e46c1bd4baf2",
+ "@id": "bids::sum_ideal.1D",
"Label": "sum_ideal.1D",
"AtLocation": "sum_ideal.1D",
- "GeneratedBy": "urn:bfddd750-a372-43d1-ae2a-a023348e8b54",
+ "GeneratedBy": "urn:3dtstat-KMyBshB8",
"digest": {
"sha256": "b2dccadcd84b2d26ec9685c4d1846baf2f11b867f31c36a08748d1c85467b01a"
}
},
{
- "@id": "urn:2cca56e2-0ca3-40d3-8b46-288d3ee06214",
+ "@id": "bids::X.stim.xmat.1D",
"Label": "X.stim.xmat.1D",
"AtLocation": "X.stim.xmat.1D",
- "GeneratedBy": "urn:2ff95f50-a969-489e-a40e-e7790f83f572",
+ "GeneratedBy": "urn:1dcat-BYaIlWxZ",
"digest": {
"sha256": "7c61b2f4bbb9eb0cecb19f81faa3a79b94d547b7fb4087ed18e368619e0004e6"
}
},
{
- "@id": "urn:61be43c2-2b91-4045-88de-c723a6db4e88",
+ "@id": "bids::blur.epits.1D",
"Label": "blur.epits.1D",
"AtLocation": "blur.epits.1D",
- "GeneratedBy": "urn:fd15a9b8-4e08-4138-bc21-ad000cf37cb5",
+ "GeneratedBy": "urn:3dfwhmx-Ud3U0uO1",
"digest": {
"sha256": "623e70a42214e56babc1f1dca156e0b11ba09865dbd6ca9549d54ca2fc601515"
}
},
{
- "@id": "urn:2272d4b8-d106-48ff-a984-c7533e17d0ab",
+ "@id": "bids::blur.errts.1D",
"Label": "blur.errts.1D",
"AtLocation": "blur.errts.1D",
- "GeneratedBy": "urn:3ccddd9f-ea57-4ce6-9092-ca4b5a77eac7",
+ "GeneratedBy": "urn:3dfwhmx-5rR4o8zi",
"digest": {
"sha256": "73969700079b5d3275536ac7eaf0e17571d7e74ec49553b6940f90d5718fc800"
}
},
{
- "@id": "urn:dc43357b-0d1e-4e30-a9ee-8be5fcb5feb2",
+ "@id": "bids::ClustSim",
"Label": "ClustSim",
"AtLocation": "ClustSim",
- "GeneratedBy": "urn:a8f3bb8f-3e44-47c6-ace2-cf65386c4b34",
+ "GeneratedBy": "urn:3dclusts-yn5oKahn",
"digest": {
"sha256": "2e0cdba2c91902ba12d742a39cb20df66cfd705ba8de767fbf68aae8eb65c6f0"
}
},
{
- "@id": "urn:779bba0c-3ae9-48cb-acab-b1e42ff2ac39",
+ "@id": "bids::pb00.$subj.r*.tcat+orig.HEAD",
"Label": "pb00.$subj.r*.tcat",
"AtLocation": "pb00.$subj.r*.tcat+orig.HEAD",
"digest": {
@@ -1342,10 +1353,10 @@
}
},
{
- "@id": "urn:de46ce68-4f74-457e-9cf6-0025743ec8ee",
+ "@id": "bids::-exit0",
"Label": "-exit0",
"AtLocation": "-exit0",
- "GeneratedBy": "urn:2c85290f-b3f2-431b-91c4-402a54caa3b8",
+ "GeneratedBy": "urn:genssrev-F0b9dXGV",
"digest": {
"sha256": "871a4d3513ed2924cbb10c1c15a196eac4a46a05bdcc248e3bcdb23327b3ad90"
}
diff --git a/examples/from_parsers/afni/afni_thr_clustunck10_proc.png b/examples/from_parsers/afni/afni_thr_clustunck10_proc.png
index 9b0528af9..0655e98bb 100644
Binary files a/examples/from_parsers/afni/afni_thr_clustunck10_proc.png and b/examples/from_parsers/afni/afni_thr_clustunck10_proc.png differ
diff --git a/examples/from_parsers/afni/afni_thr_clustunck10_proc_block.jsonld b/examples/from_parsers/afni/afni_thr_clustunck10_proc_block.jsonld
index a773c3c8e..381f84f63 100644
--- a/examples/from_parsers/afni/afni_thr_clustunck10_proc_block.jsonld
+++ b/examples/from_parsers/afni/afni_thr_clustunck10_proc_block.jsonld
@@ -4,187 +4,189 @@
"Records": {
"Software": [
{
- "@id": "urn:3e779b96-b84b-4017-9c44-e80cc9061684",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:afni-Ie70nH53",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
- "Version": "afni24"
+ "Version": "afni24",
+ "AltIdentifier": "RRID:SCR_005927"
}
],
"Activities": [
{
- "@id": "urn:ab084599-d390-45bf-900d-a3e6f4fbb20f",
+ "@id": "urn:autobloc-LgDQ5Cau",
"Label": "auto block: setup",
- "AssociatedWith": "urn:3e779b96-b84b-4017-9c44-e80cc9061684",
+ "AssociatedWith": "urn:afni-Ie70nH53",
"Command": "mkdir $output_dir; mkdir $output_dir/stimuli; cp ./afni_cluster_k10/tone_counting_onset_times.txt ./afni_cluster_k10/tone_counting_probe_duration.txt $output_dir/stimuli; 3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w; ",
"Used": [
- "urn:0f97dafe-7942-48b2-a0e1-23c0879c2780",
- "urn:b31016e4-d131-4b54-b8bb-8ffb95e1235a",
- "urn:5fb05a76-a750-4b84-98ec-1946b81a5db4"
+ "bids::afni_cluster_k10/tone_counting_onset_times.txt",
+ "bids::afni_cluster_k10/tone_counting_probe_duration.txt",
+ "bids::sub-01_T1w.nii.gz"
]
},
{
- "@id": "urn:927ff65e-1d3e-4803-8c17-18433a1607c1",
+ "@id": "urn:autobloc-gGJDCSg9",
"Label": "auto block: tcat",
- "AssociatedWith": "urn:3e779b96-b84b-4017-9c44-e80cc9061684",
+ "AssociatedWith": "urn:afni-Ie70nH53",
"Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ",
"Used": [
- "urn:5041a759-7d98-40e9-8f7a-eb9414fc0d5c"
+ "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'"
]
},
{
- "@id": "urn:7688d9d7-da55-4bd4-9043-3ecdceb1cf4e",
+ "@id": "urn:autobloc-BxTtH4fF",
"Label": "auto block: outcount",
- "AssociatedWith": "urn:3e779b96-b84b-4017-9c44-e80cc9061684",
+ "AssociatedWith": "urn:afni-Ie70nH53",
"Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ",
"Used": [
- "urn:7e8f72f4-3ab7-4e45-9686-af86309b5c18",
- "urn:955da2fc-77e8-4752-8215-2a0149f99377"
+ "bids::pb00.$subj.r$run.tcat+orig",
+ "bids::outcount.r*.1D"
]
},
{
- "@id": "urn:584dcc11-4282-4005-a233-aa247685f735",
+ "@id": "urn:tshift-XMM25khJ",
"Label": "tshift",
- "AssociatedWith": "urn:3e779b96-b84b-4017-9c44-e80cc9061684",
+ "AssociatedWith": "urn:afni-Ie70nH53",
"Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ",
"Used": [
- "urn:7e8f72f4-3ab7-4e45-9686-af86309b5c18"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:b64ae7ad-936c-47ac-a436-60fd51bc00fd",
+ "@id": "urn:align-bsB9poRV",
"Label": "align",
- "AssociatedWith": "urn:3e779b96-b84b-4017-9c44-e80cc9061684",
+ "AssociatedWith": "urn:afni-Ie70nH53",
"Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ",
"Used": [
- "urn:a876f85d-2556-4f1c-bc99-507e89425058",
- "urn:d8b2dc52-ca26-4227-aff0-f19085500225"
+ "bids::pb01.$subj.r01.tshift+orig",
+ "bids::sub-01_T1w+orig"
]
},
{
- "@id": "urn:6f070701-23cb-4ab5-a385-af737f811d7e",
+ "@id": "urn:tlrc-J1B4oPWF",
"Label": "tlrc",
- "AssociatedWith": "urn:3e779b96-b84b-4017-9c44-e80cc9061684",
+ "AssociatedWith": "urn:afni-Ie70nH53",
"Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ",
"Used": [
- "urn:458a1844-cfe6-4c0c-be41-852bc6d6ef52",
- "urn:aaa58822-55d3-41ef-936e-040f81bc9bfd",
- "urn:09a35bda-f038-4046-a2ba-bdf2ec4a47d8"
+ "bids::TT_N27+tlrc",
+ "bids::sub-01_T1w_ns+orig",
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:c62f9d14-a51a-4fee-8038-d735433b3e7c",
+ "@id": "urn:volreg-QASdhVdj",
"Label": "volreg",
- "AssociatedWith": "urn:3e779b96-b84b-4017-9c44-e80cc9061684",
+ "AssociatedWith": "urn:afni-Ie70nH53",
"Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig; 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1; cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D; 3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run; 3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run; 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc; cat dfile.r*.1D > dfile_rall.1D; 3dcopy rm.epi.min.r01+tlrc mask_epi_extents; 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg; 3dcopy sub-01_T1w_ns+tlrc anat_final.$subj; 3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped; ",
"Used": [
- "urn:0fc2ef80-a58a-4562-9768-d62b75f49c47",
- "urn:0fc2ef80-a58a-4562-9768-d62b75f49c47",
- "urn:09a35bda-f038-4046-a2ba-bdf2ec4a47d8",
- "urn:0fc2ef80-a58a-4562-9768-d62b75f49c47",
- "urn:c17b2fce-6992-45ca-8529-7c2ff62a9b35",
- "urn:b3a63d0e-6eda-41fa-a7bc-f1a91690c230",
- "urn:c17b2fce-6992-45ca-8529-7c2ff62a9b35",
- "urn:083011da-8332-4224-8b04-3e446b1d0565",
- "urn:ce136485-f2cb-4219-86c1-c4706b2d5e23",
- "urn:f42e9433-2e8b-4418-985e-0e729a4b9011",
- "urn:76f34313-4036-4758-aeb7-417bdfa5b93a",
- "urn:9866dec0-439b-443d-aa0f-09fdb0d86941",
- "urn:c17b2fce-6992-45ca-8529-7c2ff62a9b35",
- "urn:74b17bd8-cbc5-4d4f-87c3-abd4546fdc05"
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.epi.all1+orig",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.epi.1.r$run+tlrc",
+ "bids::dfile.r*.1D",
+ "bids::rm.epi.min.r01+tlrc",
+ "bids::mask_epi_extents+tlrc",
+ "bids::rm.epi.nomask.r$run+tlrc",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::anat_final.$subj+tlrc",
+ "bids::warp.anat.Xat.1D"
]
},
{
- "@id": "urn:432fd184-6d95-4966-bc34-3703aaebc045",
+ "@id": "urn:blur-Ij61bOyL",
"Label": "blur",
- "AssociatedWith": "urn:3e779b96-b84b-4017-9c44-e80cc9061684",
+ "AssociatedWith": "urn:afni-Ie70nH53",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc; ",
"Used": [
- "urn:3a654753-b045-43d9-91af-47a534e1ddf0",
- "urn:632d059b-7317-409b-bc33-1129e0fb3384"
+ "bids::pb02.$subj.r$run.volreg+tlrc",
+ "bids::pb03.$subj.r$run.blur"
]
},
{
- "@id": "urn:086efdc4-e2eb-4773-b6b6-042e622a6721",
+ "@id": "urn:mask-d0J0X9W5",
"Label": "mask",
- "AssociatedWith": "urn:3e779b96-b84b-4017-9c44-e80cc9061684",
+ "AssociatedWith": "urn:afni-Ie70nH53",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc; 3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj; 3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj; 3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt; 3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt; 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group; ",
"Used": [
- "urn:5a94b1ea-6185-4724-82e8-6a994f8b40e5",
- "urn:1d5fc7c1-5967-451b-9074-9ecff2ec0f09",
- "urn:c17b2fce-6992-45ca-8529-7c2ff62a9b35",
- "urn:4b6b1d21-b999-489b-8adf-0ef6a72be07b",
- "urn:5599d82d-e9dc-49b9-ba3d-62d2fef3c704",
- "urn:b415fe53-55a1-4e80-aead-40b447d50de0",
- "urn:5599d82d-e9dc-49b9-ba3d-62d2fef3c704",
- "urn:b415fe53-55a1-4e80-aead-40b447d50de0",
- "urn:1d5fc7c1-5967-451b-9074-9ecff2ec0f09",
- "urn:5f718118-a8b0-4b13-ac81-05ba2dd92a07",
- "urn:33ff223f-e6e1-46fb-93ae-370fded0fdba"
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.resam.anat+tlrc",
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee",
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee",
+ "bids::/Users/u1591557/abin/TT_N27+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.resam.group+tlrc"
]
},
{
- "@id": "urn:d16c50a6-7f32-4b74-b8f3-8f9c5a14d796",
+ "@id": "urn:scale-tqb4fi1p",
"Label": "scale",
- "AssociatedWith": "urn:3e779b96-b84b-4017-9c44-e80cc9061684",
+ "AssociatedWith": "urn:afni-Ie70nH53",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc; 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale; ",
"Used": [
- "urn:5a94b1ea-6185-4724-82e8-6a994f8b40e5",
- "urn:1acb59f0-d174-4fd6-add7-3662f9b53c07",
- "urn:5a94b1ea-6185-4724-82e8-6a994f8b40e5",
- "urn:9866dec0-439b-443d-aa0f-09fdb0d86941"
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::mask_epi_extents+tlrc",
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::rm.mean_r$run+tlrc"
]
},
{
- "@id": "urn:ec08b899-bdfa-4f0f-b3fd-8671c1ceea3d",
+ "@id": "urn:regress-QBMi7uo8",
"Label": "regress",
- "AssociatedWith": "urn:3e779b96-b84b-4017-9c44-e80cc9061684",
+ "AssociatedWith": "urn:afni-Ie70nH53",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}; 3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj; 1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt; 3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD; 3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"; 3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"; 3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj; 3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc; 3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D; 3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D; 3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP; 3dTstat -sum -prefix corr_brain rm.DP+tlrc; 1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D; 1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D; 3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"; 1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D; ",
"Used": [
- "urn:d4257f34-69b5-4910-a169-f8a8325c1191",
- "urn:d4257f34-69b5-4910-a169-f8a8325c1191",
- "urn:d4257f34-69b5-4910-a169-f8a8325c1191",
- "urn:8b3e58d2-01fa-49f8-a673-9431aaccfc47",
- "urn:8b3e58d2-01fa-49f8-a673-9431aaccfc47",
- "urn:4c89ad48-ba0f-45e9-b026-e813b7816d32",
- "urn:30e03dcc-204f-4159-afcc-fcd7efe4664d",
- "urn:1d5fc7c1-5967-451b-9074-9ecff2ec0f09",
- "urn:8b77e7f5-fa5d-43fe-a8c3-caf66c861b43",
- "urn:df94604f-7f06-4143-9b98-e624dab2dc66",
- "urn:41002437-cbf0-4db7-9a60-637d98c15b27",
- "urn:fcef7c15-eb1a-43d0-a496-81c1c8943ae1",
- "urn:85f2163f-cfc5-4ede-9da5-a69c4e234514",
- "urn:b66b5e86-c268-4d21-9bda-3d10f0361c09",
- "urn:d6f63e96-ea88-4593-82e8-42fed8a33dfd",
- "urn:8b5fda69-66b3-4b80-b1b8-4e9f3526efb9",
- "urn:7c5d805c-8cc9-4593-99f1-fc70e69f54c5",
- "urn:7c5d805c-8cc9-4593-99f1-fc70e69f54c5"
+ "bids::dfile_rall.1D",
+ "bids::dfile_rall.1D",
+ "bids::dfile_rall.1D",
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD",
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD",
+ "bids::all_runs.$subj+tlrc%22[$ktrs]%22",
+ "bids::errts.$%7Bsubj%7D+tlrc%22[$ktrs]%22",
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.noise.all+tlrc",
+ "bids::rm.signal.all+tlrc",
+ "bids::errts.$%7Bsubj%7D+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::out.gcor.1D",
+ "bids::rm.errts.unit+tlrc",
+ "bids::rm.DP+tlrc",
+ "bids::X.nocensor.xmat.1D'[3]'",
+ "bids::X.nocensor.xmat.1D'[4]'",
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22",
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:155a15be-dfc8-497f-bcab-b479fbce21c2",
+ "@id": "urn:bluresti-a7rUmMml",
"Label": "blur estimation",
- "AssociatedWith": "urn:3e779b96-b84b-4017-9c44-e80cc9061684",
+ "AssociatedWith": "urn:afni-Ie70nH53",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D; 3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D; 3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim; ",
"Used": [
- "urn:1d5fc7c1-5967-451b-9074-9ecff2ec0f09",
- "urn:1d5fc7c1-5967-451b-9074-9ecff2ec0f09",
- "urn:1d5fc7c1-5967-451b-9074-9ecff2ec0f09"
+ "bids::full_mask.$subj+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:f0d6e7fb-50cd-4a57-a20f-f495606ad77b",
+ "@id": "urn:autobloc-olTmkcM4",
"Label": "auto block: generate review scripts",
- "AssociatedWith": "urn:3e779b96-b84b-4017-9c44-e80cc9061684",
+ "AssociatedWith": "urn:afni-Ie70nH53",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD; gen_ss_review_scripts.py -mot_limit 0.3 -exit0; ",
"Used": [
- "urn:241187a5-ac48-4a1e-8598-30c933d02e3f"
+ "bids::pb00.$subj.r*.tcat+orig.HEAD"
]
}
],
"Entities": [
{
- "@id": "urn:b31016e4-d131-4b54-b8bb-8ffb95e1235a",
+ "@id": "bids::afni_cluster_k10/tone_counting_onset_times.txt",
"Label": "tone_counting_onset_times.txt",
"AtLocation": "./afni_cluster_k10/tone_counting_onset_times.txt",
"digest": {
@@ -192,7 +194,7 @@
}
},
{
- "@id": "urn:0f97dafe-7942-48b2-a0e1-23c0879c2780",
+ "@id": "bids::afni_cluster_k10/tone_counting_probe_duration.txt",
"Label": "tone_counting_probe_duration.txt",
"AtLocation": "./afni_cluster_k10/tone_counting_probe_duration.txt",
"digest": {
@@ -200,7 +202,7 @@
}
},
{
- "@id": "urn:5fb05a76-a750-4b84-98ec-1946b81a5db4",
+ "@id": "bids::sub-01_T1w.nii.gz",
"Label": "sub-01_T1w.nii.gz",
"AtLocation": "sub-01_T1w.nii.gz",
"digest": {
@@ -208,34 +210,34 @@
}
},
{
- "@id": "urn:24ef9e82-b791-4254-9443-63afae794945",
+ "@id": "bids::$output_dir",
"Label": "$output_dir",
"AtLocation": "$output_dir",
- "GeneratedBy": "urn:ab084599-d390-45bf-900d-a3e6f4fbb20f",
+ "GeneratedBy": "urn:autobloc-LgDQ5Cau",
"digest": {
"sha256": "9fa4c635e6533ddf2fed54295920052818d948c3ffe97bc753bd7336b453f8cb"
}
},
{
- "@id": "urn:7770962b-a499-4159-9e68-1276c1c6a1d7",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:ab084599-d390-45bf-900d-a3e6f4fbb20f"
+ "GeneratedBy": "urn:autobloc-LgDQ5Cau"
},
{
- "@id": "urn:3bcd92f6-9026-4d20-97a1-2202c2d7a417",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:ab084599-d390-45bf-900d-a3e6f4fbb20f"
+ "GeneratedBy": "urn:autobloc-LgDQ5Cau"
},
{
- "@id": "urn:33a88f78-2a21-48c5-86a8-4ae6601a7bd4",
+ "@id": "bids::$output_dir/sub-01_T1w",
"Label": "sub-01_T1w",
"AtLocation": "$output_dir/sub-01_T1w",
- "GeneratedBy": "urn:ab084599-d390-45bf-900d-a3e6f4fbb20f"
+ "GeneratedBy": "urn:autobloc-LgDQ5Cau"
},
{
- "@id": "urn:5041a759-7d98-40e9-8f7a-eb9414fc0d5c",
+ "@id": "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Label": "sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"digest": {
@@ -243,13 +245,13 @@
}
},
{
- "@id": "urn:5b3dfb16-6266-481a-8853-05f9d3d63907",
+ "@id": "bids::$output_dir/pb00.$subj.r01.tcat",
"Label": "pb00.$subj.r01.tcat",
"AtLocation": "$output_dir/pb00.$subj.r01.tcat",
- "GeneratedBy": "urn:927ff65e-1d3e-4803-8c17-18433a1607c1"
+ "GeneratedBy": "urn:autobloc-gGJDCSg9"
},
{
- "@id": "urn:7e8f72f4-3ab7-4e45-9686-af86309b5c18",
+ "@id": "bids::pb00.$subj.r$run.tcat+orig",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -257,7 +259,7 @@
}
},
{
- "@id": "urn:955da2fc-77e8-4752-8215-2a0149f99377",
+ "@id": "bids::outcount.r*.1D",
"Label": "outcount.r*.1D",
"AtLocation": "outcount.r*.1D",
"digest": {
@@ -265,25 +267,25 @@
}
},
{
- "@id": "urn:1aee3f47-2397-4b97-92ab-90d2167edbca",
+ "@id": "bids::outcount.r$run.1D",
"Label": "outcount.r$run.1D",
"AtLocation": "outcount.r$run.1D",
- "GeneratedBy": "urn:7688d9d7-da55-4bd4-9043-3ecdceb1cf4e",
+ "GeneratedBy": "urn:autobloc-BxTtH4fF",
"digest": {
"sha256": "63d9f539e5470badc625d557109f68bc4eecbb02ca2667483739d52f95e5d0dd"
}
},
{
- "@id": "urn:e2038ef4-ff24-4366-bfc1-1a9a292de9a3",
+ "@id": "bids::outcount_rall.1D",
"Label": "outcount_rall.1D",
"AtLocation": "outcount_rall.1D",
- "GeneratedBy": "urn:7688d9d7-da55-4bd4-9043-3ecdceb1cf4e",
+ "GeneratedBy": "urn:autobloc-BxTtH4fF",
"digest": {
"sha256": "cb887fd5e4d5e9acb3a24820d0f7a62ed38a5ffb0fdedd373440ac0219fb186a"
}
},
{
- "@id": "urn:7e8f72f4-3ab7-4e45-9686-af86309b5c18",
+ "@id": "bids::pb00.$subj.r$run.tcat+orig",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -291,16 +293,16 @@
}
},
{
- "@id": "urn:edf7efc4-5506-41fe-a639-b0288c6f9929",
+ "@id": "bids::pb01.$subj.r$run.tshift",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift",
- "GeneratedBy": "urn:584dcc11-4282-4005-a233-aa247685f735",
+ "GeneratedBy": "urn:tshift-XMM25khJ",
"digest": {
"sha256": "c6bf01cea8d2eac1d7a866f80b865c6e7d4b4e012dbb63d480ac9a8551162d72"
}
},
{
- "@id": "urn:d8b2dc52-ca26-4227-aff0-f19085500225",
+ "@id": "bids::sub-01_T1w+orig",
"Label": "sub-01_T1w",
"AtLocation": "sub-01_T1w+orig",
"digest": {
@@ -308,7 +310,7 @@
}
},
{
- "@id": "urn:a876f85d-2556-4f1c-bc99-507e89425058",
+ "@id": "bids::pb01.$subj.r01.tshift+orig",
"Label": "pb01.$subj.r01.tshift",
"AtLocation": "pb01.$subj.r01.tshift+orig",
"digest": {
@@ -316,16 +318,16 @@
}
},
{
- "@id": "urn:f8678cd3-2fbe-4b0a-b6ce-7a5607cf6e49",
+ "@id": "bids::_al_junk",
"Label": "_al_junk",
"AtLocation": "_al_junk",
- "GeneratedBy": "urn:b64ae7ad-936c-47ac-a436-60fd51bc00fd",
+ "GeneratedBy": "urn:align-bsB9poRV",
"digest": {
"sha256": "bd785a075a4c6446e1e54de9e628913f7f1c814e86b69a9fbfe933209e6d37b5"
}
},
{
- "@id": "urn:aaa58822-55d3-41ef-936e-040f81bc9bfd",
+ "@id": "bids::TT_N27+tlrc",
"Label": "TT_N27",
"AtLocation": "TT_N27+tlrc",
"digest": {
@@ -333,7 +335,7 @@
}
},
{
- "@id": "urn:458a1844-cfe6-4c0c-be41-852bc6d6ef52",
+ "@id": "bids::sub-01_T1w_ns+orig",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+orig",
"digest": {
@@ -341,7 +343,7 @@
}
},
{
- "@id": "urn:09a35bda-f038-4046-a2ba-bdf2ec4a47d8",
+ "@id": "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc::WARP_DATA",
"digest": {
@@ -349,16 +351,16 @@
}
},
{
- "@id": "urn:74b17bd8-cbc5-4d4f-87c3-abd4546fdc05",
+ "@id": "bids::warp.anat.Xat.1D",
"Label": "warp.anat.Xat.1D",
"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:6f070701-23cb-4ab5-a385-af737f811d7e",
+ "GeneratedBy": "urn:tlrc-J1B4oPWF",
"digest": {
"sha256": "800633fb5b4e9be64078bc181c4d5510ffb73fc5cccaf364c7fb6a294aa06728"
}
},
{
- "@id": "urn:09a35bda-f038-4046-a2ba-bdf2ec4a47d8",
+ "@id": "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc::WARP_DATA",
"digest": {
@@ -366,16 +368,16 @@
}
},
{
- "@id": "urn:74b17bd8-cbc5-4d4f-87c3-abd4546fdc05",
+ "@id": "bids::warp.anat.Xat.1D",
"Label": "warp.anat.Xat.1D",
"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:6f070701-23cb-4ab5-a385-af737f811d7e",
+ "GeneratedBy": "urn:tlrc-J1B4oPWF",
"digest": {
"sha256": "800633fb5b4e9be64078bc181c4d5510ffb73fc5cccaf364c7fb6a294aa06728"
}
},
{
- "@id": "urn:0fc2ef80-a58a-4562-9768-d62b75f49c47",
+ "@id": "bids::pb01.$subj.r$run.tshift+orig",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift+orig",
"digest": {
@@ -383,7 +385,7 @@
}
},
{
- "@id": "urn:c17b2fce-6992-45ca-8529-7c2ff62a9b35",
+ "@id": "bids::sub-01_T1w_ns+tlrc",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc",
"digest": {
@@ -391,7 +393,7 @@
}
},
{
- "@id": "urn:b3a63d0e-6eda-41fa-a7bc-f1a91690c230",
+ "@id": "bids::rm.epi.all1+orig",
"Label": "rm.epi.all1",
"AtLocation": "rm.epi.all1+orig",
"digest": {
@@ -399,7 +401,7 @@
}
},
{
- "@id": "urn:083011da-8332-4224-8b04-3e446b1d0565",
+ "@id": "bids::rm.epi.1.r$run+tlrc",
"Label": "rm.epi.1.r$run",
"AtLocation": "rm.epi.1.r$run+tlrc",
"digest": {
@@ -407,7 +409,7 @@
}
},
{
- "@id": "urn:ce136485-f2cb-4219-86c1-c4706b2d5e23",
+ "@id": "bids::dfile.r*.1D",
"Label": "dfile.r*.1D",
"AtLocation": "dfile.r*.1D",
"digest": {
@@ -415,7 +417,7 @@
}
},
{
- "@id": "urn:f42e9433-2e8b-4418-985e-0e729a4b9011",
+ "@id": "bids::rm.epi.min.r01+tlrc",
"Label": "rm.epi.min.r01",
"AtLocation": "rm.epi.min.r01+tlrc",
"digest": {
@@ -423,7 +425,7 @@
}
},
{
- "@id": "urn:76f34313-4036-4758-aeb7-417bdfa5b93a",
+ "@id": "bids::rm.epi.nomask.r$run+tlrc",
"Label": "rm.epi.nomask.r$run",
"AtLocation": "rm.epi.nomask.r$run+tlrc",
"digest": {
@@ -431,7 +433,7 @@
}
},
{
- "@id": "urn:9866dec0-439b-443d-aa0f-09fdb0d86941",
+ "@id": "bids::mask_epi_extents+tlrc",
"Label": "mask_epi_extents",
"AtLocation": "mask_epi_extents+tlrc",
"digest": {
@@ -439,97 +441,105 @@
}
},
{
- "@id": "urn:5212afa6-9451-4b1b-96ff-74703db15b8e",
+ "@id": "bids::anat_final.$subj+tlrc",
+ "Label": "anat_final.$subj",
+ "AtLocation": "anat_final.$subj+tlrc",
+ "digest": {
+ "sha256": "94eb1853614cc085b22772c011f119f6a0ad7ec06cba2850587762e7f1a6eae6"
+ }
+ },
+ {
+ "@id": "bids::mat.r$run.vr.aff12.1D",
"Label": "mat.r$run.vr.aff12.1D",
"AtLocation": "mat.r$run.vr.aff12.1D",
- "GeneratedBy": "urn:c62f9d14-a51a-4fee-8038-d735433b3e7c",
+ "GeneratedBy": "urn:volreg-QASdhVdj",
"digest": {
"sha256": "2e6e6c2ce8089cfa3c6e11dc72fca0cc8497f7a55faae2ced402de4867466c91"
}
},
{
- "@id": "urn:fd0c1922-3af4-4ff4-9e43-e101e9894067",
+ "@id": "bids::rm.epi.all1",
"Label": "rm.epi.all1",
"AtLocation": "rm.epi.all1",
- "GeneratedBy": "urn:c62f9d14-a51a-4fee-8038-d735433b3e7c",
+ "GeneratedBy": "urn:volreg-QASdhVdj",
"digest": {
"sha256": "1023e3c16cecdbdc73ea456bcf33c2e5bb4f1e07094b73d29022d651e5fa3f85"
}
},
{
- "@id": "urn:49a97bda-57b1-4235-9a78-05d841a0d0a5",
+ "@id": "bids::rm.epi.nomask.r$run",
"Label": "rm.epi.nomask.r$run",
"AtLocation": "rm.epi.nomask.r$run",
- "GeneratedBy": "urn:c62f9d14-a51a-4fee-8038-d735433b3e7c",
+ "GeneratedBy": "urn:volreg-QASdhVdj",
"digest": {
"sha256": "03d6cba0426c5545e350e6b63a19b0e46f8dfa2223fd08691753e8914a479e36"
}
},
{
- "@id": "urn:aae97d91-c38d-4bad-a44f-266f2980278e",
+ "@id": "bids::rm.epi.1.r$run",
"Label": "rm.epi.1.r$run",
"AtLocation": "rm.epi.1.r$run",
- "GeneratedBy": "urn:c62f9d14-a51a-4fee-8038-d735433b3e7c",
+ "GeneratedBy": "urn:volreg-QASdhVdj",
"digest": {
"sha256": "b1b9128c103ea246625db1a35e6f474a221ca6c1105a30df38aefdc4d5421e84"
}
},
{
- "@id": "urn:e73688be-08fe-432e-be79-af3c6e4d3fcb",
+ "@id": "bids::rm.epi.min.r$run",
"Label": "rm.epi.min.r$run",
"AtLocation": "rm.epi.min.r$run",
- "GeneratedBy": "urn:c62f9d14-a51a-4fee-8038-d735433b3e7c",
+ "GeneratedBy": "urn:volreg-QASdhVdj",
"digest": {
"sha256": "b4418a96ddbbf25afdfd01ed0506ddebe009011ba18aed10137f994260fd1a66"
}
},
{
- "@id": "urn:d4257f34-69b5-4910-a169-f8a8325c1191",
+ "@id": "bids::dfile_rall.1D",
"Label": "dfile_rall.1D",
"AtLocation": "dfile_rall.1D",
- "GeneratedBy": "urn:c62f9d14-a51a-4fee-8038-d735433b3e7c",
+ "GeneratedBy": "urn:volreg-QASdhVdj",
"digest": {
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}
},
{
- "@id": "urn:59d9b2e7-c91d-4f60-9f44-1bcf0e1670ec",
+ "@id": "bids::mask_epi_extents",
"Label": "mask_epi_extents",
"AtLocation": "mask_epi_extents",
- "GeneratedBy": "urn:c62f9d14-a51a-4fee-8038-d735433b3e7c",
+ "GeneratedBy": "urn:volreg-QASdhVdj",
"digest": {
"sha256": "a69dd71209516ec24e2b3364072ed54adff16619459b1c369866210ec642e987"
}
},
{
- "@id": "urn:5e26136f-5604-4340-8c7b-44216fd86348",
+ "@id": "bids::pb02.$subj.r$run.volreg",
"Label": "pb02.$subj.r$run.volreg",
"AtLocation": "pb02.$subj.r$run.volreg",
- "GeneratedBy": "urn:c62f9d14-a51a-4fee-8038-d735433b3e7c",
+ "GeneratedBy": "urn:volreg-QASdhVdj",
"digest": {
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}
},
{
- "@id": "urn:ba768bfc-8d83-41b6-a165-99c6551f22ac",
+ "@id": "bids::anat_final.$subj",
"Label": "anat_final.$subj",
"AtLocation": "anat_final.$subj",
- "GeneratedBy": "urn:c62f9d14-a51a-4fee-8038-d735433b3e7c",
+ "GeneratedBy": "urn:volreg-QASdhVdj",
"digest": {
"sha256": "69b750d004bdba337de0b4ffa683bd92bc8f34b854d320327839ad264b28c4c5"
}
},
{
- "@id": "urn:31054834-2460-4ad5-bfa8-309f871874ae",
+ "@id": "bids::anat_w_skull_warped",
"Label": "anat_w_skull_warped",
"AtLocation": "anat_w_skull_warped",
- "GeneratedBy": "urn:c62f9d14-a51a-4fee-8038-d735433b3e7c",
+ "GeneratedBy": "urn:volreg-QASdhVdj",
"digest": {
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}
},
{
- "@id": "urn:632d059b-7317-409b-bc33-1129e0fb3384",
+ "@id": "bids::pb03.$subj.r$run.blur",
"Label": "pb03.$subj.r$run.blur",
"AtLocation": "pb03.$subj.r$run.blur",
"digest": {
@@ -537,7 +547,7 @@
}
},
{
- "@id": "urn:3a654753-b045-43d9-91af-47a534e1ddf0",
+ "@id": "bids::pb02.$subj.r$run.volreg+tlrc",
"Label": "pb02.$subj.r$run.volreg",
"AtLocation": "pb02.$subj.r$run.volreg+tlrc",
"digest": {
@@ -545,7 +555,7 @@
}
},
{
- "@id": "urn:c17b2fce-6992-45ca-8529-7c2ff62a9b35",
+ "@id": "bids::sub-01_T1w_ns+tlrc",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc",
"digest": {
@@ -553,7 +563,7 @@
}
},
{
- "@id": "urn:5a94b1ea-6185-4724-82e8-6a994f8b40e5",
+ "@id": "bids::pb03.$subj.r$run.blur+tlrc",
"Label": "pb03.$subj.r$run.blur",
"AtLocation": "pb03.$subj.r$run.blur+tlrc",
"digest": {
@@ -561,7 +571,7 @@
}
},
{
- "@id": "urn:1d5fc7c1-5967-451b-9074-9ecff2ec0f09",
+ "@id": "bids::full_mask.$subj+tlrc",
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"digest": {
@@ -569,7 +579,7 @@
}
},
{
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+ "@id": "bids::rm.resam.anat+tlrc",
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"digest": {
@@ -577,7 +587,7 @@
}
},
{
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+ "@id": "bids::mask_anat.$subj+tlrc",
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"AtLocation": "mask_anat.$subj+tlrc",
"digest": {
@@ -585,7 +595,7 @@
}
},
{
- "@id": "urn:5599d82d-e9dc-49b9-ba3d-62d2fef3c704",
+ "@id": "bids::tee",
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"digest": {
@@ -593,7 +603,7 @@
}
},
{
- "@id": "urn:5f718118-a8b0-4b13-ac81-05ba2dd92a07",
+ "@id": "bids::/Users/u1591557/abin/TT_N27+tlrc",
"Label": "TT_N27",
"AtLocation": "/Users/u1591557/abin/TT_N27+tlrc",
"digest": {
@@ -601,7 +611,7 @@
}
},
{
- "@id": "urn:33ff223f-e6e1-46fb-93ae-370fded0fdba",
+ "@id": "bids::rm.resam.group+tlrc",
"Label": "rm.resam.group",
"AtLocation": "rm.resam.group+tlrc",
"digest": {
@@ -609,61 +619,61 @@
}
},
{
- "@id": "urn:e9b09628-d956-4771-99c5-61c5151eb24e",
+ "@id": "bids::rm.mask_r$run",
"Label": "rm.mask_r$run",
"AtLocation": "rm.mask_r$run",
- "GeneratedBy": "urn:086efdc4-e2eb-4773-b6b6-042e622a6721",
+ "GeneratedBy": "urn:mask-d0J0X9W5",
"digest": {
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}
},
{
- "@id": "urn:45ad5d74-508c-4c18-bae0-c2b973d3c784",
+ "@id": "bids::full_mask.$subj",
"Label": "full_mask.$subj",
"AtLocation": "full_mask.$subj",
- "GeneratedBy": "urn:086efdc4-e2eb-4773-b6b6-042e622a6721",
+ "GeneratedBy": "urn:mask-d0J0X9W5",
"digest": {
"sha256": "02da8c6ed741c00cb6ccb8da25bf6ca853afb9100b992c854209afde9e30918f"
}
},
{
- "@id": "urn:c79be97e-b015-4120-b508-621e5bd01049",
+ "@id": "bids::rm.resam.anat",
"Label": "rm.resam.anat",
"AtLocation": "rm.resam.anat",
- "GeneratedBy": "urn:086efdc4-e2eb-4773-b6b6-042e622a6721",
+ "GeneratedBy": "urn:mask-d0J0X9W5",
"digest": {
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}
},
{
- "@id": "urn:22644854-5b21-46b9-8f42-4e730f48909b",
+ "@id": "bids::mask_anat.$subj",
"Label": "mask_anat.$subj",
"AtLocation": "mask_anat.$subj",
- "GeneratedBy": "urn:086efdc4-e2eb-4773-b6b6-042e622a6721",
+ "GeneratedBy": "urn:mask-d0J0X9W5",
"digest": {
"sha256": "d3f1becfb7c7d234361e002cc34c3ca5b5333640259f572993b773f6973f0e98"
}
},
{
- "@id": "urn:39abacfe-7ecb-410e-bfc2-89bb11de297b",
+ "@id": "bids::rm.resam.group",
"Label": "rm.resam.group",
"AtLocation": "./rm.resam.group",
- "GeneratedBy": "urn:086efdc4-e2eb-4773-b6b6-042e622a6721",
+ "GeneratedBy": "urn:mask-d0J0X9W5",
"digest": {
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}
},
{
- "@id": "urn:dc0b0f52-290f-4c61-b4d9-9f39ad232080",
+ "@id": "bids::mask_group",
"Label": "mask_group",
"AtLocation": "mask_group",
- "GeneratedBy": "urn:086efdc4-e2eb-4773-b6b6-042e622a6721",
+ "GeneratedBy": "urn:mask-d0J0X9W5",
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}
},
{
- "@id": "urn:9866dec0-439b-443d-aa0f-09fdb0d86941",
+ "@id": "bids::mask_epi_extents+tlrc",
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"digest": {
@@ -671,7 +681,7 @@
}
},
{
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+ "@id": "bids::pb03.$subj.r$run.blur+tlrc",
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"digest": {
@@ -679,7 +689,7 @@
}
},
{
- "@id": "urn:1acb59f0-d174-4fd6-add7-3662f9b53c07",
+ "@id": "bids::rm.mean_r$run+tlrc",
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"digest": {
@@ -687,34 +697,34 @@
}
},
{
- "@id": "urn:7bcc4566-fca1-49a5-88eb-00f9726c62a7",
+ "@id": "bids::rm.mean_r$run",
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"AtLocation": "rm.mean_r$run",
- "GeneratedBy": "urn:d16c50a6-7f32-4b74-b8f3-8f9c5a14d796",
+ "GeneratedBy": "urn:scale-tqb4fi1p",
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},
{
- "@id": "urn:f59a50ab-7372-4da2-bb77-52336a109fac",
+ "@id": "bids::pb04.$subj.r$run.scale",
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"AtLocation": "pb04.$subj.r$run.scale",
- "GeneratedBy": "urn:d16c50a6-7f32-4b74-b8f3-8f9c5a14d796",
+ "GeneratedBy": "urn:scale-tqb4fi1p",
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}
},
{
- "@id": "urn:d4257f34-69b5-4910-a169-f8a8325c1191",
+ "@id": "bids::dfile_rall.1D",
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"AtLocation": "dfile_rall.1D",
- "GeneratedBy": "urn:c62f9d14-a51a-4fee-8038-d735433b3e7c",
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{
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"digest": {
@@ -722,7 +732,7 @@
}
},
{
- "@id": "urn:8b3e58d2-01fa-49f8-a673-9431aaccfc47",
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"AtLocation": "pb04.$subj.r*.scale+tlrc.HEAD",
"digest": {
@@ -730,7 +740,7 @@
}
},
{
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+ "@id": "bids::all_runs.$subj+tlrc%22[$ktrs]%22",
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"digest": {
@@ -738,7 +748,7 @@
}
},
{
- "@id": "urn:30e03dcc-204f-4159-afcc-fcd7efe4664d",
+ "@id": "bids::errts.$%7Bsubj%7D+tlrc%22[$ktrs]%22",
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"AtLocation": "errts.${subj}+tlrc\"[$ktrs]\"",
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@@ -746,7 +756,7 @@
}
},
{
- "@id": "urn:8b77e7f5-fa5d-43fe-a8c3-caf66c861b43",
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"digest": {
@@ -754,7 +764,7 @@
}
},
{
- "@id": "urn:df94604f-7f06-4143-9b98-e624dab2dc66",
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"AtLocation": "rm.noise.all+tlrc",
"digest": {
@@ -762,7 +772,7 @@
}
},
{
- "@id": "urn:41002437-cbf0-4db7-9a60-637d98c15b27",
+ "@id": "bids::errts.$%7Bsubj%7D+tlrc",
"Label": "errts.${subj}",
"AtLocation": "errts.${subj}+tlrc",
"digest": {
@@ -770,7 +780,7 @@
}
},
{
- "@id": "urn:fcef7c15-eb1a-43d0-a496-81c1c8943ae1",
+ "@id": "bids::out.gcor.1D",
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"digest": {
@@ -778,7 +788,7 @@
}
},
{
- "@id": "urn:85f2163f-cfc5-4ede-9da5-a69c4e234514",
+ "@id": "bids::rm.errts.unit+tlrc",
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@@ -786,7 +796,7 @@
}
},
{
- "@id": "urn:b66b5e86-c268-4d21-9bda-3d10f0361c09",
+ "@id": "bids::rm.DP+tlrc",
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"AtLocation": "rm.DP+tlrc",
"digest": {
@@ -794,7 +804,7 @@
}
},
{
- "@id": "urn:d6f63e96-ea88-4593-82e8-42fed8a33dfd",
+ "@id": "bids::X.nocensor.xmat.1D'[3]'",
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@@ -802,7 +812,7 @@
}
},
{
- "@id": "urn:8b5fda69-66b3-4b80-b1b8-4e9f3526efb9",
+ "@id": "bids::X.nocensor.xmat.1D'[4]'",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D'[4]'",
"digest": {
@@ -810,7 +820,7 @@
}
},
{
- "@id": "urn:7c5d805c-8cc9-4593-99f1-fc70e69f54c5",
+ "@id": "bids::X.nocensor.xmat.1D%22[$reg_cols]%22",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D\"[$reg_cols]\"",
"digest": {
@@ -818,133 +828,133 @@
}
},
{
- "@id": "urn:0c2f6818-7e94-4d28-8d58-046bef4826bd",
+ "@id": "bids::motion_demean.1D",
"Label": "motion_demean.1D",
"AtLocation": "motion_demean.1D",
- "GeneratedBy": "urn:ec08b899-bdfa-4f0f-b3fd-8671c1ceea3d",
+ "GeneratedBy": "urn:regress-QBMi7uo8",
"digest": {
"sha256": "1de1e10c0120caa7b6cf441bd141a5a76716e458676ae56ce693039eecb79c85"
}
},
{
- "@id": "urn:224754da-1ea0-40db-a26f-bf12ec3e2c9f",
+ "@id": "bids::motion_deriv.1D",
"Label": "motion_deriv.1D",
"AtLocation": "motion_deriv.1D",
- "GeneratedBy": "urn:ec08b899-bdfa-4f0f-b3fd-8671c1ceea3d",
+ "GeneratedBy": "urn:regress-QBMi7uo8",
"digest": {
"sha256": "47185bf319e91642ad6f2a396a43fc9f8db7b82f2a9aef326bfe4a955120038b"
}
},
{
- "@id": "urn:9daf71b2-6838-42b4-a3e4-bd1d76fe79f9",
+ "@id": "bids::all_runs.$subj",
"Label": "all_runs.$subj",
"AtLocation": "all_runs.$subj",
- "GeneratedBy": "urn:ec08b899-bdfa-4f0f-b3fd-8671c1ceea3d",
+ "GeneratedBy": "urn:regress-QBMi7uo8",
"digest": {
"sha256": "bcf27fc2e339e751d0ea9bba931674c21fd9d434ff411330f4df55f872a8cc7e"
}
},
{
- "@id": "urn:5808802e-2ed8-4307-966b-e5ca05b9ce35",
+ "@id": "bids::rm.signal.all",
"Label": "rm.signal.all",
"AtLocation": "rm.signal.all",
- "GeneratedBy": "urn:ec08b899-bdfa-4f0f-b3fd-8671c1ceea3d",
+ "GeneratedBy": "urn:regress-QBMi7uo8",
"digest": {
"sha256": "bda68a16c0afd5e55d4d7415c8c959e61a9aad7898dd456b0f3bb597363dde31"
}
},
{
- "@id": "urn:66596f41-21e7-4190-82a8-de0697b8d0c6",
+ "@id": "bids::rm.noise.all",
"Label": "rm.noise.all",
"AtLocation": "rm.noise.all",
- "GeneratedBy": "urn:ec08b899-bdfa-4f0f-b3fd-8671c1ceea3d",
+ "GeneratedBy": "urn:regress-QBMi7uo8",
"digest": {
"sha256": "431314eb75d086ce08373b3a374427969e89414c4a2d607e449c1f6485c547af"
}
},
{
- "@id": "urn:29e0b780-0d6b-4417-9475-2753d3da59a3",
+ "@id": "bids::TSNR.$subj",
"Label": "TSNR.$subj",
"AtLocation": "TSNR.$subj",
- "GeneratedBy": "urn:ec08b899-bdfa-4f0f-b3fd-8671c1ceea3d",
+ "GeneratedBy": "urn:regress-QBMi7uo8",
"digest": {
"sha256": "303f183145a1e295686c08335d3b70753777cf0fa0b3f9628cf8de5471359a00"
}
},
{
- "@id": "urn:b463f3ce-4f90-4f0c-8df8-992655455333",
+ "@id": "bids::rm.errts.unit",
"Label": "rm.errts.unit",
"AtLocation": "rm.errts.unit",
- "GeneratedBy": "urn:ec08b899-bdfa-4f0f-b3fd-8671c1ceea3d",
+ "GeneratedBy": "urn:regress-QBMi7uo8",
"digest": {
"sha256": "03b570ad773a00f51ab7e6cdedfebdeca45f5356de0c25f9e3be44d7bf2c7151"
}
},
{
- "@id": "urn:338b602f-d83f-4655-8404-32c1d8fb3a51",
+ "@id": "urn:uuid:98b6f611-15c9-4e5c-9ec8-65792920c9df",
"Label": "-",
"AtLocation": "-",
- "GeneratedBy": "urn:ec08b899-bdfa-4f0f-b3fd-8671c1ceea3d",
+ "GeneratedBy": "urn:regress-QBMi7uo8",
"digest": {
"sha256": "dac304c9f20899ca1ef5aa403e565345fd0ff4ed80c35f82007c9b03a68292b3"
}
},
{
- "@id": "urn:3717a4e1-99f6-4b60-9f13-13f30a9f180d",
+ "@id": "bids::rm.DP",
"Label": "rm.DP",
"AtLocation": "rm.DP",
- "GeneratedBy": "urn:ec08b899-bdfa-4f0f-b3fd-8671c1ceea3d",
+ "GeneratedBy": "urn:regress-QBMi7uo8",
"digest": {
"sha256": "06a0bfbc609c1a06ecf93c479a3288d2911c7f5f3e93cf49c5d26f721c2035ed"
}
},
{
- "@id": "urn:d66f2975-367e-471e-b934-9427c9784ed2",
+ "@id": "bids::corr_brain",
"Label": "corr_brain",
"AtLocation": "corr_brain",
- "GeneratedBy": "urn:ec08b899-bdfa-4f0f-b3fd-8671c1ceea3d",
+ "GeneratedBy": "urn:regress-QBMi7uo8",
"digest": {
"sha256": "74e3aeae0da338b871ab5dc9e8859a4e81fcf1b3c0042cd22fe337eb7baf5eae"
}
},
{
- "@id": "urn:d839cce9-09a1-4f7f-98a1-1111d118824c",
+ "@id": "bids::ideal_tone_counting.1D",
"Label": "ideal_tone_counting.1D",
"AtLocation": "ideal_tone_counting.1D",
- "GeneratedBy": "urn:ec08b899-bdfa-4f0f-b3fd-8671c1ceea3d",
+ "GeneratedBy": "urn:regress-QBMi7uo8",
"digest": {
"sha256": "9bb1cabac5ce7ca19dffa5cd6336a9bf82d362fea2ce9341978406e421b5333c"
}
},
{
- "@id": "urn:18090ee8-2b42-44ac-a89c-2bbc77ce84d2",
+ "@id": "bids::ideal_probe.1D",
"Label": "ideal_probe.1D",
"AtLocation": "ideal_probe.1D",
- "GeneratedBy": "urn:ec08b899-bdfa-4f0f-b3fd-8671c1ceea3d",
+ "GeneratedBy": "urn:regress-QBMi7uo8",
"digest": {
"sha256": "705d93afa8b6ded9f4f572db3f967b54e9906942669af51dd8287a9863bb4288"
}
},
{
- "@id": "urn:813625a1-5cd9-48f5-b1fd-a31afcc8ab5c",
+ "@id": "bids::sum_ideal.1D",
"Label": "sum_ideal.1D",
"AtLocation": "sum_ideal.1D",
- "GeneratedBy": "urn:ec08b899-bdfa-4f0f-b3fd-8671c1ceea3d",
+ "GeneratedBy": "urn:regress-QBMi7uo8",
"digest": {
"sha256": "b2dccadcd84b2d26ec9685c4d1846baf2f11b867f31c36a08748d1c85467b01a"
}
},
{
- "@id": "urn:9f9a7b54-8e6c-416f-9fde-1ef0401fb67a",
+ "@id": "bids::X.stim.xmat.1D",
"Label": "X.stim.xmat.1D",
"AtLocation": "X.stim.xmat.1D",
- "GeneratedBy": "urn:ec08b899-bdfa-4f0f-b3fd-8671c1ceea3d",
+ "GeneratedBy": "urn:regress-QBMi7uo8",
"digest": {
"sha256": "7c61b2f4bbb9eb0cecb19f81faa3a79b94d547b7fb4087ed18e368619e0004e6"
}
},
{
- "@id": "urn:1d5fc7c1-5967-451b-9074-9ecff2ec0f09",
+ "@id": "bids::full_mask.$subj+tlrc",
"Label": "full_mask.$subj",
"AtLocation": "full_mask.$subj+tlrc",
"digest": {
@@ -952,34 +962,34 @@
}
},
{
- "@id": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "@id": "bids::blur.epits.1D",
"Label": "blur.epits.1D",
"AtLocation": "blur.epits.1D",
- "GeneratedBy": "urn:155a15be-dfc8-497f-bcab-b479fbce21c2",
+ "GeneratedBy": "urn:bluresti-a7rUmMml",
"digest": {
"sha256": "623e70a42214e56babc1f1dca156e0b11ba09865dbd6ca9549d54ca2fc601515"
}
},
{
- "@id": "urn:e78b162c-1f30-4cdf-863a-8e2c248887f0",
+ "@id": "bids::blur.errts.1D",
"Label": "blur.errts.1D",
"AtLocation": "blur.errts.1D",
- "GeneratedBy": "urn:155a15be-dfc8-497f-bcab-b479fbce21c2",
+ "GeneratedBy": "urn:bluresti-a7rUmMml",
"digest": {
"sha256": "73969700079b5d3275536ac7eaf0e17571d7e74ec49553b6940f90d5718fc800"
}
},
{
- "@id": "urn:219450be-d458-4eb8-80d4-d28e1d78b728",
+ "@id": "bids::ClustSim",
"Label": "ClustSim",
"AtLocation": "ClustSim",
- "GeneratedBy": "urn:155a15be-dfc8-497f-bcab-b479fbce21c2",
+ "GeneratedBy": "urn:bluresti-a7rUmMml",
"digest": {
"sha256": "2e0cdba2c91902ba12d742a39cb20df66cfd705ba8de767fbf68aae8eb65c6f0"
}
},
{
- "@id": "urn:241187a5-ac48-4a1e-8598-30c933d02e3f",
+ "@id": "bids::pb00.$subj.r*.tcat+orig.HEAD",
"Label": "pb00.$subj.r*.tcat",
"AtLocation": "pb00.$subj.r*.tcat+orig.HEAD",
"digest": {
@@ -987,10 +997,10 @@
}
},
{
- "@id": "urn:711c3b2d-51b7-457e-af1a-8d07e299e9b9",
+ "@id": "bids::-exit0",
"Label": "-exit0",
"AtLocation": "-exit0",
- "GeneratedBy": "urn:f0d6e7fb-50cd-4a57-a20f-f495606ad77b",
+ "GeneratedBy": "urn:autobloc-olTmkcM4",
"digest": {
"sha256": "871a4d3513ed2924cbb10c1c15a196eac4a46a05bdcc248e3bcdb23327b3ad90"
}
diff --git a/examples/from_parsers/afni/afni_thr_clustunck10_proc_block.png b/examples/from_parsers/afni/afni_thr_clustunck10_proc_block.png
index a23521184..cdcf2806e 100644
Binary files a/examples/from_parsers/afni/afni_thr_clustunck10_proc_block.png and b/examples/from_parsers/afni/afni_thr_clustunck10_proc_block.png differ
diff --git a/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc.jsonld b/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc.jsonld
index d4907343f..0197e4aa9 100644
--- a/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc.jsonld
+++ b/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc.jsonld
@@ -4,578 +4,581 @@
"Records": {
"Software": [
{
- "@id": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:afni-tLT3AXf7",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
- "Version": "afni24"
+ "Version": "afni24",
+ "AltIdentifier": "RRID:SCR_005927"
}
],
"Activities": [
{
- "@id": "urn:d2ea33ae-1f76-4b44-890c-f3d725d21da4",
+ "@id": "urn:makedire-xHouasWb",
"Label": "Make directory",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "mkdir $output_dir",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:92b61693-efb7-4c2d-aebb-8faad94ac4ed",
+ "@id": "urn:makedire-ikqUgOGP",
"Label": "Make directory",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "mkdir $output_dir/stimuli",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:8456e1f8-f2ca-4e15-ba7d-728b19b628b1",
+ "@id": "urn:cp-6qkwf0q0",
"Label": "cp",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "cp ./afni_voxelwise_fdr_p005/tone_counting_onset_times.txt ./afni_voxelwise_fdr_p005/tone_counting_probe_duration.txt $output_dir/stimuli",
"Parameters": {},
"Used": [
- "urn:8be00b9f-a0ec-4b9b-9f74-afa0e2539204",
- "urn:d49a081f-daeb-41bb-9197-1595d0e07b8c"
+ "bids::afni_voxelwise_fdr_p005/tone_counting_onset_times.txt",
+ "bids::afni_voxelwise_fdr_p005/tone_counting_probe_duration.txt"
]
},
{
- "@id": "urn:5e17a001-8b17-426f-b998-3a9e2f1ac345",
+ "@id": "urn:3dcopy-8N2iEpYo",
"Label": "3dcopy",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w",
"Parameters": {},
"Used": [
- "urn:2bce5358-e3e1-4ebc-b87f-e4997de984a5"
+ "bids::sub-01_T1w.nii.gz"
]
},
{
- "@id": "urn:680dcb93-a5e5-4c9c-90c1-fc944c597c01",
+ "@id": "urn:3dtcat-zECB7UZU",
"Label": "3dTcat",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Parameters": {},
"Used": [
- "urn:a436f385-0f2b-4f63-9e9f-3fc989a38ba4"
+ "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'"
]
},
{
- "@id": "urn:bfcf1d25-38e5-4fc5-8102-eaf19af9b7e3",
+ "@id": "urn:3dtoutco-zhAFS3NH",
"Label": "3dToutcount",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D",
"Parameters": {},
"Used": [
- "urn:1493a23b-141b-40c4-8fce-42e43fa48cab"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:636ec98c-3655-4048-9bb0-284bea060001",
+ "@id": "urn:cat-pNK8q7O6",
"Label": "cat",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "cat outcount.r*.1D > outcount_rall.1D",
"Parameters": {},
"Used": [
- "urn:be104b26-6320-4707-bd15-ad1549f178d7"
+ "bids::outcount.r*.1D"
]
},
{
- "@id": "urn:beb88253-3826-420a-a7ff-4cd2d080b8a2",
+ "@id": "urn:3dtshift-CbynrLCD",
"Label": "3dTshift",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig",
"Parameters": {},
"Used": [
- "urn:1493a23b-141b-40c4-8fce-42e43fa48cab"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:286200ad-d727-41c1-9a52-8425ccd365e5",
+ "@id": "urn:alignepi-NMFGrarO",
"Label": "align_epi_anat.py",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off",
"Parameters": {},
"Used": [
- "urn:4bfa309f-9cfd-4a8e-a067-25197776aa14",
- "urn:4cc9fc91-8348-47c7-a8b1-4d3afb013835"
+ "bids::pb01.$subj.r01.tshift+orig",
+ "bids::sub-01_T1w+orig"
]
},
{
- "@id": "urn:afe142bc-c35a-4051-910a-ef29f94fd623",
+ "@id": "urn:autotlrc-TSlycvih",
"Label": "@auto_tlrc",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss",
"Parameters": {},
"Used": [
- "urn:6eadba50-fb9c-4d7e-bf72-1b88f1ca5a88",
- "urn:86049fdc-651f-4842-9c9c-97843fe0758a"
+ "bids::TT_N27+tlrc",
+ "bids::sub-01_T1w_ns+orig"
]
},
{
- "@id": "urn:cb8c893f-e445-4427-95f7-59c56cd97693",
+ "@id": "urn:catmatve-HCS5IUyZ",
"Label": "cat_matvec",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D",
"Parameters": {},
"Used": [
- "urn:e05cbe53-170e-4a16-85f7-af70818b0819"
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:a915c231-05a8-4b3d-b46a-4b0fc16d7322",
+ "@id": "urn:3dvolreg-vv7XX0yk",
"Label": "3dvolreg",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig",
"Parameters": {},
"Used": [
- "urn:78ef53dc-3b7e-49d2-aab1-b1fe345584d8"
+ "bids::pb01.$subj.r$run.tshift+orig"
]
},
{
- "@id": "urn:116b6207-b3d0-4d3a-9ab7-aff0a2a05816",
+ "@id": "urn:3dcalc-Cxm5xD74",
"Label": "3dcalc",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1",
"Parameters": {},
"Used": [
- "urn:78ef53dc-3b7e-49d2-aab1-b1fe345584d8"
+ "bids::pb01.$subj.r$run.tshift+orig"
]
},
{
- "@id": "urn:1bcc182c-0ac5-4413-9b83-eecb1f34e34b",
+ "@id": "urn:catmatve-3uuUHbaW",
"Label": "cat_matvec",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D",
"Parameters": {},
"Used": [
- "urn:e05cbe53-170e-4a16-85f7-af70818b0819"
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:9d68b561-06ce-47ff-9fa6-4ac57965c20e",
+ "@id": "urn:3dalline-jEXn2s4t",
"Label": "3dAllineate",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run",
"Parameters": {},
"Used": [
- "urn:6b074efa-a20c-49fa-a8c6-75535054c1d1",
- "urn:78ef53dc-3b7e-49d2-aab1-b1fe345584d8",
- "urn:e2bedf66-d8ac-4e5e-9971-d9e5cca47454"
+ "bids::mat.r$run.warp.aff12.1D",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:685fe902-3622-47ca-a82d-f1576dce6155",
+ "@id": "urn:3dalline-p9hWi9Rx",
"Label": "3dAllineate",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run",
"Parameters": {},
"Used": [
- "urn:6b074efa-a20c-49fa-a8c6-75535054c1d1",
- "urn:e2bedf66-d8ac-4e5e-9971-d9e5cca47454",
- "urn:f8b90f86-9945-4f05-90ee-eefb98cb45a9"
+ "bids::mat.r$run.warp.aff12.1D",
+ "bids::rm.epi.all1+orig",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:7f5afc7c-5e37-484d-b2fb-6e381999e4ef",
+ "@id": "urn:3dtstat-42xTJb5v",
"Label": "3dTstat",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc",
"Parameters": {},
"Used": [
- "urn:d4f48c80-1f94-4011-b6f1-94fc0faed774"
+ "bids::rm.epi.1.r$run+tlrc"
]
},
{
- "@id": "urn:e35beaab-57a1-420d-9217-bf152a1e2ede",
+ "@id": "urn:cat-QxDklpDH",
"Label": "cat",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "cat dfile.r*.1D > dfile_rall.1D",
"Parameters": {},
"Used": [
- "urn:da60e1fe-01dc-4dd7-a2e7-2daf34e5c853"
+ "bids::dfile.r*.1D"
]
},
{
- "@id": "urn:1f1ad99c-0e00-4a95-ba36-5d0dd79158d6",
+ "@id": "urn:3dcopy-YqLNlgfd",
"Label": "3dcopy",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents",
"Parameters": {},
"Used": [
- "urn:4d0b4182-47ba-4a78-bd74-e3f99493f451"
+ "bids::rm.epi.min.r01+tlrc"
]
},
{
- "@id": "urn:e86ccae2-61ff-42f0-b150-66e5f24bf34b",
+ "@id": "urn:3dcalc-nwnpdeD8",
"Label": "3dcalc",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg",
"Parameters": {},
"Used": [
- "urn:1a3eab84-6a4d-46a9-9d8e-4f75db8644f4",
- "urn:678c01d1-55b3-48e4-80a7-50bd58e40b65"
+ "bids::mask_epi_extents+tlrc",
+ "bids::rm.epi.nomask.r$run+tlrc"
]
},
{
- "@id": "urn:97c24bcb-3fcd-4a5e-bd82-05e213699d99",
+ "@id": "urn:3dcopy-sWazpmol",
"Label": "3dcopy",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj",
"Parameters": {},
"Used": [
- "urn:e2bedf66-d8ac-4e5e-9971-d9e5cca47454"
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:798285b2-c0b7-47ff-9dd9-cd8db08a6f5a",
+ "@id": "urn:3dalline-Gkr9wZce",
"Label": "3dAllineate",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped",
"Parameters": {},
"Used": [
- "urn:d7c888ac-cfa4-4ad6-b0f2-68da3b23253d"
+ "bids::anat_final.$subj+tlrc",
+ "bids::warp.anat.Xat.1D"
]
},
{
- "@id": "urn:4d3e09b8-a6d1-4cae-ab6e-518c9140be14",
+ "@id": "urn:3dmerge-DuWTIduU",
"Label": "3dmerge",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc",
"Parameters": {},
"Used": [
- "urn:7ba4e7c7-b024-4437-89fb-12b9fd6d684e",
- "urn:bc261f1d-b44d-4663-8826-2438b4367d0b"
+ "bids::pb02.$subj.r$run.volreg+tlrc",
+ "bids::pb03.$subj.r$run.blur"
]
},
{
- "@id": "urn:9a5ec82b-4187-43d9-9c8e-a2884b7f56c6",
+ "@id": "urn:3dautoma-9uASZijc",
"Label": "3dAutomask",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:74badce5-1fae-46aa-b055-750279abb84b"
+ "bids::pb03.$subj.r$run.blur+tlrc"
]
},
{
- "@id": "urn:93b166eb-4469-4dae-9d65-435cb8462de2",
+ "@id": "urn:3dmaskto-sfwNoLLZ",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:77eff1ab-01eb-4ea7-8085-3efbc9667ede",
+ "@id": "urn:3dresamp-xA6d9Uf6",
"Label": "3dresample",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat",
"Parameters": {},
"Used": [
- "urn:3864259f-5550-45d1-b33a-9df348637636",
- "urn:e2bedf66-d8ac-4e5e-9971-d9e5cca47454"
+ "bids::full_mask.$subj+tlrc",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:312cb241-708c-4709-a23a-9dac9490ae33",
+ "@id": "urn:3dmaskto-ZfejqHaM",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj",
"Parameters": {},
"Used": [
- "urn:01fb4cd3-71f1-4d76-86fb-813344b065d1"
+ "bids::rm.resam.anat+tlrc"
]
},
{
- "@id": "urn:87f188df-c23d-4aa0-bfb6-eb6dd111eab2",
+ "@id": "urn:3dabover-vvyh4Nym",
"Label": "3dABoverlap",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt",
"Parameters": {},
"Used": [
- "urn:7798a257-63de-4a1e-9e79-f2c54807c99f",
- "urn:b134ff18-cea0-4fd7-ba7c-462a43576f99"
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee"
]
},
{
- "@id": "urn:4354a546-b446-40de-b1c1-b7b8dc8dff65",
+ "@id": "urn:3ddot-Yg3gmlJA",
"Label": "3ddot",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt",
"Parameters": {},
"Used": [
- "urn:7798a257-63de-4a1e-9e79-f2c54807c99f",
- "urn:b134ff18-cea0-4fd7-ba7c-462a43576f99"
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee"
]
},
{
- "@id": "urn:5c12f4d7-c86c-4d81-8952-2716bd7cab63",
+ "@id": "urn:3dresamp-XCEnyeM1",
"Label": "3dresample",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc",
"Parameters": {},
"Used": [
- "urn:0056d03a-3a4e-4ad8-a792-e032a7a1b1d4",
- "urn:3864259f-5550-45d1-b33a-9df348637636"
+ "bids::/Users/u1591557/abin/TT_N27+tlrc",
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:06fc7b28-440a-443f-a1ac-d27d1cd48948",
+ "@id": "urn:3dmaskto-MkN1j1sE",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group",
"Parameters": {},
"Used": [
- "urn:a9d7e700-eb28-4f95-96f4-fbb2d456c47a"
+ "bids::rm.resam.group+tlrc"
]
},
{
- "@id": "urn:b4232f97-2855-4e32-bf87-c66ce2b5c029",
+ "@id": "urn:3dtstat-44rAL5NV",
"Label": "3dTstat",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:74badce5-1fae-46aa-b055-750279abb84b"
+ "bids::pb03.$subj.r$run.blur+tlrc"
]
},
{
- "@id": "urn:5f462872-6e3d-45c2-9084-135b50b7d687",
+ "@id": "urn:3dcalc-9DYdW41e",
"Label": "3dcalc",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale",
"Parameters": {},
"Used": [
- "urn:07255a93-153e-49f8-9bc0-72c6b0ffbe4f",
- "urn:1a3eab84-6a4d-46a9-9d8e-4f75db8644f4",
- "urn:74badce5-1fae-46aa-b055-750279abb84b"
+ "bids::mask_epi_extents+tlrc",
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::rm.mean_r$run+tlrc"
]
},
{
- "@id": "urn:05718fb0-06ad-47cc-ba24-7bede3b7fa5f",
+ "@id": "urn:1dtoolpy-3LqsoK7f",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D",
"Parameters": {},
"Used": [
- "urn:a4173802-b0fc-4eb5-9016-9013f1a1852f"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:39a676f4-77df-40f8-acb2-7e28c6080cb9",
+ "@id": "urn:1dtoolpy-EJ9CJXoE",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D",
"Parameters": {},
"Used": [
- "urn:a4173802-b0fc-4eb5-9016-9013f1a1852f"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:aaff34bb-d1d7-4bc8-8027-7b2e3324634d",
+ "@id": "urn:1dtoolpy-gqPPMiGB",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}",
"Parameters": {},
"Used": [
- "urn:a4173802-b0fc-4eb5-9016-9013f1a1852f"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:16931ede-5125-43d4-9542-c658eabfe815",
+ "@id": "urn:3ddeconv-zxISCpbR",
"Label": "3dDeconvolve",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj",
"Parameters": {},
"Used": [
- "urn:b86e0b5f-d758-45a8-8e37-5d1b161349dc"
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD"
]
},
{
- "@id": "urn:b9006899-0e5a-4b73-bba5-5fbe62aaaf70",
+ "@id": "urn:1dtoolpy-VMxL9qLW",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt",
"Parameters": {},
"Used": [
- "urn:5f22ddf2-67d3-4126-8597-d39382d590d7"
+ "bids::X.xmat.1D"
]
},
{
- "@id": "urn:612ba8e4-a321-4ed5-a8db-f058c9714ee1",
+ "@id": "urn:3dtcat-bXpUL2kv",
"Label": "3dTcat",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD",
"Parameters": {},
"Used": [
- "urn:b86e0b5f-d758-45a8-8e37-5d1b161349dc"
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD"
]
},
{
- "@id": "urn:b71fedb7-1f28-46dd-babc-b3262aaed8e3",
+ "@id": "urn:3dtstat-IKAKcmGw",
"Label": "3dTstat",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:6f18de40-659b-4703-ac67-3e1ef791e7dd"
+ "bids::all_runs.$subj+tlrc%22[$ktrs]%22"
]
},
{
- "@id": "urn:fd044b55-392f-4640-b3f2-3b65833d67cc",
+ "@id": "urn:3dtstat-GTXQ0NaI",
"Label": "3dTstat",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:8965832a-ae7b-4dd0-a768-07c2add9c69a"
+ "bids::errts.$%7Bsubj%7D+tlrc%22[$ktrs]%22"
]
},
{
- "@id": "urn:81b58bf8-24f5-4583-852e-b7717232a36c",
+ "@id": "urn:3dcalc-5aWFRDAY",
"Label": "3dcalc",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj",
"Parameters": {},
"Used": [
- "urn:3864259f-5550-45d1-b33a-9df348637636",
- "urn:49bf439f-38c7-4199-8e87-69c80fac13b1",
- "urn:c1e1e658-7814-4772-9a8e-1f78cc2304f6"
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.noise.all+tlrc",
+ "bids::rm.signal.all+tlrc"
]
},
{
- "@id": "urn:3be0b06d-d28f-40c3-ae8f-7e5ee3a243bc",
+ "@id": "urn:3dtnorm-C8LjardN",
"Label": "3dTnorm",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc",
"Parameters": {},
"Used": [
- "urn:c458d0e0-760b-477e-ba6e-3738fb12899d"
+ "bids::errts.$%7Bsubj%7D+tlrc"
]
},
{
- "@id": "urn:3ed53110-62f4-4afb-b4d4-e532ba05c06d",
+ "@id": "urn:3dmaskav-PGPxFIWj",
"Label": "3dmaskave",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D",
"Parameters": {},
- "Used": []
+ "Used": [
+ "bids::full_mask.$subj+tlrc"
+ ]
},
{
- "@id": "urn:630c11dd-1330-4b11-acf6-38a25866bf9b",
+ "@id": "urn:3dtstat-U3O8J2lt",
"Label": "3dTstat",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D",
"Parameters": {},
"Used": [
- "urn:fc0613fa-5fd4-4495-8357-0cd8529d8039"
+ "bids::out.gcor.1D"
]
},
{
- "@id": "urn:de06699c-4240-4cb5-ac86-00f497114b13",
+ "@id": "urn:3dcalc-dnHEfxzV",
"Label": "3dcalc",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP",
"Parameters": {},
"Used": [
- "urn:2145b1ec-29c9-4f38-8fae-e22b03e9d510",
- "urn:9d1166fb-e484-48db-a28a-5096b6f510ac"
+ "bids::gmean.errts.unit.1D",
+ "bids::rm.errts.unit+tlrc"
]
},
{
- "@id": "urn:5ea303c9-2001-4005-8ea5-e21dc774c2ed",
+ "@id": "urn:3dtstat-o7tC0mIS",
"Label": "3dTstat",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc",
"Parameters": {},
"Used": [
- "urn:351af4c6-0a25-41b8-a04a-f7a9e1fbe0f4"
+ "bids::rm.DP+tlrc"
]
},
{
- "@id": "urn:c6d90bd6-3dfb-4883-8769-e2c8ee94f629",
+ "@id": "urn:1dcat-vWKWYGl9",
"Label": "1dcat",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D",
"Parameters": {},
"Used": [
- "urn:e0f7df09-b3b6-46ed-bb81-f50f98b456b3"
+ "bids::X.nocensor.xmat.1D'[3]'"
]
},
{
- "@id": "urn:6b322220-2c90-483b-993b-6483d77b8a9d",
+ "@id": "urn:1dcat-LuD2LyAl",
"Label": "1dcat",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D",
"Parameters": {},
"Used": [
- "urn:37563603-83e1-4a1b-b5fd-3e44180f457c"
+ "bids::X.nocensor.xmat.1D'[4]'"
]
},
{
- "@id": "urn:bce0e9d4-45fc-4c6f-9aa7-73b7ed67b6d6",
+ "@id": "urn:3dtstat-dbJoftKk",
"Label": "3dTstat",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"",
"Parameters": {},
"Used": [
- "urn:5fc04da0-5344-458d-a448-2f39ee9b1aa8"
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:f9a48e5b-69cd-4f1a-97e0-20b485db7038",
+ "@id": "urn:1dcat-JsZglSmL",
"Label": "1dcat",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D",
"Parameters": {},
"Used": [
- "urn:5fc04da0-5344-458d-a448-2f39ee9b1aa8"
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:0a988fde-cf11-40a4-b860-ab7fffd2f7f5",
+ "@id": "urn:3dfwhmx-GscTV8E7",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D",
"Parameters": {},
"Used": [
- "urn:3864259f-5550-45d1-b33a-9df348637636"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:3ae6d58b-af74-4aba-b551-beafc94b9403",
+ "@id": "urn:3dfwhmx-tozyQ3za",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D",
"Parameters": {},
"Used": [
- "urn:3864259f-5550-45d1-b33a-9df348637636"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:53d6fe42-943b-4412-a88b-59d60f4676ce",
+ "@id": "urn:3dclusts-pDD8OMkd",
"Label": "3dClustSim",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim",
"Parameters": {},
"Used": [
- "urn:3864259f-5550-45d1-b33a-9df348637636"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:1e4af6db-76e5-4f56-bb88-54a17fafc89d",
+ "@id": "urn:genepire-JofLi2Iv",
"Label": "gen_epi_review.py",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD",
"Parameters": {},
"Used": [
- "urn:3d020ecb-fd28-407c-b4ee-5440d1a2c024"
+ "bids::pb00.$subj.r*.tcat+orig.HEAD"
]
},
{
- "@id": "urn:3da27e70-7531-4071-b13c-dfa3d43a7765",
+ "@id": "urn:genssrev-6zZrgJp6",
"Label": "gen_ss_review_scripts.py",
- "AssociatedWith": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "AssociatedWith": "urn:afni-tLT3AXf7",
"Command": "gen_ss_review_scripts.py -mot_limit 0.3 -exit0",
"Parameters": {
"-mot_limit": "0.3",
@@ -586,22 +589,22 @@
],
"Entities": [
{
- "@id": "urn:27dbbdf7-0766-4b4c-8637-2b5ce6f14689",
+ "@id": "bids::$output_dir",
"Label": "$output_dir",
"AtLocation": "$output_dir",
- "GeneratedBy": "urn:d2ea33ae-1f76-4b44-890c-f3d725d21da4",
+ "GeneratedBy": "urn:makedire-xHouasWb",
"digest": {
"sha256": "9fa4c635e6533ddf2fed54295920052818d948c3ffe97bc753bd7336b453f8cb"
}
},
{
- "@id": "urn:efbf8bd2-204f-4308-a8a6-b38ea3ed3659",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:92b61693-efb7-4c2d-aebb-8faad94ac4ed"
+ "GeneratedBy": "urn:makedire-ikqUgOGP"
},
{
- "@id": "urn:8be00b9f-a0ec-4b9b-9f74-afa0e2539204",
+ "@id": "bids::afni_voxelwise_fdr_p005/tone_counting_onset_times.txt",
"Label": "tone_counting_onset_times.txt",
"AtLocation": "./afni_voxelwise_fdr_p005/tone_counting_onset_times.txt",
"digest": {
@@ -609,7 +612,7 @@
}
},
{
- "@id": "urn:d49a081f-daeb-41bb-9197-1595d0e07b8c",
+ "@id": "bids::afni_voxelwise_fdr_p005/tone_counting_probe_duration.txt",
"Label": "tone_counting_probe_duration.txt",
"AtLocation": "./afni_voxelwise_fdr_p005/tone_counting_probe_duration.txt",
"digest": {
@@ -617,13 +620,13 @@
}
},
{
- "@id": "urn:9aaf2d76-fdcb-465d-9248-7743685b85e0",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:8456e1f8-f2ca-4e15-ba7d-728b19b628b1"
+ "GeneratedBy": "urn:cp-6qkwf0q0"
},
{
- "@id": "urn:2bce5358-e3e1-4ebc-b87f-e4997de984a5",
+ "@id": "bids::sub-01_T1w.nii.gz",
"Label": "sub-01_T1w.nii.gz",
"AtLocation": "sub-01_T1w.nii.gz",
"digest": {
@@ -631,13 +634,13 @@
}
},
{
- "@id": "urn:9aaacc92-ad1f-44d1-b791-010d10a306c4",
+ "@id": "bids::$output_dir/sub-01_T1w",
"Label": "sub-01_T1w",
"AtLocation": "$output_dir/sub-01_T1w",
- "GeneratedBy": "urn:5e17a001-8b17-426f-b998-3a9e2f1ac345"
+ "GeneratedBy": "urn:3dcopy-8N2iEpYo"
},
{
- "@id": "urn:a436f385-0f2b-4f63-9e9f-3fc989a38ba4",
+ "@id": "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Label": "sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"digest": {
@@ -645,13 +648,13 @@
}
},
{
- "@id": "urn:e7565259-771d-4514-b0f8-511867fdf0d4",
+ "@id": "bids::$output_dir/pb00.$subj.r01.tcat",
"Label": "pb00.$subj.r01.tcat",
"AtLocation": "$output_dir/pb00.$subj.r01.tcat",
- "GeneratedBy": "urn:680dcb93-a5e5-4c9c-90c1-fc944c597c01"
+ "GeneratedBy": "urn:3dtcat-zECB7UZU"
},
{
- "@id": "urn:1493a23b-141b-40c4-8fce-42e43fa48cab",
+ "@id": "bids::pb00.$subj.r$run.tcat+orig",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -659,16 +662,16 @@
}
},
{
- "@id": "urn:9ea288a7-91a6-4d8b-a363-f91ed2bb234d",
+ "@id": "bids::outcount.r$run.1D",
"Label": "outcount.r$run.1D",
"AtLocation": "outcount.r$run.1D",
- "GeneratedBy": "urn:bfcf1d25-38e5-4fc5-8102-eaf19af9b7e3",
+ "GeneratedBy": "urn:3dtoutco-zhAFS3NH",
"digest": {
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}
},
{
- "@id": "urn:be104b26-6320-4707-bd15-ad1549f178d7",
+ "@id": "bids::outcount.r*.1D",
"Label": "outcount.r*.1D",
"AtLocation": "outcount.r*.1D",
"digest": {
@@ -676,25 +679,25 @@
}
},
{
- "@id": "urn:89dafdd6-e4c2-414e-8682-1fff8940a2aa",
+ "@id": "bids::outcount_rall.1D",
"Label": "outcount_rall.1D",
"AtLocation": "outcount_rall.1D",
- "GeneratedBy": "urn:636ec98c-3655-4048-9bb0-284bea060001",
+ "GeneratedBy": "urn:cat-pNK8q7O6",
"digest": {
"sha256": "cb887fd5e4d5e9acb3a24820d0f7a62ed38a5ffb0fdedd373440ac0219fb186a"
}
},
{
- "@id": "urn:c6382124-21af-41e5-8d48-6db6ccdc8117",
+ "@id": "bids::pb01.$subj.r$run.tshift",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift",
- "GeneratedBy": "urn:beb88253-3826-420a-a7ff-4cd2d080b8a2",
+ "GeneratedBy": "urn:3dtshift-CbynrLCD",
"digest": {
"sha256": "c6bf01cea8d2eac1d7a866f80b865c6e7d4b4e012dbb63d480ac9a8551162d72"
}
},
{
- "@id": "urn:4bfa309f-9cfd-4a8e-a067-25197776aa14",
+ "@id": "bids::sub-01_T1w+orig",
"Label": "sub-01_T1w",
"AtLocation": "sub-01_T1w+orig",
"digest": {
@@ -702,7 +705,7 @@
}
},
{
- "@id": "urn:4cc9fc91-8348-47c7-a8b1-4d3afb013835",
+ "@id": "bids::pb01.$subj.r01.tshift+orig",
"Label": "pb01.$subj.r01.tshift",
"AtLocation": "pb01.$subj.r01.tshift+orig",
"digest": {
@@ -710,16 +713,16 @@
}
},
{
- "@id": "urn:1f2a2915-43a9-4fe1-b64f-de93ec4d4b9f",
+ "@id": "bids::_al_junk",
"Label": "_al_junk",
"AtLocation": "_al_junk",
- "GeneratedBy": "urn:286200ad-d727-41c1-9a52-8425ccd365e5",
+ "GeneratedBy": "urn:alignepi-NMFGrarO",
"digest": {
"sha256": "bd785a075a4c6446e1e54de9e628913f7f1c814e86b69a9fbfe933209e6d37b5"
}
},
{
- "@id": "urn:6eadba50-fb9c-4d7e-bf72-1b88f1ca5a88",
+ "@id": "bids::TT_N27+tlrc",
"Label": "TT_N27",
"AtLocation": "TT_N27+tlrc",
"digest": {
@@ -727,7 +730,7 @@
}
},
{
- "@id": "urn:86049fdc-651f-4842-9c9c-97843fe0758a",
+ "@id": "bids::sub-01_T1w_ns+orig",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+orig",
"digest": {
@@ -735,7 +738,7 @@
}
},
{
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@@ -743,16 +746,16 @@
}
},
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+ "@id": "bids::warp.anat.Xat.1D",
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"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:cb8c893f-e445-4427-95f7-59c56cd97693",
+ "GeneratedBy": "urn:catmatve-HCS5IUyZ",
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"AtLocation": "pb01.$subj.r$run.tshift+orig",
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@@ -760,34 +763,34 @@
}
},
{
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"AtLocation": "mat.r$run.vr.aff12.1D",
- "GeneratedBy": "urn:a915c231-05a8-4b3d-b46a-4b0fc16d7322",
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{
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+ "@id": "bids::rm.epi.all1",
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"AtLocation": "rm.epi.all1",
- "GeneratedBy": "urn:116b6207-b3d0-4d3a-9ab7-aff0a2a05816",
+ "GeneratedBy": "urn:3dcalc-Cxm5xD74",
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{
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"AtLocation": "mat.r$run.warp.aff12.1D",
- "GeneratedBy": "urn:1bcc182c-0ac5-4413-9b83-eecb1f34e34b",
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{
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"digest": {
@@ -795,16 +798,16 @@
}
},
{
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"AtLocation": "rm.epi.nomask.r$run",
- "GeneratedBy": "urn:9d68b561-06ce-47ff-9fa6-4ac57965c20e",
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@@ -812,16 +815,16 @@
}
},
{
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- "GeneratedBy": "urn:685fe902-3622-47ca-a82d-f1576dce6155",
+ "GeneratedBy": "urn:3dalline-p9hWi9Rx",
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@@ -829,16 +832,16 @@
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- "GeneratedBy": "urn:7f5afc7c-5e37-484d-b2fb-6e381999e4ef",
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"digest": {
@@ -846,16 +849,16 @@
}
},
{
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- "GeneratedBy": "urn:e35beaab-57a1-420d-9217-bf152a1e2ede",
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@@ -863,16 +866,16 @@
}
},
{
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- "GeneratedBy": "urn:1f1ad99c-0e00-4a95-ba36-5d0dd79158d6",
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{
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@@ -880,7 +883,7 @@
}
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{
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"digest": {
@@ -888,34 +891,42 @@
}
},
{
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"AtLocation": "pb02.$subj.r$run.volreg",
- "GeneratedBy": "urn:e86ccae2-61ff-42f0-b150-66e5f24bf34b",
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{
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"AtLocation": "anat_final.$subj",
- "GeneratedBy": "urn:97c24bcb-3fcd-4a5e-bd82-05e213699d99",
+ "GeneratedBy": "urn:3dcopy-sWazpmol",
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{
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+ "AtLocation": "anat_final.$subj+tlrc",
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- "GeneratedBy": "urn:798285b2-c0b7-47ff-9dd9-cd8db08a6f5a",
+ "GeneratedBy": "urn:3dalline-Gkr9wZce",
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{
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@@ -923,7 +934,7 @@
}
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{
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@@ -931,7 +942,7 @@
}
},
{
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"digest": {
@@ -939,25 +950,25 @@
}
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{
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{
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- "GeneratedBy": "urn:93b166eb-4469-4dae-9d65-435cb8462de2",
+ "GeneratedBy": "urn:3dmaskto-sfwNoLLZ",
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"digest": {
@@ -965,16 +976,16 @@
}
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{
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@@ -982,16 +993,16 @@
}
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{
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{
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"digest": {
@@ -999,7 +1010,7 @@
}
},
{
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@@ -1007,7 +1018,7 @@
}
},
{
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+ "@id": "bids::/Users/u1591557/abin/TT_N27+tlrc",
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"digest": {
@@ -1015,16 +1026,16 @@
}
},
{
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+ "@id": "bids::rm.resam.group",
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- "GeneratedBy": "urn:5c12f4d7-c86c-4d81-8952-2716bd7cab63",
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{
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@@ -1032,25 +1043,25 @@
}
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{
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- "GeneratedBy": "urn:06fc7b28-440a-443f-a1ac-d27d1cd48948",
+ "GeneratedBy": "urn:3dmaskto-MkN1j1sE",
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{
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+ "@id": "bids::rm.mean_r$run",
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- "GeneratedBy": "urn:b4232f97-2855-4e32-bf87-c66ce2b5c029",
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@@ -1058,34 +1069,34 @@
}
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{
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{
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+ "@id": "bids::motion_demean.1D",
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+ "GeneratedBy": "urn:1dtoolpy-3LqsoK7f",
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{
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- "GeneratedBy": "urn:39a676f4-77df-40f8-acb2-7e28c6080cb9",
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@@ -1093,25 +1104,25 @@
}
},
{
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- "GeneratedBy": "urn:16931ede-5125-43d4-9542-c658eabfe815",
+ "GeneratedBy": "urn:3ddeconv-zxISCpbR",
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{
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- "GeneratedBy": "urn:612ba8e4-a321-4ed5-a8db-f058c9714ee1",
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{
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"digest": {
@@ -1119,16 +1130,16 @@
}
},
{
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- "GeneratedBy": "urn:b71fedb7-1f28-46dd-babc-b3262aaed8e3",
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{
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+ "@id": "bids::errts.$%7Bsubj%7D+tlrc%22[$ktrs]%22",
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"digest": {
@@ -1136,16 +1147,16 @@
}
},
{
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+ "@id": "bids::rm.noise.all",
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- "GeneratedBy": "urn:fd044b55-392f-4640-b3f2-3b65833d67cc",
+ "GeneratedBy": "urn:3dtstat-GTXQ0NaI",
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@@ -1153,7 +1164,7 @@
}
},
{
- "@id": "urn:c1e1e658-7814-4772-9a8e-1f78cc2304f6",
+ "@id": "bids::rm.noise.all+tlrc",
"Label": "rm.noise.all",
"AtLocation": "rm.noise.all+tlrc",
"digest": {
@@ -1161,16 +1172,16 @@
}
},
{
- "@id": "urn:375c7dcd-2880-43fb-8f1b-194947fd0df1",
+ "@id": "bids::TSNR.$subj",
"Label": "TSNR.$subj",
"AtLocation": "TSNR.$subj",
- "GeneratedBy": "urn:81b58bf8-24f5-4583-852e-b7717232a36c",
+ "GeneratedBy": "urn:3dcalc-5aWFRDAY",
"digest": {
"sha256": "303f183145a1e295686c08335d3b70753777cf0fa0b3f9628cf8de5471359a00"
}
},
{
- "@id": "urn:c458d0e0-760b-477e-ba6e-3738fb12899d",
+ "@id": "bids::errts.$%7Bsubj%7D+tlrc",
"Label": "errts.${subj}",
"AtLocation": "errts.${subj}+tlrc",
"digest": {
@@ -1178,25 +1189,25 @@
}
},
{
- "@id": "urn:5b3c5241-a423-4108-baa3-13f05f4fff33",
+ "@id": "bids::rm.errts.unit",
"Label": "rm.errts.unit",
"AtLocation": "rm.errts.unit",
- "GeneratedBy": "urn:3be0b06d-d28f-40c3-ae8f-7e5ee3a243bc",
+ "GeneratedBy": "urn:3dtnorm-C8LjardN",
"digest": {
"sha256": "03b570ad773a00f51ab7e6cdedfebdeca45f5356de0c25f9e3be44d7bf2c7151"
}
},
{
- "@id": "urn:9d1166fb-e484-48db-a28a-5096b6f510ac",
+ "@id": "bids::gmean.errts.unit.1D",
"Label": "gmean.errts.unit.1D",
"AtLocation": "gmean.errts.unit.1D",
- "GeneratedBy": "urn:3ed53110-62f4-4afb-b4d4-e532ba05c06d",
+ "GeneratedBy": "urn:3dmaskav-PGPxFIWj",
"digest": {
"sha256": "a35a66cce2e2d487762823c197ca1edc450a9887f46f125826b69c5021662f95"
}
},
{
- "@id": "urn:fc0613fa-5fd4-4495-8357-0cd8529d8039",
+ "@id": "bids::out.gcor.1D",
"Label": "out.gcor.1D",
"AtLocation": "out.gcor.1D",
"digest": {
@@ -1204,16 +1215,16 @@
}
},
{
- "@id": "urn:7b132978-d935-41d5-8649-09988bf6e150",
+ "@id": "urn:uuid:ca75045e-e6e1-4f42-b342-11111042cfd4",
"Label": "-",
"AtLocation": "-",
- "GeneratedBy": "urn:630c11dd-1330-4b11-acf6-38a25866bf9b",
+ "GeneratedBy": "urn:3dtstat-U3O8J2lt",
"digest": {
"sha256": "dac304c9f20899ca1ef5aa403e565345fd0ff4ed80c35f82007c9b03a68292b3"
}
},
{
- "@id": "urn:2145b1ec-29c9-4f38-8fae-e22b03e9d510",
+ "@id": "bids::rm.errts.unit+tlrc",
"Label": "rm.errts.unit",
"AtLocation": "rm.errts.unit+tlrc",
"digest": {
@@ -1221,16 +1232,16 @@
}
},
{
- "@id": "urn:9db814a8-1bcc-44c3-983e-9df4ee6fe2dd",
+ "@id": "bids::rm.DP",
"Label": "rm.DP",
"AtLocation": "rm.DP",
- "GeneratedBy": "urn:de06699c-4240-4cb5-ac86-00f497114b13",
+ "GeneratedBy": "urn:3dcalc-dnHEfxzV",
"digest": {
"sha256": "06a0bfbc609c1a06ecf93c479a3288d2911c7f5f3e93cf49c5d26f721c2035ed"
}
},
{
- "@id": "urn:351af4c6-0a25-41b8-a04a-f7a9e1fbe0f4",
+ "@id": "bids::rm.DP+tlrc",
"Label": "rm.DP",
"AtLocation": "rm.DP+tlrc",
"digest": {
@@ -1238,16 +1249,16 @@
}
},
{
- "@id": "urn:7ade7234-672e-4949-8cac-ddb7c085f8e3",
+ "@id": "bids::corr_brain",
"Label": "corr_brain",
"AtLocation": "corr_brain",
- "GeneratedBy": "urn:5ea303c9-2001-4005-8ea5-e21dc774c2ed",
+ "GeneratedBy": "urn:3dtstat-o7tC0mIS",
"digest": {
"sha256": "74e3aeae0da338b871ab5dc9e8859a4e81fcf1b3c0042cd22fe337eb7baf5eae"
}
},
{
- "@id": "urn:e0f7df09-b3b6-46ed-bb81-f50f98b456b3",
+ "@id": "bids::X.nocensor.xmat.1D'[3]'",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D'[3]'",
"digest": {
@@ -1255,16 +1266,16 @@
}
},
{
- "@id": "urn:ecb26611-af49-4f77-9041-82a002d7c2d5",
+ "@id": "bids::ideal_tone_counting.1D",
"Label": "ideal_tone_counting.1D",
"AtLocation": "ideal_tone_counting.1D",
- "GeneratedBy": "urn:c6d90bd6-3dfb-4883-8769-e2c8ee94f629",
+ "GeneratedBy": "urn:1dcat-vWKWYGl9",
"digest": {
"sha256": "9bb1cabac5ce7ca19dffa5cd6336a9bf82d362fea2ce9341978406e421b5333c"
}
},
{
- "@id": "urn:37563603-83e1-4a1b-b5fd-3e44180f457c",
+ "@id": "bids::X.nocensor.xmat.1D'[4]'",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D'[4]'",
"digest": {
@@ -1272,16 +1283,16 @@
}
},
{
- "@id": "urn:83c705c4-10e0-4063-9745-7ebce793f929",
+ "@id": "bids::ideal_probe.1D",
"Label": "ideal_probe.1D",
"AtLocation": "ideal_probe.1D",
- "GeneratedBy": "urn:6b322220-2c90-483b-993b-6483d77b8a9d",
+ "GeneratedBy": "urn:1dcat-LuD2LyAl",
"digest": {
"sha256": "705d93afa8b6ded9f4f572db3f967b54e9906942669af51dd8287a9863bb4288"
}
},
{
- "@id": "urn:5fc04da0-5344-458d-a448-2f39ee9b1aa8",
+ "@id": "bids::X.nocensor.xmat.1D%22[$reg_cols]%22",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D\"[$reg_cols]\"",
"digest": {
@@ -1289,52 +1300,52 @@
}
},
{
- "@id": "urn:3fa86845-cc78-4a61-9b14-b2b6cd058b34",
+ "@id": "bids::sum_ideal.1D",
"Label": "sum_ideal.1D",
"AtLocation": "sum_ideal.1D",
- "GeneratedBy": "urn:bce0e9d4-45fc-4c6f-9aa7-73b7ed67b6d6",
+ "GeneratedBy": "urn:3dtstat-dbJoftKk",
"digest": {
"sha256": "b2dccadcd84b2d26ec9685c4d1846baf2f11b867f31c36a08748d1c85467b01a"
}
},
{
- "@id": "urn:70d7aa44-9486-4d80-a553-314541d0689f",
+ "@id": "bids::X.stim.xmat.1D",
"Label": "X.stim.xmat.1D",
"AtLocation": "X.stim.xmat.1D",
- "GeneratedBy": "urn:f9a48e5b-69cd-4f1a-97e0-20b485db7038",
+ "GeneratedBy": "urn:1dcat-JsZglSmL",
"digest": {
"sha256": "7c61b2f4bbb9eb0cecb19f81faa3a79b94d547b7fb4087ed18e368619e0004e6"
}
},
{
- "@id": "urn:4d776027-1b79-454d-b119-8be7428aa40a",
+ "@id": "bids::blur.epits.1D",
"Label": "blur.epits.1D",
"AtLocation": "blur.epits.1D",
- "GeneratedBy": "urn:0a988fde-cf11-40a4-b860-ab7fffd2f7f5",
+ "GeneratedBy": "urn:3dfwhmx-GscTV8E7",
"digest": {
"sha256": "623e70a42214e56babc1f1dca156e0b11ba09865dbd6ca9549d54ca2fc601515"
}
},
{
- "@id": "urn:37fc37c6-0fb5-4dfd-a2db-533863b130fc",
+ "@id": "bids::blur.errts.1D",
"Label": "blur.errts.1D",
"AtLocation": "blur.errts.1D",
- "GeneratedBy": "urn:3ae6d58b-af74-4aba-b551-beafc94b9403",
+ "GeneratedBy": "urn:3dfwhmx-tozyQ3za",
"digest": {
"sha256": "73969700079b5d3275536ac7eaf0e17571d7e74ec49553b6940f90d5718fc800"
}
},
{
- "@id": "urn:056dd331-56c7-4481-9025-6a972c52f7af",
+ "@id": "bids::ClustSim",
"Label": "ClustSim",
"AtLocation": "ClustSim",
- "GeneratedBy": "urn:53d6fe42-943b-4412-a88b-59d60f4676ce",
+ "GeneratedBy": "urn:3dclusts-pDD8OMkd",
"digest": {
"sha256": "2e0cdba2c91902ba12d742a39cb20df66cfd705ba8de767fbf68aae8eb65c6f0"
}
},
{
- "@id": "urn:3d020ecb-fd28-407c-b4ee-5440d1a2c024",
+ "@id": "bids::pb00.$subj.r*.tcat+orig.HEAD",
"Label": "pb00.$subj.r*.tcat",
"AtLocation": "pb00.$subj.r*.tcat+orig.HEAD",
"digest": {
@@ -1342,10 +1353,10 @@
}
},
{
- "@id": "urn:b85723e2-2634-41a2-b745-ce014c138e48",
+ "@id": "bids::-exit0",
"Label": "-exit0",
"AtLocation": "-exit0",
- "GeneratedBy": "urn:3da27e70-7531-4071-b13c-dfa3d43a7765",
+ "GeneratedBy": "urn:genssrev-6zZrgJp6",
"digest": {
"sha256": "871a4d3513ed2924cbb10c1c15a196eac4a46a05bdcc248e3bcdb23327b3ad90"
}
diff --git a/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc.png b/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc.png
index aabdb8171..64037be11 100644
Binary files a/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc.png and b/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc.png differ
diff --git a/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc_block.jsonld b/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc_block.jsonld
index e27677c1c..9d6700ce9 100644
--- a/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc_block.jsonld
+++ b/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc_block.jsonld
@@ -4,187 +4,189 @@
"Records": {
"Software": [
{
- "@id": "urn:2f56c0f2-f0d5-4997-9cb7-dc9136310252",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:afni-bx6q4Oas",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
- "Version": "afni24"
+ "Version": "afni24",
+ "AltIdentifier": "RRID:SCR_005927"
}
],
"Activities": [
{
- "@id": "urn:5e4c7270-4828-4ea5-9229-b98f490e9bbc",
+ "@id": "urn:autobloc-Lb7mU4cg",
"Label": "auto block: setup",
- "AssociatedWith": "urn:2f56c0f2-f0d5-4997-9cb7-dc9136310252",
+ "AssociatedWith": "urn:afni-bx6q4Oas",
"Command": "mkdir $output_dir; mkdir $output_dir/stimuli; cp ./afni_voxelwise_fdr_p005/tone_counting_onset_times.txt ./afni_voxelwise_fdr_p005/tone_counting_probe_duration.txt $output_dir/stimuli; 3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w; ",
"Used": [
- "urn:5634518e-8272-499c-ab40-b15f1a0d7d8a",
- "urn:c78c31e5-b426-479e-962a-b525066ac296",
- "urn:3e6bfd7e-087f-4f51-afb1-882eb4cbe149"
+ "bids::afni_voxelwise_fdr_p005/tone_counting_onset_times.txt",
+ "bids::afni_voxelwise_fdr_p005/tone_counting_probe_duration.txt",
+ "bids::sub-01_T1w.nii.gz"
]
},
{
- "@id": "urn:54e53611-1185-4cbc-a135-6669556584ba",
+ "@id": "urn:autobloc-rUFvnhtZ",
"Label": "auto block: tcat",
- "AssociatedWith": "urn:2f56c0f2-f0d5-4997-9cb7-dc9136310252",
+ "AssociatedWith": "urn:afni-bx6q4Oas",
"Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ",
"Used": [
- "urn:9a8a0caf-982f-4090-b178-7415ef5842b0"
+ "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'"
]
},
{
- "@id": "urn:6441239c-3ff4-45ce-a136-41bf8e6fd33a",
+ "@id": "urn:autobloc-MMJBhghb",
"Label": "auto block: outcount",
- "AssociatedWith": "urn:2f56c0f2-f0d5-4997-9cb7-dc9136310252",
+ "AssociatedWith": "urn:afni-bx6q4Oas",
"Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ",
"Used": [
- "urn:150a7ce4-f3d0-43dd-81a6-637409ba5481",
- "urn:7abc0423-3682-48cf-8806-fee1a3fb186c"
+ "bids::pb00.$subj.r$run.tcat+orig",
+ "bids::outcount.r*.1D"
]
},
{
- "@id": "urn:c8f49f12-8b13-478c-80d8-2e5352fe372b",
+ "@id": "urn:tshift-9jkHUP80",
"Label": "tshift",
- "AssociatedWith": "urn:2f56c0f2-f0d5-4997-9cb7-dc9136310252",
+ "AssociatedWith": "urn:afni-bx6q4Oas",
"Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ",
"Used": [
- "urn:150a7ce4-f3d0-43dd-81a6-637409ba5481"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:8ae18fa4-72c3-4ea6-9635-4c952e84bbcc",
+ "@id": "urn:align-j9wdpba6",
"Label": "align",
- "AssociatedWith": "urn:2f56c0f2-f0d5-4997-9cb7-dc9136310252",
+ "AssociatedWith": "urn:afni-bx6q4Oas",
"Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ",
"Used": [
- "urn:420cd2a7-49c9-4fcb-a221-45d7da289ec3",
- "urn:6db2c440-a1c5-4be4-be37-c75b9faba368"
+ "bids::pb01.$subj.r01.tshift+orig",
+ "bids::sub-01_T1w+orig"
]
},
{
- "@id": "urn:f1f9f4c6-2c36-47a6-afba-6dedde47c8e1",
+ "@id": "urn:tlrc-D1HWOqFx",
"Label": "tlrc",
- "AssociatedWith": "urn:2f56c0f2-f0d5-4997-9cb7-dc9136310252",
+ "AssociatedWith": "urn:afni-bx6q4Oas",
"Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ",
"Used": [
- "urn:8dc86011-0121-48e3-945d-edfafd138b17",
- "urn:cb8bda64-2c63-42e4-8f16-df3a7449ba41",
- "urn:58675ac0-241a-40e0-8600-1775c2221c7b"
+ "bids::TT_N27+tlrc",
+ "bids::sub-01_T1w_ns+orig",
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:75cc4aa9-4afb-4375-9045-4fc9c45c506a",
+ "@id": "urn:volreg-z9mTiN6d",
"Label": "volreg",
- "AssociatedWith": "urn:2f56c0f2-f0d5-4997-9cb7-dc9136310252",
+ "AssociatedWith": "urn:afni-bx6q4Oas",
"Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig; 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1; cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D; 3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run; 3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run; 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc; cat dfile.r*.1D > dfile_rall.1D; 3dcopy rm.epi.min.r01+tlrc mask_epi_extents; 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg; 3dcopy sub-01_T1w_ns+tlrc anat_final.$subj; 3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped; ",
"Used": [
- "urn:ac224873-aa4f-43e1-bce8-57961761c3b5",
- "urn:ac224873-aa4f-43e1-bce8-57961761c3b5",
- "urn:58675ac0-241a-40e0-8600-1775c2221c7b",
- "urn:6c939c93-038f-484b-8362-0d7ccb01dfa4",
- "urn:ac224873-aa4f-43e1-bce8-57961761c3b5",
- "urn:6c939c93-038f-484b-8362-0d7ccb01dfa4",
- "urn:915a73a0-d2c9-476c-bb2b-55f6b431b745",
- "urn:d9f85d96-c33c-411a-8cfa-c8de426d250a",
- "urn:576ad643-bad3-45b6-a625-e9823c45c0af",
- "urn:48aae18d-fcff-4f4d-bbd4-d8262dc89ce4",
- "urn:48863a0d-1cea-4233-887c-2754a9ff4167",
- "urn:48a66e58-4e4c-451e-9433-857a97c1851c",
- "urn:6c939c93-038f-484b-8362-0d7ccb01dfa4",
- "urn:05033224-1bed-4f2e-904f-113e6309a493"
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.epi.all1+orig",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.epi.1.r$run+tlrc",
+ "bids::dfile.r*.1D",
+ "bids::rm.epi.min.r01+tlrc",
+ "bids::mask_epi_extents+tlrc",
+ "bids::rm.epi.nomask.r$run+tlrc",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::anat_final.$subj+tlrc",
+ "bids::warp.anat.Xat.1D"
]
},
{
- "@id": "urn:00952bcd-b9f3-4b91-8e31-bc58ddbf8082",
+ "@id": "urn:blur-ZFrDByJZ",
"Label": "blur",
- "AssociatedWith": "urn:2f56c0f2-f0d5-4997-9cb7-dc9136310252",
+ "AssociatedWith": "urn:afni-bx6q4Oas",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc; ",
"Used": [
- "urn:19e29262-d365-463f-971e-ea6537b869f9",
- "urn:69de28c5-0c0c-45ce-8afb-bd975bea590c"
+ "bids::pb02.$subj.r$run.volreg+tlrc",
+ "bids::pb03.$subj.r$run.blur"
]
},
{
- "@id": "urn:63610069-101d-41c4-ac02-dde249b45c74",
+ "@id": "urn:mask-2jbzY0kR",
"Label": "mask",
- "AssociatedWith": "urn:2f56c0f2-f0d5-4997-9cb7-dc9136310252",
+ "AssociatedWith": "urn:afni-bx6q4Oas",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc; 3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj; 3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj; 3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt; 3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt; 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group; ",
"Used": [
- "urn:b83b346d-bbf3-4ad0-bf40-e52d3ebfca17",
- "urn:6c939c93-038f-484b-8362-0d7ccb01dfa4",
- "urn:cb2c6935-c344-43e3-8766-cf55331e5fdb",
- "urn:825794b7-217b-455b-8d55-754a7cea5c55",
- "urn:36267516-ae53-4c72-80b2-9670e20b5dc5",
- "urn:4ca2274b-4907-4b0a-9929-b002870fc68f",
- "urn:36267516-ae53-4c72-80b2-9670e20b5dc5",
- "urn:4ca2274b-4907-4b0a-9929-b002870fc68f",
- "urn:91373dd3-513c-4e6a-a1a1-b11ca3ab6fd7",
- "urn:cb2c6935-c344-43e3-8766-cf55331e5fdb",
- "urn:e5e65692-048e-4f65-ad68-27b7c20b876b"
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.resam.anat+tlrc",
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee",
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee",
+ "bids::/Users/u1591557/abin/TT_N27+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.resam.group+tlrc"
]
},
{
- "@id": "urn:dba88ff1-79ae-4867-97c3-3685b147c297",
+ "@id": "urn:scale-3YoozkFZ",
"Label": "scale",
- "AssociatedWith": "urn:2f56c0f2-f0d5-4997-9cb7-dc9136310252",
+ "AssociatedWith": "urn:afni-bx6q4Oas",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc; 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale; ",
"Used": [
- "urn:b83b346d-bbf3-4ad0-bf40-e52d3ebfca17",
- "urn:04d86c72-4729-4d2f-b96e-5528baeb3bb0",
- "urn:48a66e58-4e4c-451e-9433-857a97c1851c",
- "urn:b83b346d-bbf3-4ad0-bf40-e52d3ebfca17"
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::mask_epi_extents+tlrc",
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::rm.mean_r$run+tlrc"
]
},
{
- "@id": "urn:a2872607-ec43-4a31-9ead-e326632837bf",
+ "@id": "urn:regress-TUuT4CNb",
"Label": "regress",
- "AssociatedWith": "urn:2f56c0f2-f0d5-4997-9cb7-dc9136310252",
+ "AssociatedWith": "urn:afni-bx6q4Oas",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}; 3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj; 1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt; 3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD; 3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"; 3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"; 3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj; 3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc; 3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D; 3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D; 3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP; 3dTstat -sum -prefix corr_brain rm.DP+tlrc; 1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D; 1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D; 3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"; 1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D; ",
"Used": [
- "urn:340ac867-6732-4a1b-a9db-70fd07d8285f",
- "urn:340ac867-6732-4a1b-a9db-70fd07d8285f",
- "urn:340ac867-6732-4a1b-a9db-70fd07d8285f",
- "urn:155cfa56-dccb-49ee-954d-0d5fae018142",
- "urn:155cfa56-dccb-49ee-954d-0d5fae018142",
- "urn:8106c673-1b79-48c9-ae6b-659c565e75c5",
- "urn:c2efd8eb-72e0-41e9-921d-fec41f42856b",
- "urn:b40ccf75-ad84-4a4b-9482-2c31e4498ef0",
- "urn:cb2c6935-c344-43e3-8766-cf55331e5fdb",
- "urn:cef3da7d-292c-4710-b2bd-4f672b9326e7",
- "urn:9d505fad-bfb4-4d42-9041-d332f14f09ef",
- "urn:087865c4-2517-4b7c-a084-f175c515884c",
- "urn:87456180-00b3-4cc9-994f-62bb929164b8",
- "urn:9d464330-204c-4836-8e63-7577201ac4c2",
- "urn:117d50be-276e-44b9-a974-59a90cdc308c",
- "urn:f43ec009-6d83-4fde-8637-cfda36cba7c8",
- "urn:b41c1cc8-933c-4a8b-85d4-3a9f80498340",
- "urn:b41c1cc8-933c-4a8b-85d4-3a9f80498340"
+ "bids::dfile_rall.1D",
+ "bids::dfile_rall.1D",
+ "bids::dfile_rall.1D",
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD",
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD",
+ "bids::all_runs.$subj+tlrc%22[$ktrs]%22",
+ "bids::errts.$%7Bsubj%7D+tlrc%22[$ktrs]%22",
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.noise.all+tlrc",
+ "bids::rm.signal.all+tlrc",
+ "bids::errts.$%7Bsubj%7D+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::out.gcor.1D",
+ "bids::rm.errts.unit+tlrc",
+ "bids::rm.DP+tlrc",
+ "bids::X.nocensor.xmat.1D'[3]'",
+ "bids::X.nocensor.xmat.1D'[4]'",
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22",
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:85eb274e-9de4-49ad-a020-b3fc4932276b",
+ "@id": "urn:bluresti-0pPC1AJS",
"Label": "blur estimation",
- "AssociatedWith": "urn:2f56c0f2-f0d5-4997-9cb7-dc9136310252",
+ "AssociatedWith": "urn:afni-bx6q4Oas",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D; 3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D; 3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim; ",
"Used": [
- "urn:cb2c6935-c344-43e3-8766-cf55331e5fdb",
- "urn:cb2c6935-c344-43e3-8766-cf55331e5fdb",
- "urn:cb2c6935-c344-43e3-8766-cf55331e5fdb"
+ "bids::full_mask.$subj+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:ea295298-15e9-4553-a615-29f04d8138b1",
+ "@id": "urn:autobloc-3hupkewz",
"Label": "auto block: generate review scripts",
- "AssociatedWith": "urn:2f56c0f2-f0d5-4997-9cb7-dc9136310252",
+ "AssociatedWith": "urn:afni-bx6q4Oas",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD; gen_ss_review_scripts.py -mot_limit 0.3 -exit0; ",
"Used": [
- "urn:894cab31-3c91-43df-aa22-fcb41742d2e4"
+ "bids::pb00.$subj.r*.tcat+orig.HEAD"
]
}
],
"Entities": [
{
- "@id": "urn:5634518e-8272-499c-ab40-b15f1a0d7d8a",
+ "@id": "bids::afni_voxelwise_fdr_p005/tone_counting_onset_times.txt",
"Label": "tone_counting_onset_times.txt",
"AtLocation": "./afni_voxelwise_fdr_p005/tone_counting_onset_times.txt",
"digest": {
@@ -192,7 +194,7 @@
}
},
{
- "@id": "urn:c78c31e5-b426-479e-962a-b525066ac296",
+ "@id": "bids::afni_voxelwise_fdr_p005/tone_counting_probe_duration.txt",
"Label": "tone_counting_probe_duration.txt",
"AtLocation": "./afni_voxelwise_fdr_p005/tone_counting_probe_duration.txt",
"digest": {
@@ -200,7 +202,7 @@
}
},
{
- "@id": "urn:3e6bfd7e-087f-4f51-afb1-882eb4cbe149",
+ "@id": "bids::sub-01_T1w.nii.gz",
"Label": "sub-01_T1w.nii.gz",
"AtLocation": "sub-01_T1w.nii.gz",
"digest": {
@@ -208,34 +210,34 @@
}
},
{
- "@id": "urn:b86afaa0-9f58-422b-a895-1d2c7f5252c1",
+ "@id": "bids::$output_dir",
"Label": "$output_dir",
"AtLocation": "$output_dir",
- "GeneratedBy": "urn:5e4c7270-4828-4ea5-9229-b98f490e9bbc",
+ "GeneratedBy": "urn:autobloc-Lb7mU4cg",
"digest": {
"sha256": "9fa4c635e6533ddf2fed54295920052818d948c3ffe97bc753bd7336b453f8cb"
}
},
{
- "@id": "urn:95e20196-ea50-47d2-85d2-5ca1fceaeb1e",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:5e4c7270-4828-4ea5-9229-b98f490e9bbc"
+ "GeneratedBy": "urn:autobloc-Lb7mU4cg"
},
{
- "@id": "urn:7924b172-2309-4669-ae81-a988e591655e",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:5e4c7270-4828-4ea5-9229-b98f490e9bbc"
+ "GeneratedBy": "urn:autobloc-Lb7mU4cg"
},
{
- "@id": "urn:7d6d5f29-98cb-4f1e-a0b4-748891d45584",
+ "@id": "bids::$output_dir/sub-01_T1w",
"Label": "sub-01_T1w",
"AtLocation": "$output_dir/sub-01_T1w",
- "GeneratedBy": "urn:5e4c7270-4828-4ea5-9229-b98f490e9bbc"
+ "GeneratedBy": "urn:autobloc-Lb7mU4cg"
},
{
- "@id": "urn:9a8a0caf-982f-4090-b178-7415ef5842b0",
+ "@id": "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Label": "sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"digest": {
@@ -243,13 +245,13 @@
}
},
{
- "@id": "urn:b97f8a1e-186a-4b15-bab1-ee845c16352d",
+ "@id": "bids::$output_dir/pb00.$subj.r01.tcat",
"Label": "pb00.$subj.r01.tcat",
"AtLocation": "$output_dir/pb00.$subj.r01.tcat",
- "GeneratedBy": "urn:54e53611-1185-4cbc-a135-6669556584ba"
+ "GeneratedBy": "urn:autobloc-rUFvnhtZ"
},
{
- "@id": "urn:150a7ce4-f3d0-43dd-81a6-637409ba5481",
+ "@id": "bids::pb00.$subj.r$run.tcat+orig",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -257,7 +259,7 @@
}
},
{
- "@id": "urn:7abc0423-3682-48cf-8806-fee1a3fb186c",
+ "@id": "bids::outcount.r*.1D",
"Label": "outcount.r*.1D",
"AtLocation": "outcount.r*.1D",
"digest": {
@@ -265,25 +267,25 @@
}
},
{
- "@id": "urn:5fb06023-e8e1-439e-9746-ceaedfd29f11",
+ "@id": "bids::outcount.r$run.1D",
"Label": "outcount.r$run.1D",
"AtLocation": "outcount.r$run.1D",
- "GeneratedBy": "urn:6441239c-3ff4-45ce-a136-41bf8e6fd33a",
+ "GeneratedBy": "urn:autobloc-MMJBhghb",
"digest": {
"sha256": "63d9f539e5470badc625d557109f68bc4eecbb02ca2667483739d52f95e5d0dd"
}
},
{
- "@id": "urn:ceb18837-f089-46e0-8d15-f53ebe8394c7",
+ "@id": "bids::outcount_rall.1D",
"Label": "outcount_rall.1D",
"AtLocation": "outcount_rall.1D",
- "GeneratedBy": "urn:6441239c-3ff4-45ce-a136-41bf8e6fd33a",
+ "GeneratedBy": "urn:autobloc-MMJBhghb",
"digest": {
"sha256": "cb887fd5e4d5e9acb3a24820d0f7a62ed38a5ffb0fdedd373440ac0219fb186a"
}
},
{
- "@id": "urn:150a7ce4-f3d0-43dd-81a6-637409ba5481",
+ "@id": "bids::pb00.$subj.r$run.tcat+orig",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -291,16 +293,16 @@
}
},
{
- "@id": "urn:41b4dd62-a1d6-471a-9459-b7c3d9e66545",
+ "@id": "bids::pb01.$subj.r$run.tshift",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift",
- "GeneratedBy": "urn:c8f49f12-8b13-478c-80d8-2e5352fe372b",
+ "GeneratedBy": "urn:tshift-9jkHUP80",
"digest": {
"sha256": "c6bf01cea8d2eac1d7a866f80b865c6e7d4b4e012dbb63d480ac9a8551162d72"
}
},
{
- "@id": "urn:420cd2a7-49c9-4fcb-a221-45d7da289ec3",
+ "@id": "bids::sub-01_T1w+orig",
"Label": "sub-01_T1w",
"AtLocation": "sub-01_T1w+orig",
"digest": {
@@ -308,7 +310,7 @@
}
},
{
- "@id": "urn:6db2c440-a1c5-4be4-be37-c75b9faba368",
+ "@id": "bids::pb01.$subj.r01.tshift+orig",
"Label": "pb01.$subj.r01.tshift",
"AtLocation": "pb01.$subj.r01.tshift+orig",
"digest": {
@@ -316,16 +318,16 @@
}
},
{
- "@id": "urn:d9236ad7-4bbc-4dad-ad64-95059a111499",
+ "@id": "bids::_al_junk",
"Label": "_al_junk",
"AtLocation": "_al_junk",
- "GeneratedBy": "urn:8ae18fa4-72c3-4ea6-9635-4c952e84bbcc",
+ "GeneratedBy": "urn:align-j9wdpba6",
"digest": {
"sha256": "bd785a075a4c6446e1e54de9e628913f7f1c814e86b69a9fbfe933209e6d37b5"
}
},
{
- "@id": "urn:8dc86011-0121-48e3-945d-edfafd138b17",
+ "@id": "bids::TT_N27+tlrc",
"Label": "TT_N27",
"AtLocation": "TT_N27+tlrc",
"digest": {
@@ -333,7 +335,7 @@
}
},
{
- "@id": "urn:cb8bda64-2c63-42e4-8f16-df3a7449ba41",
+ "@id": "bids::sub-01_T1w_ns+orig",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+orig",
"digest": {
@@ -341,7 +343,7 @@
}
},
{
- "@id": "urn:58675ac0-241a-40e0-8600-1775c2221c7b",
+ "@id": "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc::WARP_DATA",
"digest": {
@@ -349,16 +351,16 @@
}
},
{
- "@id": "urn:05033224-1bed-4f2e-904f-113e6309a493",
+ "@id": "bids::warp.anat.Xat.1D",
"Label": "warp.anat.Xat.1D",
"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:f1f9f4c6-2c36-47a6-afba-6dedde47c8e1",
+ "GeneratedBy": "urn:tlrc-D1HWOqFx",
"digest": {
"sha256": "800633fb5b4e9be64078bc181c4d5510ffb73fc5cccaf364c7fb6a294aa06728"
}
},
{
- "@id": "urn:58675ac0-241a-40e0-8600-1775c2221c7b",
+ "@id": "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc::WARP_DATA",
"digest": {
@@ -366,16 +368,16 @@
}
},
{
- "@id": "urn:05033224-1bed-4f2e-904f-113e6309a493",
+ "@id": "bids::warp.anat.Xat.1D",
"Label": "warp.anat.Xat.1D",
"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:f1f9f4c6-2c36-47a6-afba-6dedde47c8e1",
+ "GeneratedBy": "urn:tlrc-D1HWOqFx",
"digest": {
"sha256": "800633fb5b4e9be64078bc181c4d5510ffb73fc5cccaf364c7fb6a294aa06728"
}
},
{
- "@id": "urn:ac224873-aa4f-43e1-bce8-57961761c3b5",
+ "@id": "bids::pb01.$subj.r$run.tshift+orig",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift+orig",
"digest": {
@@ -383,7 +385,7 @@
}
},
{
- "@id": "urn:6c939c93-038f-484b-8362-0d7ccb01dfa4",
+ "@id": "bids::sub-01_T1w_ns+tlrc",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc",
"digest": {
@@ -391,7 +393,7 @@
}
},
{
- "@id": "urn:915a73a0-d2c9-476c-bb2b-55f6b431b745",
+ "@id": "bids::rm.epi.all1+orig",
"Label": "rm.epi.all1",
"AtLocation": "rm.epi.all1+orig",
"digest": {
@@ -399,7 +401,7 @@
}
},
{
- "@id": "urn:d9f85d96-c33c-411a-8cfa-c8de426d250a",
+ "@id": "bids::rm.epi.1.r$run+tlrc",
"Label": "rm.epi.1.r$run",
"AtLocation": "rm.epi.1.r$run+tlrc",
"digest": {
@@ -407,7 +409,7 @@
}
},
{
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@@ -415,7 +417,7 @@
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@@ -423,7 +425,7 @@
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@@ -431,7 +433,7 @@
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@@ -439,97 +441,105 @@
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- "GeneratedBy": "urn:75cc4aa9-4afb-4375-9045-4fc9c45c506a",
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@@ -537,7 +547,7 @@
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@@ -545,7 +555,7 @@
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@@ -553,7 +563,7 @@
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@@ -561,7 +571,7 @@
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@@ -569,7 +579,7 @@
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@@ -577,7 +587,7 @@
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@@ -585,7 +595,7 @@
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{
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@@ -593,7 +603,7 @@
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@@ -601,7 +611,7 @@
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@@ -609,61 +619,61 @@
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{
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- "GeneratedBy": "urn:63610069-101d-41c4-ac02-dde249b45c74",
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- "GeneratedBy": "urn:63610069-101d-41c4-ac02-dde249b45c74",
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@@ -671,7 +681,7 @@
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@@ -679,7 +689,7 @@
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@@ -687,34 +697,34 @@
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@@ -722,7 +732,7 @@
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@@ -730,7 +740,7 @@
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@@ -738,7 +748,7 @@
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@@ -746,7 +756,7 @@
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@@ -754,7 +764,7 @@
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@@ -762,7 +772,7 @@
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@@ -770,7 +780,7 @@
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@@ -778,7 +788,7 @@
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@@ -786,7 +796,7 @@
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@@ -794,7 +804,7 @@
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{
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@@ -802,7 +812,7 @@
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@@ -810,7 +820,7 @@
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@@ -818,133 +828,133 @@
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{
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- "GeneratedBy": "urn:a2872607-ec43-4a31-9ead-e326632837bf",
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- "GeneratedBy": "urn:a2872607-ec43-4a31-9ead-e326632837bf",
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- "GeneratedBy": "urn:a2872607-ec43-4a31-9ead-e326632837bf",
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- "GeneratedBy": "urn:a2872607-ec43-4a31-9ead-e326632837bf",
+ "GeneratedBy": "urn:regress-TUuT4CNb",
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"sha256": "bda68a16c0afd5e55d4d7415c8c959e61a9aad7898dd456b0f3bb597363dde31"
}
},
{
- "@id": "urn:33ea97ed-7601-42c3-99f1-bdad2cd7a2fa",
+ "@id": "bids::rm.noise.all",
"Label": "rm.noise.all",
"AtLocation": "rm.noise.all",
- "GeneratedBy": "urn:a2872607-ec43-4a31-9ead-e326632837bf",
+ "GeneratedBy": "urn:regress-TUuT4CNb",
"digest": {
"sha256": "431314eb75d086ce08373b3a374427969e89414c4a2d607e449c1f6485c547af"
}
},
{
- "@id": "urn:2ae53466-3149-42f2-9c04-cf5c54bf55d1",
+ "@id": "bids::TSNR.$subj",
"Label": "TSNR.$subj",
"AtLocation": "TSNR.$subj",
- "GeneratedBy": "urn:a2872607-ec43-4a31-9ead-e326632837bf",
+ "GeneratedBy": "urn:regress-TUuT4CNb",
"digest": {
"sha256": "303f183145a1e295686c08335d3b70753777cf0fa0b3f9628cf8de5471359a00"
}
},
{
- "@id": "urn:e22719b6-d4be-48ce-b94a-24c556ee69a8",
+ "@id": "bids::rm.errts.unit",
"Label": "rm.errts.unit",
"AtLocation": "rm.errts.unit",
- "GeneratedBy": "urn:a2872607-ec43-4a31-9ead-e326632837bf",
+ "GeneratedBy": "urn:regress-TUuT4CNb",
"digest": {
"sha256": "03b570ad773a00f51ab7e6cdedfebdeca45f5356de0c25f9e3be44d7bf2c7151"
}
},
{
- "@id": "urn:29aba15c-e988-4938-8925-3e1516f516a3",
+ "@id": "urn:uuid:3462266c-b562-44db-8643-4e59b1296c05",
"Label": "-",
"AtLocation": "-",
- "GeneratedBy": "urn:a2872607-ec43-4a31-9ead-e326632837bf",
+ "GeneratedBy": "urn:regress-TUuT4CNb",
"digest": {
"sha256": "dac304c9f20899ca1ef5aa403e565345fd0ff4ed80c35f82007c9b03a68292b3"
}
},
{
- "@id": "urn:c71305e5-49ab-4bec-9a88-4837edc1e558",
+ "@id": "bids::rm.DP",
"Label": "rm.DP",
"AtLocation": "rm.DP",
- "GeneratedBy": "urn:a2872607-ec43-4a31-9ead-e326632837bf",
+ "GeneratedBy": "urn:regress-TUuT4CNb",
"digest": {
"sha256": "06a0bfbc609c1a06ecf93c479a3288d2911c7f5f3e93cf49c5d26f721c2035ed"
}
},
{
- "@id": "urn:b33646b2-646b-45ae-a449-43a0c28b1a6d",
+ "@id": "bids::corr_brain",
"Label": "corr_brain",
"AtLocation": "corr_brain",
- "GeneratedBy": "urn:a2872607-ec43-4a31-9ead-e326632837bf",
+ "GeneratedBy": "urn:regress-TUuT4CNb",
"digest": {
"sha256": "74e3aeae0da338b871ab5dc9e8859a4e81fcf1b3c0042cd22fe337eb7baf5eae"
}
},
{
- "@id": "urn:75bdbb93-ecf8-4707-b568-3acb8cd49ddc",
+ "@id": "bids::ideal_tone_counting.1D",
"Label": "ideal_tone_counting.1D",
"AtLocation": "ideal_tone_counting.1D",
- "GeneratedBy": "urn:a2872607-ec43-4a31-9ead-e326632837bf",
+ "GeneratedBy": "urn:regress-TUuT4CNb",
"digest": {
"sha256": "9bb1cabac5ce7ca19dffa5cd6336a9bf82d362fea2ce9341978406e421b5333c"
}
},
{
- "@id": "urn:b9bd9710-5122-4098-9acf-8d228dce9a76",
+ "@id": "bids::ideal_probe.1D",
"Label": "ideal_probe.1D",
"AtLocation": "ideal_probe.1D",
- "GeneratedBy": "urn:a2872607-ec43-4a31-9ead-e326632837bf",
+ "GeneratedBy": "urn:regress-TUuT4CNb",
"digest": {
"sha256": "705d93afa8b6ded9f4f572db3f967b54e9906942669af51dd8287a9863bb4288"
}
},
{
- "@id": "urn:3ca35147-dc66-46af-bd2a-ca466dc5c4f9",
+ "@id": "bids::sum_ideal.1D",
"Label": "sum_ideal.1D",
"AtLocation": "sum_ideal.1D",
- "GeneratedBy": "urn:a2872607-ec43-4a31-9ead-e326632837bf",
+ "GeneratedBy": "urn:regress-TUuT4CNb",
"digest": {
"sha256": "b2dccadcd84b2d26ec9685c4d1846baf2f11b867f31c36a08748d1c85467b01a"
}
},
{
- "@id": "urn:0aefca75-8457-4b37-9220-9065a676cc39",
+ "@id": "bids::X.stim.xmat.1D",
"Label": "X.stim.xmat.1D",
"AtLocation": "X.stim.xmat.1D",
- "GeneratedBy": "urn:a2872607-ec43-4a31-9ead-e326632837bf",
+ "GeneratedBy": "urn:regress-TUuT4CNb",
"digest": {
"sha256": "7c61b2f4bbb9eb0cecb19f81faa3a79b94d547b7fb4087ed18e368619e0004e6"
}
},
{
- "@id": "urn:cb2c6935-c344-43e3-8766-cf55331e5fdb",
+ "@id": "bids::full_mask.$subj+tlrc",
"Label": "full_mask.$subj",
"AtLocation": "full_mask.$subj+tlrc",
"digest": {
@@ -952,34 +962,34 @@
}
},
{
- "@id": "urn:7b40b911-8757-4a00-bae1-fb3d68382e7b",
+ "@id": "bids::blur.epits.1D",
"Label": "blur.epits.1D",
"AtLocation": "blur.epits.1D",
- "GeneratedBy": "urn:85eb274e-9de4-49ad-a020-b3fc4932276b",
+ "GeneratedBy": "urn:bluresti-0pPC1AJS",
"digest": {
"sha256": "623e70a42214e56babc1f1dca156e0b11ba09865dbd6ca9549d54ca2fc601515"
}
},
{
- "@id": "urn:bb968bcf-419b-4bf7-a6c7-5ac98405a73f",
+ "@id": "bids::blur.errts.1D",
"Label": "blur.errts.1D",
"AtLocation": "blur.errts.1D",
- "GeneratedBy": "urn:85eb274e-9de4-49ad-a020-b3fc4932276b",
+ "GeneratedBy": "urn:bluresti-0pPC1AJS",
"digest": {
"sha256": "73969700079b5d3275536ac7eaf0e17571d7e74ec49553b6940f90d5718fc800"
}
},
{
- "@id": "urn:0cac31cc-159f-4927-b0dd-f1a7166d6614",
+ "@id": "bids::ClustSim",
"Label": "ClustSim",
"AtLocation": "ClustSim",
- "GeneratedBy": "urn:85eb274e-9de4-49ad-a020-b3fc4932276b",
+ "GeneratedBy": "urn:bluresti-0pPC1AJS",
"digest": {
"sha256": "2e0cdba2c91902ba12d742a39cb20df66cfd705ba8de767fbf68aae8eb65c6f0"
}
},
{
- "@id": "urn:894cab31-3c91-43df-aa22-fcb41742d2e4",
+ "@id": "bids::pb00.$subj.r*.tcat+orig.HEAD",
"Label": "pb00.$subj.r*.tcat",
"AtLocation": "pb00.$subj.r*.tcat+orig.HEAD",
"digest": {
@@ -987,10 +997,10 @@
}
},
{
- "@id": "urn:2c73cf58-a76c-4b38-8157-b945a6fc64be",
+ "@id": "bids::-exit0",
"Label": "-exit0",
"AtLocation": "-exit0",
- "GeneratedBy": "urn:ea295298-15e9-4553-a615-29f04d8138b1",
+ "GeneratedBy": "urn:autobloc-3hupkewz",
"digest": {
"sha256": "871a4d3513ed2924cbb10c1c15a196eac4a46a05bdcc248e3bcdb23327b3ad90"
}
diff --git a/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc_block.png b/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc_block.png
index 521d49838..6233fc351 100644
Binary files a/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc_block.png and b/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc_block.png differ
diff --git a/examples/from_parsers/afni/afni_thr_voxelunct4_proc.jsonld b/examples/from_parsers/afni/afni_thr_voxelunct4_proc.jsonld
index eacdc7d64..7a4e6d3fa 100644
--- a/examples/from_parsers/afni/afni_thr_voxelunct4_proc.jsonld
+++ b/examples/from_parsers/afni/afni_thr_voxelunct4_proc.jsonld
@@ -4,578 +4,581 @@
"Records": {
"Software": [
{
- "@id": "urn:5929d021-c389-40b8-805a-044f09a71d42",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:afni-SFNElAFI",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
- "Version": "afni24"
+ "Version": "afni24",
+ "AltIdentifier": "RRID:SCR_005927"
}
],
"Activities": [
{
- "@id": "urn:25ce9b2f-e8fb-434d-8cdd-dfc62a03929e",
+ "@id": "urn:makedire-iFdm4p5Y",
"Label": "Make directory",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "mkdir $output_dir",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:2c8bf5db-37af-4b00-92a0-d2310ccc0371",
+ "@id": "urn:makedire-7b1I4rvH",
"Label": "Make directory",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "mkdir $output_dir/stimuli",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:25a1d29c-00ee-4032-a4b3-83e6e044f54e",
+ "@id": "urn:cp-ca6PNsvH",
"Label": "cp",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "cp ./afni_voxelwise_t4/tone_counting_onset_times.txt ./afni_voxelwise_t4/tone_counting_probe_duration.txt $output_dir/stimuli",
"Parameters": {},
"Used": [
- "urn:10a59a9e-d688-4beb-904f-a9f05eb85774",
- "urn:82749c15-7a83-4b5d-abb9-b74aae16fa81"
+ "bids::afni_voxelwise_t4/tone_counting_onset_times.txt",
+ "bids::afni_voxelwise_t4/tone_counting_probe_duration.txt"
]
},
{
- "@id": "urn:71f9e9f7-19e5-459e-94c6-05e44e3cc474",
+ "@id": "urn:3dcopy-9k58WpVo",
"Label": "3dcopy",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w",
"Parameters": {},
"Used": [
- "urn:72122e17-9b35-403d-b214-abe7be549e59"
+ "bids::sub-01_T1w.nii.gz"
]
},
{
- "@id": "urn:c98fa04c-7ddd-4442-8682-39ae8cbe4f03",
+ "@id": "urn:3dtcat-0ZxXYorR",
"Label": "3dTcat",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Parameters": {},
"Used": [
- "urn:1e5f5881-04e7-40df-85b6-db6338a8b9e1"
+ "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'"
]
},
{
- "@id": "urn:24b57a63-58d3-4788-abf9-202b9094696c",
+ "@id": "urn:3dtoutco-ik1bRskW",
"Label": "3dToutcount",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D",
"Parameters": {},
"Used": [
- "urn:a1b863ef-5a4f-4406-b100-3dddd647ef1c"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:38359f0d-0376-4cd9-b242-9c4b33dc6392",
+ "@id": "urn:cat-pkAOeENL",
"Label": "cat",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "cat outcount.r*.1D > outcount_rall.1D",
"Parameters": {},
"Used": [
- "urn:9f31b8ab-69ee-49ec-82c4-c8359d7de3c8"
+ "bids::outcount.r*.1D"
]
},
{
- "@id": "urn:5abb2ca1-a8ca-400d-9fc6-4d55b714f708",
+ "@id": "urn:3dtshift-1s3mZhmF",
"Label": "3dTshift",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig",
"Parameters": {},
"Used": [
- "urn:a1b863ef-5a4f-4406-b100-3dddd647ef1c"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:165bae48-7dae-427e-b10a-d1e238d9a17a",
+ "@id": "urn:alignepi-dTIk7nk3",
"Label": "align_epi_anat.py",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off",
"Parameters": {},
"Used": [
- "urn:28317228-ec2f-447f-8c78-e171c1cbb61d",
- "urn:6f8fe425-239f-4dfa-8b97-95d38d64b317"
+ "bids::pb01.$subj.r01.tshift+orig",
+ "bids::sub-01_T1w+orig"
]
},
{
- "@id": "urn:7af713f3-b8a5-4a79-95fd-8e6c5f25a64b",
+ "@id": "urn:autotlrc-mvmK1Bz8",
"Label": "@auto_tlrc",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss",
"Parameters": {},
"Used": [
- "urn:68079d2a-f99a-4365-a455-48bcf66b0699",
- "urn:f3ec8a03-ff2c-4d67-af27-aebcebd30f5d"
+ "bids::TT_N27+tlrc",
+ "bids::sub-01_T1w_ns+orig"
]
},
{
- "@id": "urn:b5ab0ba4-4889-4f87-a5c8-817a91c4de71",
+ "@id": "urn:catmatve-IJzNefhm",
"Label": "cat_matvec",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D",
"Parameters": {},
"Used": [
- "urn:3cb24f05-3dce-4413-98ce-0b5f694af482"
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:647f8a33-8bc6-49e6-a24b-f19e4afe80b5",
+ "@id": "urn:3dvolreg-O6tLmVdq",
"Label": "3dvolreg",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig",
"Parameters": {},
"Used": [
- "urn:c6a57e08-7b1d-4b28-aa5c-fc678f8a6bfe"
+ "bids::pb01.$subj.r$run.tshift+orig"
]
},
{
- "@id": "urn:2fca9e42-28fe-4360-bfe7-d3f1e1490b0f",
+ "@id": "urn:3dcalc-abvVqlYS",
"Label": "3dcalc",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1",
"Parameters": {},
"Used": [
- "urn:c6a57e08-7b1d-4b28-aa5c-fc678f8a6bfe"
+ "bids::pb01.$subj.r$run.tshift+orig"
]
},
{
- "@id": "urn:fbc766f7-c85d-42e4-af8d-a0b99b746f1d",
+ "@id": "urn:catmatve-O5GbwUs0",
"Label": "cat_matvec",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D",
"Parameters": {},
"Used": [
- "urn:3cb24f05-3dce-4413-98ce-0b5f694af482"
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:4e42c1fa-6371-4fdc-b15f-6334c00a93a5",
+ "@id": "urn:3dalline-D00HrQEK",
"Label": "3dAllineate",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run",
"Parameters": {},
"Used": [
- "urn:3790699d-27ec-4cd2-b718-ba21560d41e5",
- "urn:5fafa766-c98b-4270-a2d7-7245919ec15c",
- "urn:c6a57e08-7b1d-4b28-aa5c-fc678f8a6bfe"
+ "bids::mat.r$run.warp.aff12.1D",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:beae24c7-c164-4607-a1dd-53aeaa3faa50",
+ "@id": "urn:3dalline-MSx3Xfbr",
"Label": "3dAllineate",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run",
"Parameters": {},
"Used": [
- "urn:3790699d-27ec-4cd2-b718-ba21560d41e5",
- "urn:5fafa766-c98b-4270-a2d7-7245919ec15c",
- "urn:ae3269b4-3935-49e8-b0ba-f5b592e2f46f"
+ "bids::mat.r$run.warp.aff12.1D",
+ "bids::rm.epi.all1+orig",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:92d36e57-fdf4-41be-ac3f-ff88ff2caa71",
+ "@id": "urn:3dtstat-gdzMud8a",
"Label": "3dTstat",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc",
"Parameters": {},
"Used": [
- "urn:72309cbc-a1ff-4ece-b74d-7ab14d5329ec"
+ "bids::rm.epi.1.r$run+tlrc"
]
},
{
- "@id": "urn:f0f4353c-7637-4227-92b0-58e0afa1d0b9",
+ "@id": "urn:cat-kWtH0mNC",
"Label": "cat",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "cat dfile.r*.1D > dfile_rall.1D",
"Parameters": {},
"Used": [
- "urn:5a10086e-715a-46fb-a249-a2bb0dae791c"
+ "bids::dfile.r*.1D"
]
},
{
- "@id": "urn:c108b15e-d09b-48b6-99b8-a0aa3bcaa657",
+ "@id": "urn:3dcopy-IAV4FmmX",
"Label": "3dcopy",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents",
"Parameters": {},
"Used": [
- "urn:6aeb1fae-cce5-4617-a260-14ede7ddafd0"
+ "bids::rm.epi.min.r01+tlrc"
]
},
{
- "@id": "urn:43d395c3-1ccd-4588-ac63-d743e9d3d44d",
+ "@id": "urn:3dcalc-gllFh2IY",
"Label": "3dcalc",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg",
"Parameters": {},
"Used": [
- "urn:4dc65753-932f-49f4-b53e-3d8855fa336e",
- "urn:68a18c08-3b1d-4a17-92bf-7211f35d75f9"
+ "bids::mask_epi_extents+tlrc",
+ "bids::rm.epi.nomask.r$run+tlrc"
]
},
{
- "@id": "urn:31afdc2f-30f8-4682-a3d6-58f886590e75",
+ "@id": "urn:3dcopy-mWiPsmH7",
"Label": "3dcopy",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj",
"Parameters": {},
"Used": [
- "urn:5fafa766-c98b-4270-a2d7-7245919ec15c"
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:39d91d05-0337-4cde-8b33-86c43a213344",
+ "@id": "urn:3dalline-y5OXIUGU",
"Label": "3dAllineate",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped",
"Parameters": {},
"Used": [
- "urn:4728686d-9548-4cfa-b106-3de60ed831c1"
+ "bids::anat_final.$subj+tlrc",
+ "bids::warp.anat.Xat.1D"
]
},
{
- "@id": "urn:8465e4d8-80f6-4f0f-b165-cb30f2704a4d",
+ "@id": "urn:3dmerge-i0saPomM",
"Label": "3dmerge",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc",
"Parameters": {},
"Used": [
- "urn:27efb73c-c0cf-4c10-9047-b4ff9de6bad4",
- "urn:83e679fa-bc45-496a-b380-e64dbf09045e"
+ "bids::pb02.$subj.r$run.volreg+tlrc",
+ "bids::pb03.$subj.r$run.blur"
]
},
{
- "@id": "urn:cb3177ed-bc4b-431f-a111-dee5794e9478",
+ "@id": "urn:3dautoma-QrU9lY5P",
"Label": "3dAutomask",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:63b1ead7-b09f-4f03-8bc6-1d1d547c045f"
+ "bids::pb03.$subj.r$run.blur+tlrc"
]
},
{
- "@id": "urn:32ca811a-225c-43e8-a31c-2546ee3ada58",
+ "@id": "urn:3dmaskto-Aeh3ucUx",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:4ae04bd2-f829-465d-967b-51490c165efc",
+ "@id": "urn:3dresamp-SwGWI41p",
"Label": "3dresample",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat",
"Parameters": {},
"Used": [
- "urn:5fafa766-c98b-4270-a2d7-7245919ec15c",
- "urn:73d43f31-95c3-4568-b492-5ca4371c4f13"
+ "bids::full_mask.$subj+tlrc",
+ "bids::sub-01_T1w_ns+tlrc"
]
},
{
- "@id": "urn:9d77733e-7a2d-451f-970e-c6292ca36386",
+ "@id": "urn:3dmaskto-mRybVZG4",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj",
"Parameters": {},
"Used": [
- "urn:536112dd-62ec-4f7c-bad8-95c16e582d83"
+ "bids::rm.resam.anat+tlrc"
]
},
{
- "@id": "urn:53e45275-0dd2-4380-89b0-e06263477c86",
+ "@id": "urn:3dabover-lHAbRJGu",
"Label": "3dABoverlap",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt",
"Parameters": {},
"Used": [
- "urn:12dfa6ff-144e-4f66-9fd4-2409d56c120d",
- "urn:8fe8a3f1-b285-4417-b942-d9a281060918"
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee"
]
},
{
- "@id": "urn:f4fa8ecb-fe15-40ca-92ed-74c9e1fe18df",
+ "@id": "urn:3ddot-FMfjPWlg",
"Label": "3ddot",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt",
"Parameters": {},
"Used": [
- "urn:12dfa6ff-144e-4f66-9fd4-2409d56c120d",
- "urn:8fe8a3f1-b285-4417-b942-d9a281060918"
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee"
]
},
{
- "@id": "urn:36bb8644-008c-45bd-8c8e-ce0fd687b486",
+ "@id": "urn:3dresamp-8r8ElSpK",
"Label": "3dresample",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc",
"Parameters": {},
"Used": [
- "urn:068a56ed-fa24-4ab2-9781-d333a439bf94",
- "urn:73d43f31-95c3-4568-b492-5ca4371c4f13"
+ "bids::/Users/u1591557/abin/TT_N27+tlrc",
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:0a4cb941-af52-4ed0-883f-ad9d4e7b316c",
+ "@id": "urn:3dmaskto-G8eA3DDQ",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group",
"Parameters": {},
"Used": [
- "urn:8679d689-6609-4dd7-85a2-330a667c96e9"
+ "bids::rm.resam.group+tlrc"
]
},
{
- "@id": "urn:9d964c85-58a1-40e2-8ea1-06c596be6661",
+ "@id": "urn:3dtstat-SCph0awI",
"Label": "3dTstat",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:63b1ead7-b09f-4f03-8bc6-1d1d547c045f"
+ "bids::pb03.$subj.r$run.blur+tlrc"
]
},
{
- "@id": "urn:32bbae9d-fb30-4902-bf42-a34d51ac5989",
+ "@id": "urn:3dcalc-neUl0mA2",
"Label": "3dcalc",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale",
"Parameters": {},
"Used": [
- "urn:0e2f2522-9df7-4407-a50e-04e4fc9f4475",
- "urn:4dc65753-932f-49f4-b53e-3d8855fa336e",
- "urn:63b1ead7-b09f-4f03-8bc6-1d1d547c045f"
+ "bids::mask_epi_extents+tlrc",
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::rm.mean_r$run+tlrc"
]
},
{
- "@id": "urn:3f5fcc63-c232-47b9-9bfe-231b359c95b9",
+ "@id": "urn:1dtoolpy-L9OtMQxy",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D",
"Parameters": {},
"Used": [
- "urn:3d6b5432-45bd-4528-81c3-dcd551a5b5f8"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:949d043a-545a-4b78-b266-8885d981bf99",
+ "@id": "urn:1dtoolpy-VrRbA8c5",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D",
"Parameters": {},
"Used": [
- "urn:3d6b5432-45bd-4528-81c3-dcd551a5b5f8"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:6c68e7db-4b96-4b16-b064-fbf79cad5a41",
+ "@id": "urn:1dtoolpy-AIN7Of4w",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}",
"Parameters": {},
"Used": [
- "urn:3d6b5432-45bd-4528-81c3-dcd551a5b5f8"
+ "bids::dfile_rall.1D"
]
},
{
- "@id": "urn:aae4ed70-8823-4964-83b4-5d2f17e7fcc3",
+ "@id": "urn:3ddeconv-IjQMt3QN",
"Label": "3dDeconvolve",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj",
"Parameters": {},
"Used": [
- "urn:1e5abde0-a6bf-4444-81f8-23433fbd770a"
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD"
]
},
{
- "@id": "urn:703d1215-6aca-48fc-b9b0-5ae629fcaade",
+ "@id": "urn:1dtoolpy-J0cOwMKf",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt",
"Parameters": {},
"Used": [
- "urn:394e603e-0619-459e-a1c1-6dffeac3be20"
+ "bids::X.xmat.1D"
]
},
{
- "@id": "urn:a99a3cf5-8910-4304-91cd-19b94fd29c69",
+ "@id": "urn:3dtcat-llsqdBCU",
"Label": "3dTcat",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD",
"Parameters": {},
"Used": [
- "urn:1e5abde0-a6bf-4444-81f8-23433fbd770a"
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD"
]
},
{
- "@id": "urn:1c4d8379-a962-4530-b203-961ea5164edd",
+ "@id": "urn:3dtstat-t3hTw7tN",
"Label": "3dTstat",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:055e6616-8da2-44c5-aeb2-418931734dc0"
+ "bids::all_runs.$subj+tlrc%22[$ktrs]%22"
]
},
{
- "@id": "urn:f0febda5-28f8-4a7a-970e-4517c40e4ee5",
+ "@id": "urn:3dtstat-n6gcZwl0",
"Label": "3dTstat",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:9ec24ab3-4b92-46b9-9266-3c5e655db29c"
+ "bids::errts.$%7Bsubj%7D+tlrc%22[$ktrs]%22"
]
},
{
- "@id": "urn:0db9f667-31ec-4cc1-b7d6-ddb0ea21f714",
+ "@id": "urn:3dcalc-6uQ9g5pA",
"Label": "3dcalc",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj",
"Parameters": {},
"Used": [
- "urn:6f845091-280e-49cb-9947-2af6d2e7b4d3",
- "urn:73d43f31-95c3-4568-b492-5ca4371c4f13",
- "urn:f7d845ee-066a-455c-b70e-0a693a186017"
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.noise.all+tlrc",
+ "bids::rm.signal.all+tlrc"
]
},
{
- "@id": "urn:446e55f7-85e1-46c5-93b0-3352c67424e9",
+ "@id": "urn:3dtnorm-JskZiYfq",
"Label": "3dTnorm",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc",
"Parameters": {},
"Used": [
- "urn:63f0031d-eb88-40a7-9545-42781f2da105"
+ "bids::errts.$%7Bsubj%7D+tlrc"
]
},
{
- "@id": "urn:6ef4ad96-4836-4a98-a268-4a7432f14d2e",
+ "@id": "urn:3dmaskav-Y2YKe8wv",
"Label": "3dmaskave",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D",
"Parameters": {},
- "Used": []
+ "Used": [
+ "bids::full_mask.$subj+tlrc"
+ ]
},
{
- "@id": "urn:55fdee03-e7de-4695-b54a-3b1f4f92149e",
+ "@id": "urn:3dtstat-0Gkaz1x2",
"Label": "3dTstat",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D",
"Parameters": {},
"Used": [
- "urn:a5bb8cf2-12e7-4eec-95de-1d20dceb808b"
+ "bids::out.gcor.1D"
]
},
{
- "@id": "urn:da2217a7-aee1-45a1-a872-1a94157cd6c3",
+ "@id": "urn:3dcalc-Uxphk1Ou",
"Label": "3dcalc",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP",
"Parameters": {},
"Used": [
- "urn:18577179-bd3c-4dbb-b1eb-6a32757ed46f",
- "urn:775c1fd8-bd01-4511-a0a0-ccbb75a6b43c"
+ "bids::gmean.errts.unit.1D",
+ "bids::rm.errts.unit+tlrc"
]
},
{
- "@id": "urn:9a6b936f-0fad-4390-bf3e-71423676502a",
+ "@id": "urn:3dtstat-Or9t5EsD",
"Label": "3dTstat",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc",
"Parameters": {},
"Used": [
- "urn:798791af-c988-414c-b76e-7d4b43099a24"
+ "bids::rm.DP+tlrc"
]
},
{
- "@id": "urn:13e5912f-05c3-476e-8f43-f0b19c8158e6",
+ "@id": "urn:1dcat-9pGZCsRu",
"Label": "1dcat",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D",
"Parameters": {},
"Used": [
- "urn:018a0115-b414-4a52-8b4a-dcc8ddd77f1e"
+ "bids::X.nocensor.xmat.1D'[3]'"
]
},
{
- "@id": "urn:78ac9ac3-ab64-48ed-9595-5a8da7c4a7cc",
+ "@id": "urn:1dcat-Bh8sgUNo",
"Label": "1dcat",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D",
"Parameters": {},
"Used": [
- "urn:c90da9d4-20ab-48ab-8118-62616738a6a6"
+ "bids::X.nocensor.xmat.1D'[4]'"
]
},
{
- "@id": "urn:fdcf607b-137a-4f04-807b-a47104dff267",
+ "@id": "urn:3dtstat-BDL1Mvqp",
"Label": "3dTstat",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"",
"Parameters": {},
"Used": [
- "urn:087295b0-2f4b-4955-a595-429f14d9d263"
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:ae232832-f515-4065-9319-c6c9a8f92921",
+ "@id": "urn:1dcat-1H6PkvZy",
"Label": "1dcat",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D",
"Parameters": {},
"Used": [
- "urn:087295b0-2f4b-4955-a595-429f14d9d263"
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:0ac84f61-aaa5-4bd2-aab9-06b005e382ee",
+ "@id": "urn:3dfwhmx-0bHZEnGq",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D",
"Parameters": {},
"Used": [
- "urn:73d43f31-95c3-4568-b492-5ca4371c4f13"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:449d68ef-002c-4c72-890e-200c2ca7deae",
+ "@id": "urn:3dfwhmx-aUiJXUtM",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D",
"Parameters": {},
"Used": [
- "urn:73d43f31-95c3-4568-b492-5ca4371c4f13"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:4350385e-083c-468c-b204-ff7ce3734c0e",
+ "@id": "urn:3dclusts-Zh1od73U",
"Label": "3dClustSim",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim",
"Parameters": {},
"Used": [
- "urn:73d43f31-95c3-4568-b492-5ca4371c4f13"
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:5eea3323-cc6b-47fc-8e6a-c7b742bf7f6b",
+ "@id": "urn:genepire-pYUpG6e9",
"Label": "gen_epi_review.py",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD",
"Parameters": {},
"Used": [
- "urn:17db490b-6935-4543-9638-2df1ae98971d"
+ "bids::pb00.$subj.r*.tcat+orig.HEAD"
]
},
{
- "@id": "urn:3ccfec6d-e2ec-4c67-b5b7-d49da48a2e61",
+ "@id": "urn:genssrev-3Wv3HhIo",
"Label": "gen_ss_review_scripts.py",
- "AssociatedWith": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "AssociatedWith": "urn:afni-SFNElAFI",
"Command": "gen_ss_review_scripts.py -mot_limit 0.3 -exit0",
"Parameters": {
"-mot_limit": "0.3",
@@ -586,22 +589,22 @@
],
"Entities": [
{
- "@id": "urn:d426af81-e857-4106-9f89-3122622dc357",
+ "@id": "bids::$output_dir",
"Label": "$output_dir",
"AtLocation": "$output_dir",
- "GeneratedBy": "urn:25ce9b2f-e8fb-434d-8cdd-dfc62a03929e",
+ "GeneratedBy": "urn:makedire-iFdm4p5Y",
"digest": {
"sha256": "9fa4c635e6533ddf2fed54295920052818d948c3ffe97bc753bd7336b453f8cb"
}
},
{
- "@id": "urn:24a199cf-30a1-4540-a7d5-9830fee1989a",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:2c8bf5db-37af-4b00-92a0-d2310ccc0371"
+ "GeneratedBy": "urn:makedire-7b1I4rvH"
},
{
- "@id": "urn:10a59a9e-d688-4beb-904f-a9f05eb85774",
+ "@id": "bids::afni_voxelwise_t4/tone_counting_onset_times.txt",
"Label": "tone_counting_onset_times.txt",
"AtLocation": "./afni_voxelwise_t4/tone_counting_onset_times.txt",
"digest": {
@@ -609,7 +612,7 @@
}
},
{
- "@id": "urn:82749c15-7a83-4b5d-abb9-b74aae16fa81",
+ "@id": "bids::afni_voxelwise_t4/tone_counting_probe_duration.txt",
"Label": "tone_counting_probe_duration.txt",
"AtLocation": "./afni_voxelwise_t4/tone_counting_probe_duration.txt",
"digest": {
@@ -617,13 +620,13 @@
}
},
{
- "@id": "urn:d91e85e4-9f42-47b9-a05e-c8d2c1a91f3d",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:25a1d29c-00ee-4032-a4b3-83e6e044f54e"
+ "GeneratedBy": "urn:cp-ca6PNsvH"
},
{
- "@id": "urn:72122e17-9b35-403d-b214-abe7be549e59",
+ "@id": "bids::sub-01_T1w.nii.gz",
"Label": "sub-01_T1w.nii.gz",
"AtLocation": "sub-01_T1w.nii.gz",
"digest": {
@@ -631,13 +634,13 @@
}
},
{
- "@id": "urn:7f936015-cc31-482d-92ab-c03bd1250386",
+ "@id": "bids::$output_dir/sub-01_T1w",
"Label": "sub-01_T1w",
"AtLocation": "$output_dir/sub-01_T1w",
- "GeneratedBy": "urn:71f9e9f7-19e5-459e-94c6-05e44e3cc474"
+ "GeneratedBy": "urn:3dcopy-9k58WpVo"
},
{
- "@id": "urn:1e5f5881-04e7-40df-85b6-db6338a8b9e1",
+ "@id": "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Label": "sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"digest": {
@@ -645,13 +648,13 @@
}
},
{
- "@id": "urn:dd1ab2f3-4b39-4b1d-a6b1-d963de21e821",
+ "@id": "bids::$output_dir/pb00.$subj.r01.tcat",
"Label": "pb00.$subj.r01.tcat",
"AtLocation": "$output_dir/pb00.$subj.r01.tcat",
- "GeneratedBy": "urn:c98fa04c-7ddd-4442-8682-39ae8cbe4f03"
+ "GeneratedBy": "urn:3dtcat-0ZxXYorR"
},
{
- "@id": "urn:a1b863ef-5a4f-4406-b100-3dddd647ef1c",
+ "@id": "bids::pb00.$subj.r$run.tcat+orig",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -659,16 +662,16 @@
}
},
{
- "@id": "urn:d2a1e303-a574-44e4-84ac-85293d3844d3",
+ "@id": "bids::outcount.r$run.1D",
"Label": "outcount.r$run.1D",
"AtLocation": "outcount.r$run.1D",
- "GeneratedBy": "urn:24b57a63-58d3-4788-abf9-202b9094696c",
+ "GeneratedBy": "urn:3dtoutco-ik1bRskW",
"digest": {
"sha256": "63d9f539e5470badc625d557109f68bc4eecbb02ca2667483739d52f95e5d0dd"
}
},
{
- "@id": "urn:9f31b8ab-69ee-49ec-82c4-c8359d7de3c8",
+ "@id": "bids::outcount.r*.1D",
"Label": "outcount.r*.1D",
"AtLocation": "outcount.r*.1D",
"digest": {
@@ -676,25 +679,25 @@
}
},
{
- "@id": "urn:1a432389-11df-4575-9e20-37d785264cda",
+ "@id": "bids::outcount_rall.1D",
"Label": "outcount_rall.1D",
"AtLocation": "outcount_rall.1D",
- "GeneratedBy": "urn:38359f0d-0376-4cd9-b242-9c4b33dc6392",
+ "GeneratedBy": "urn:cat-pkAOeENL",
"digest": {
"sha256": "cb887fd5e4d5e9acb3a24820d0f7a62ed38a5ffb0fdedd373440ac0219fb186a"
}
},
{
- "@id": "urn:d6b8b109-1b37-4302-ba5c-7de9ea37de91",
+ "@id": "bids::pb01.$subj.r$run.tshift",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift",
- "GeneratedBy": "urn:5abb2ca1-a8ca-400d-9fc6-4d55b714f708",
+ "GeneratedBy": "urn:3dtshift-1s3mZhmF",
"digest": {
"sha256": "c6bf01cea8d2eac1d7a866f80b865c6e7d4b4e012dbb63d480ac9a8551162d72"
}
},
{
- "@id": "urn:6f8fe425-239f-4dfa-8b97-95d38d64b317",
+ "@id": "bids::sub-01_T1w+orig",
"Label": "sub-01_T1w",
"AtLocation": "sub-01_T1w+orig",
"digest": {
@@ -702,7 +705,7 @@
}
},
{
- "@id": "urn:28317228-ec2f-447f-8c78-e171c1cbb61d",
+ "@id": "bids::pb01.$subj.r01.tshift+orig",
"Label": "pb01.$subj.r01.tshift",
"AtLocation": "pb01.$subj.r01.tshift+orig",
"digest": {
@@ -710,16 +713,16 @@
}
},
{
- "@id": "urn:68cdaeb7-59fc-440a-9c6b-7f7df63da8f4",
+ "@id": "bids::_al_junk",
"Label": "_al_junk",
"AtLocation": "_al_junk",
- "GeneratedBy": "urn:165bae48-7dae-427e-b10a-d1e238d9a17a",
+ "GeneratedBy": "urn:alignepi-dTIk7nk3",
"digest": {
"sha256": "bd785a075a4c6446e1e54de9e628913f7f1c814e86b69a9fbfe933209e6d37b5"
}
},
{
- "@id": "urn:68079d2a-f99a-4365-a455-48bcf66b0699",
+ "@id": "bids::TT_N27+tlrc",
"Label": "TT_N27",
"AtLocation": "TT_N27+tlrc",
"digest": {
@@ -727,7 +730,7 @@
}
},
{
- "@id": "urn:f3ec8a03-ff2c-4d67-af27-aebcebd30f5d",
+ "@id": "bids::sub-01_T1w_ns+orig",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+orig",
"digest": {
@@ -735,7 +738,7 @@
}
},
{
- "@id": "urn:3cb24f05-3dce-4413-98ce-0b5f694af482",
+ "@id": "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc::WARP_DATA",
"digest": {
@@ -743,16 +746,16 @@
}
},
{
- "@id": "urn:4728686d-9548-4cfa-b106-3de60ed831c1",
+ "@id": "bids::warp.anat.Xat.1D",
"Label": "warp.anat.Xat.1D",
"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:b5ab0ba4-4889-4f87-a5c8-817a91c4de71",
+ "GeneratedBy": "urn:catmatve-IJzNefhm",
"digest": {
"sha256": "800633fb5b4e9be64078bc181c4d5510ffb73fc5cccaf364c7fb6a294aa06728"
}
},
{
- "@id": "urn:c6a57e08-7b1d-4b28-aa5c-fc678f8a6bfe",
+ "@id": "bids::pb01.$subj.r$run.tshift+orig",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift+orig",
"digest": {
@@ -760,34 +763,34 @@
}
},
{
- "@id": "urn:1df39d7b-6ed2-411a-8e61-043c3cd59339",
+ "@id": "bids::mat.r$run.vr.aff12.1D",
"Label": "mat.r$run.vr.aff12.1D",
"AtLocation": "mat.r$run.vr.aff12.1D",
- "GeneratedBy": "urn:647f8a33-8bc6-49e6-a24b-f19e4afe80b5",
+ "GeneratedBy": "urn:3dvolreg-O6tLmVdq",
"digest": {
"sha256": "2e6e6c2ce8089cfa3c6e11dc72fca0cc8497f7a55faae2ced402de4867466c91"
}
},
{
- "@id": "urn:bacd31a3-804a-4288-ac9a-a0a655acb9ef",
+ "@id": "bids::rm.epi.all1",
"Label": "rm.epi.all1",
"AtLocation": "rm.epi.all1",
- "GeneratedBy": "urn:2fca9e42-28fe-4360-bfe7-d3f1e1490b0f",
+ "GeneratedBy": "urn:3dcalc-abvVqlYS",
"digest": {
"sha256": "1023e3c16cecdbdc73ea456bcf33c2e5bb4f1e07094b73d29022d651e5fa3f85"
}
},
{
- "@id": "urn:3790699d-27ec-4cd2-b718-ba21560d41e5",
+ "@id": "bids::mat.r$run.warp.aff12.1D",
"Label": "mat.r$run.warp.aff12.1D",
"AtLocation": "mat.r$run.warp.aff12.1D",
- "GeneratedBy": "urn:fbc766f7-c85d-42e4-af8d-a0b99b746f1d",
+ "GeneratedBy": "urn:catmatve-O5GbwUs0",
"digest": {
"sha256": "7c536b6f582a067c718f9e5ea2566cb535c73b43b4e15116c4c46045734d6eee"
}
},
{
- "@id": "urn:5fafa766-c98b-4270-a2d7-7245919ec15c",
+ "@id": "bids::sub-01_T1w_ns+tlrc",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc",
"digest": {
@@ -795,16 +798,16 @@
}
},
{
- "@id": "urn:8ddb9164-7c2d-4c97-a86b-2b3ce2a96d47",
+ "@id": "bids::rm.epi.nomask.r$run",
"Label": "rm.epi.nomask.r$run",
"AtLocation": "rm.epi.nomask.r$run",
- "GeneratedBy": "urn:4e42c1fa-6371-4fdc-b15f-6334c00a93a5",
+ "GeneratedBy": "urn:3dalline-D00HrQEK",
"digest": {
"sha256": "03d6cba0426c5545e350e6b63a19b0e46f8dfa2223fd08691753e8914a479e36"
}
},
{
- "@id": "urn:ae3269b4-3935-49e8-b0ba-f5b592e2f46f",
+ "@id": "bids::rm.epi.all1+orig",
"Label": "rm.epi.all1",
"AtLocation": "rm.epi.all1+orig",
"digest": {
@@ -812,16 +815,16 @@
}
},
{
- "@id": "urn:a6fb9f0f-15e6-4a8f-8544-b59c36ef72cb",
+ "@id": "bids::rm.epi.1.r$run",
"Label": "rm.epi.1.r$run",
"AtLocation": "rm.epi.1.r$run",
- "GeneratedBy": "urn:beae24c7-c164-4607-a1dd-53aeaa3faa50",
+ "GeneratedBy": "urn:3dalline-MSx3Xfbr",
"digest": {
"sha256": "b1b9128c103ea246625db1a35e6f474a221ca6c1105a30df38aefdc4d5421e84"
}
},
{
- "@id": "urn:72309cbc-a1ff-4ece-b74d-7ab14d5329ec",
+ "@id": "bids::rm.epi.1.r$run+tlrc",
"Label": "rm.epi.1.r$run",
"AtLocation": "rm.epi.1.r$run+tlrc",
"digest": {
@@ -829,16 +832,16 @@
}
},
{
- "@id": "urn:3cbf8658-8f8b-41a9-b24b-9549cac8b6a1",
+ "@id": "bids::rm.epi.min.r$run",
"Label": "rm.epi.min.r$run",
"AtLocation": "rm.epi.min.r$run",
- "GeneratedBy": "urn:92d36e57-fdf4-41be-ac3f-ff88ff2caa71",
+ "GeneratedBy": "urn:3dtstat-gdzMud8a",
"digest": {
"sha256": "b4418a96ddbbf25afdfd01ed0506ddebe009011ba18aed10137f994260fd1a66"
}
},
{
- "@id": "urn:5a10086e-715a-46fb-a249-a2bb0dae791c",
+ "@id": "bids::dfile.r*.1D",
"Label": "dfile.r*.1D",
"AtLocation": "dfile.r*.1D",
"digest": {
@@ -846,16 +849,16 @@
}
},
{
- "@id": "urn:3d6b5432-45bd-4528-81c3-dcd551a5b5f8",
+ "@id": "bids::dfile_rall.1D",
"Label": "dfile_rall.1D",
"AtLocation": "dfile_rall.1D",
- "GeneratedBy": "urn:f0f4353c-7637-4227-92b0-58e0afa1d0b9",
+ "GeneratedBy": "urn:cat-kWtH0mNC",
"digest": {
"sha256": "011e7296870a1ac7e15377fb0d529ed68710bb16b138bef6aeb6c645f437dcf2"
}
},
{
- "@id": "urn:6aeb1fae-cce5-4617-a260-14ede7ddafd0",
+ "@id": "bids::rm.epi.min.r01+tlrc",
"Label": "rm.epi.min.r01",
"AtLocation": "rm.epi.min.r01+tlrc",
"digest": {
@@ -863,16 +866,16 @@
}
},
{
- "@id": "urn:3c8bd9ea-f940-4527-8bf8-7e2f9a190099",
+ "@id": "bids::mask_epi_extents",
"Label": "mask_epi_extents",
"AtLocation": "mask_epi_extents",
- "GeneratedBy": "urn:c108b15e-d09b-48b6-99b8-a0aa3bcaa657",
+ "GeneratedBy": "urn:3dcopy-IAV4FmmX",
"digest": {
"sha256": "a69dd71209516ec24e2b3364072ed54adff16619459b1c369866210ec642e987"
}
},
{
- "@id": "urn:68a18c08-3b1d-4a17-92bf-7211f35d75f9",
+ "@id": "bids::rm.epi.nomask.r$run+tlrc",
"Label": "rm.epi.nomask.r$run",
"AtLocation": "rm.epi.nomask.r$run+tlrc",
"digest": {
@@ -880,7 +883,7 @@
}
},
{
- "@id": "urn:4dc65753-932f-49f4-b53e-3d8855fa336e",
+ "@id": "bids::mask_epi_extents+tlrc",
"Label": "mask_epi_extents",
"AtLocation": "mask_epi_extents+tlrc",
"digest": {
@@ -888,34 +891,42 @@
}
},
{
- "@id": "urn:98b17263-9c83-441a-8036-eae0e019e728",
+ "@id": "bids::pb02.$subj.r$run.volreg",
"Label": "pb02.$subj.r$run.volreg",
"AtLocation": "pb02.$subj.r$run.volreg",
- "GeneratedBy": "urn:43d395c3-1ccd-4588-ac63-d743e9d3d44d",
+ "GeneratedBy": "urn:3dcalc-gllFh2IY",
"digest": {
"sha256": "8821927190ac1b3f8f9d9a5ec74f6468ae6c1cb736e58e5de2cdbe3543d5cc0c"
}
},
{
- "@id": "urn:27c5e77b-c388-49ac-8e7c-da3fd292e0ae",
+ "@id": "bids::anat_final.$subj",
"Label": "anat_final.$subj",
"AtLocation": "anat_final.$subj",
- "GeneratedBy": "urn:31afdc2f-30f8-4682-a3d6-58f886590e75",
+ "GeneratedBy": "urn:3dcopy-mWiPsmH7",
"digest": {
"sha256": "69b750d004bdba337de0b4ffa683bd92bc8f34b854d320327839ad264b28c4c5"
}
},
{
- "@id": "urn:226bd3cb-3e0d-4c85-82cc-7baa47c0f26e",
+ "@id": "bids::anat_final.$subj+tlrc",
+ "Label": "anat_final.$subj",
+ "AtLocation": "anat_final.$subj+tlrc",
+ "digest": {
+ "sha256": "94eb1853614cc085b22772c011f119f6a0ad7ec06cba2850587762e7f1a6eae6"
+ }
+ },
+ {
+ "@id": "bids::anat_w_skull_warped",
"Label": "anat_w_skull_warped",
"AtLocation": "anat_w_skull_warped",
- "GeneratedBy": "urn:39d91d05-0337-4cde-8b33-86c43a213344",
+ "GeneratedBy": "urn:3dalline-y5OXIUGU",
"digest": {
"sha256": "462fdb8cd2b882e250fee3c6adb7acf0b0b9a9edb3e1cadf9d45d16180871105"
}
},
{
- "@id": "urn:27efb73c-c0cf-4c10-9047-b4ff9de6bad4",
+ "@id": "bids::pb03.$subj.r$run.blur",
"Label": "pb03.$subj.r$run.blur",
"AtLocation": "pb03.$subj.r$run.blur",
"digest": {
@@ -923,7 +934,7 @@
}
},
{
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@@ -931,7 +942,7 @@
}
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@@ -939,25 +950,25 @@
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@@ -965,16 +976,16 @@
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@@ -982,16 +993,16 @@
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{
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@@ -999,7 +1010,7 @@
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@@ -1007,7 +1018,7 @@
}
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{
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@@ -1015,16 +1026,16 @@
}
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{
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- "GeneratedBy": "urn:36bb8644-008c-45bd-8c8e-ce0fd687b486",
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@@ -1032,25 +1043,25 @@
}
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{
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- "GeneratedBy": "urn:0a4cb941-af52-4ed0-883f-ad9d4e7b316c",
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{
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- "GeneratedBy": "urn:9d964c85-58a1-40e2-8ea1-06c596be6661",
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@@ -1058,34 +1069,34 @@
}
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{
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"AtLocation": "pb04.$subj.r$run.scale",
- "GeneratedBy": "urn:32bbae9d-fb30-4902-bf42-a34d51ac5989",
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{
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- "GeneratedBy": "urn:3f5fcc63-c232-47b9-9bfe-231b359c95b9",
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{
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- "GeneratedBy": "urn:949d043a-545a-4b78-b266-8885d981bf99",
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{
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@@ -1093,25 +1104,25 @@
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{
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{
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- "GeneratedBy": "urn:a99a3cf5-8910-4304-91cd-19b94fd29c69",
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{
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@@ -1119,16 +1130,16 @@
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{
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- "GeneratedBy": "urn:1c4d8379-a962-4530-b203-961ea5164edd",
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{
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@@ -1136,16 +1147,16 @@
}
},
{
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{
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@@ -1153,7 +1164,7 @@
}
},
{
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@@ -1161,16 +1172,16 @@
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{
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- "GeneratedBy": "urn:0db9f667-31ec-4cc1-b7d6-ddb0ea21f714",
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{
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@@ -1178,25 +1189,25 @@
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{
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- "GeneratedBy": "urn:446e55f7-85e1-46c5-93b0-3352c67424e9",
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@@ -1204,16 +1215,16 @@
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- "GeneratedBy": "urn:55fdee03-e7de-4695-b54a-3b1f4f92149e",
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@@ -1221,16 +1232,16 @@
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{
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@@ -1238,16 +1249,16 @@
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{
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- "GeneratedBy": "urn:9a6b936f-0fad-4390-bf3e-71423676502a",
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@@ -1255,16 +1266,16 @@
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{
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- "GeneratedBy": "urn:13e5912f-05c3-476e-8f43-f0b19c8158e6",
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@@ -1272,16 +1283,16 @@
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{
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- "GeneratedBy": "urn:78ac9ac3-ab64-48ed-9595-5a8da7c4a7cc",
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@@ -1289,52 +1300,52 @@
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{
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- "GeneratedBy": "urn:fdcf607b-137a-4f04-807b-a47104dff267",
+ "GeneratedBy": "urn:3dtstat-BDL1Mvqp",
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{
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- "GeneratedBy": "urn:ae232832-f515-4065-9319-c6c9a8f92921",
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{
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- "GeneratedBy": "urn:0ac84f61-aaa5-4bd2-aab9-06b005e382ee",
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- "GeneratedBy": "urn:449d68ef-002c-4c72-890e-200c2ca7deae",
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{
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+ "@id": "bids::ClustSim",
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- "GeneratedBy": "urn:4350385e-083c-468c-b204-ff7ce3734c0e",
+ "GeneratedBy": "urn:3dclusts-Zh1od73U",
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{
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+ "@id": "bids::pb00.$subj.r*.tcat+orig.HEAD",
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"digest": {
@@ -1342,10 +1353,10 @@
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},
{
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- "GeneratedBy": "urn:3ccfec6d-e2ec-4c67-b5b7-d49da48a2e61",
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"sha256": "871a4d3513ed2924cbb10c1c15a196eac4a46a05bdcc248e3bcdb23327b3ad90"
}
diff --git a/examples/from_parsers/afni/afni_thr_voxelunct4_proc.png b/examples/from_parsers/afni/afni_thr_voxelunct4_proc.png
index b456c989f..3887c2316 100644
Binary files a/examples/from_parsers/afni/afni_thr_voxelunct4_proc.png and b/examples/from_parsers/afni/afni_thr_voxelunct4_proc.png differ
diff --git a/examples/from_parsers/afni/afni_thr_voxelunct4_proc_block.jsonld b/examples/from_parsers/afni/afni_thr_voxelunct4_proc_block.jsonld
index 819d02b9d..3092341d6 100644
--- a/examples/from_parsers/afni/afni_thr_voxelunct4_proc_block.jsonld
+++ b/examples/from_parsers/afni/afni_thr_voxelunct4_proc_block.jsonld
@@ -4,187 +4,189 @@
"Records": {
"Software": [
{
- "@id": "urn:bf062820-dfad-4ff5-a794-14bfe43fd48b",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:afni-Azo4OHIC",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
- "Version": "afni24"
+ "Version": "afni24",
+ "AltIdentifier": "RRID:SCR_005927"
}
],
"Activities": [
{
- "@id": "urn:5ab4d3ac-a283-4eb9-a6fe-522e161c6524",
+ "@id": "urn:autobloc-XPw5Ibf6",
"Label": "auto block: setup",
- "AssociatedWith": "urn:bf062820-dfad-4ff5-a794-14bfe43fd48b",
+ "AssociatedWith": "urn:afni-Azo4OHIC",
"Command": "mkdir $output_dir; mkdir $output_dir/stimuli; cp ./afni_voxelwise_t4/tone_counting_onset_times.txt ./afni_voxelwise_t4/tone_counting_probe_duration.txt $output_dir/stimuli; 3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w; ",
"Used": [
- "urn:886f9970-4f49-49db-a6af-44441c2d0b8e",
- "urn:a1eac4c0-76c2-4aaa-b595-fd3b0fe7292b",
- "urn:e5aab2e8-72a6-4fb6-9085-b63d22e335a2"
+ "bids::afni_voxelwise_t4/tone_counting_onset_times.txt",
+ "bids::afni_voxelwise_t4/tone_counting_probe_duration.txt",
+ "bids::sub-01_T1w.nii.gz"
]
},
{
- "@id": "urn:879c60d0-7bda-4e04-ad3c-36641b548b96",
+ "@id": "urn:autobloc-Xsbsvk4k",
"Label": "auto block: tcat",
- "AssociatedWith": "urn:bf062820-dfad-4ff5-a794-14bfe43fd48b",
+ "AssociatedWith": "urn:afni-Azo4OHIC",
"Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ",
"Used": [
- "urn:85de85e6-c096-4520-be17-2ef38ee27ba4"
+ "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'"
]
},
{
- "@id": "urn:c9d55f80-276d-4292-ac96-5869007a076f",
+ "@id": "urn:autobloc-8DXvAoHU",
"Label": "auto block: outcount",
- "AssociatedWith": "urn:bf062820-dfad-4ff5-a794-14bfe43fd48b",
+ "AssociatedWith": "urn:afni-Azo4OHIC",
"Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ",
"Used": [
- "urn:cf35e9bf-17a2-4078-9ef0-07b72bc70c29",
- "urn:4634275d-8f31-4429-bf23-59bfd3c12e74"
+ "bids::pb00.$subj.r$run.tcat+orig",
+ "bids::outcount.r*.1D"
]
},
{
- "@id": "urn:58710505-ae1c-4e15-8b8d-49eb446c14c6",
+ "@id": "urn:tshift-4PWunAHR",
"Label": "tshift",
- "AssociatedWith": "urn:bf062820-dfad-4ff5-a794-14bfe43fd48b",
+ "AssociatedWith": "urn:afni-Azo4OHIC",
"Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ",
"Used": [
- "urn:cf35e9bf-17a2-4078-9ef0-07b72bc70c29"
+ "bids::pb00.$subj.r$run.tcat+orig"
]
},
{
- "@id": "urn:f99457e7-83a1-4e36-9139-6343f87a9a6b",
+ "@id": "urn:align-H9dKW59q",
"Label": "align",
- "AssociatedWith": "urn:bf062820-dfad-4ff5-a794-14bfe43fd48b",
+ "AssociatedWith": "urn:afni-Azo4OHIC",
"Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ",
"Used": [
- "urn:18e33185-877f-4a53-a606-a91ceab1b3ca",
- "urn:acd749a0-2d7c-4376-98d0-74a4bf206371"
+ "bids::pb01.$subj.r01.tshift+orig",
+ "bids::sub-01_T1w+orig"
]
},
{
- "@id": "urn:763b7462-e409-4572-ab59-5401b92a5da6",
+ "@id": "urn:tlrc-8Ob4ZRGu",
"Label": "tlrc",
- "AssociatedWith": "urn:bf062820-dfad-4ff5-a794-14bfe43fd48b",
+ "AssociatedWith": "urn:afni-Azo4OHIC",
"Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ",
"Used": [
- "urn:07c230b3-a6ca-4c45-9fb4-593e85fba620",
- "urn:5ecbb2f9-d628-4980-8bed-9166dcee801a",
- "urn:623eb35c-21fa-4b31-8073-dfdba666871f"
+ "bids::TT_N27+tlrc",
+ "bids::sub-01_T1w_ns+orig",
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA"
]
},
{
- "@id": "urn:20835fc2-3de2-4f26-a384-721971a8011c",
+ "@id": "urn:volreg-XniyBbVH",
"Label": "volreg",
- "AssociatedWith": "urn:bf062820-dfad-4ff5-a794-14bfe43fd48b",
+ "AssociatedWith": "urn:afni-Azo4OHIC",
"Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig; 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1; cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D; 3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run; 3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run; 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc; cat dfile.r*.1D > dfile_rall.1D; 3dcopy rm.epi.min.r01+tlrc mask_epi_extents; 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg; 3dcopy sub-01_T1w_ns+tlrc anat_final.$subj; 3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped; ",
"Used": [
- "urn:5620cc29-8198-4896-98b0-1649f1f44ded",
- "urn:5620cc29-8198-4896-98b0-1649f1f44ded",
- "urn:623eb35c-21fa-4b31-8073-dfdba666871f",
- "urn:5620cc29-8198-4896-98b0-1649f1f44ded",
- "urn:f529c4f5-fab8-406d-98a0-0472739c6b6f",
- "urn:146689d0-63e8-4509-9d49-e9189c351ef4",
- "urn:f529c4f5-fab8-406d-98a0-0472739c6b6f",
- "urn:8331d741-04e7-4367-ab1f-0e51decade3a",
- "urn:987e241d-ef25-4cbc-a063-20943d5391b1",
- "urn:f7c6cade-4218-4595-9786-416f1729ab69",
- "urn:10dfb433-94b4-4ea4-b283-3fec0ed1cbd2",
- "urn:ef0a17e7-2410-459e-aa85-dd27e49780c9",
- "urn:f529c4f5-fab8-406d-98a0-0472739c6b6f",
- "urn:e4344175-20ec-4b1d-b49f-7542d37e6caa"
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
+ "bids::pb01.$subj.r$run.tshift+orig",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.epi.all1+orig",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.epi.1.r$run+tlrc",
+ "bids::dfile.r*.1D",
+ "bids::rm.epi.min.r01+tlrc",
+ "bids::mask_epi_extents+tlrc",
+ "bids::rm.epi.nomask.r$run+tlrc",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::anat_final.$subj+tlrc",
+ "bids::warp.anat.Xat.1D"
]
},
{
- "@id": "urn:2597f5fb-2041-4dda-b508-1b29f72a5376",
+ "@id": "urn:blur-5nvxP9to",
"Label": "blur",
- "AssociatedWith": "urn:bf062820-dfad-4ff5-a794-14bfe43fd48b",
+ "AssociatedWith": "urn:afni-Azo4OHIC",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc; ",
"Used": [
- "urn:d8dbbd9f-bb1b-4993-b567-a239b9bfc293",
- "urn:ee9492d3-dd42-42d4-8ccd-d465757bf39e"
+ "bids::pb02.$subj.r$run.volreg+tlrc",
+ "bids::pb03.$subj.r$run.blur"
]
},
{
- "@id": "urn:7e5081e7-c009-4256-9c58-49b629cdadd5",
+ "@id": "urn:mask-6s6g20Wz",
"Label": "mask",
- "AssociatedWith": "urn:bf062820-dfad-4ff5-a794-14bfe43fd48b",
+ "AssociatedWith": "urn:afni-Azo4OHIC",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc; 3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj; 3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj; 3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt; 3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt; 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group; ",
"Used": [
- "urn:d0c4406f-db80-4b51-8651-292b0bd35f81",
- "urn:9cfed3d2-3adb-4e38-8d3e-24dda4043257",
- "urn:f529c4f5-fab8-406d-98a0-0472739c6b6f",
- "urn:aae0a1f9-bf6f-45ac-88dc-8bb6df4ed04d",
- "urn:27ffde96-4f34-45ef-902d-38cfe55597c7",
- "urn:b97857bc-8e1c-448e-82f9-d862603dac3a",
- "urn:27ffde96-4f34-45ef-902d-38cfe55597c7",
- "urn:b97857bc-8e1c-448e-82f9-d862603dac3a",
- "urn:5a69a194-ad94-4bf6-92b3-5ad04ca71792",
- "urn:9cfed3d2-3adb-4e38-8d3e-24dda4043257",
- "urn:b4ea6769-7f32-4487-8166-0a5c9640f230"
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::sub-01_T1w_ns+tlrc",
+ "bids::rm.resam.anat+tlrc",
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee",
+ "bids::mask_anat.$subj+tlrc",
+ "bids::tee",
+ "bids::/Users/u1591557/abin/TT_N27+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.resam.group+tlrc"
]
},
{
- "@id": "urn:f6d1f866-f52d-40b0-a893-4ba09265a1ce",
+ "@id": "urn:scale-CYGvfYfG",
"Label": "scale",
- "AssociatedWith": "urn:bf062820-dfad-4ff5-a794-14bfe43fd48b",
+ "AssociatedWith": "urn:afni-Azo4OHIC",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc; 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale; ",
"Used": [
- "urn:d0c4406f-db80-4b51-8651-292b0bd35f81",
- "urn:76cbe384-e9c5-4aee-a9eb-7366d46724c1",
- "urn:d0c4406f-db80-4b51-8651-292b0bd35f81",
- "urn:ef0a17e7-2410-459e-aa85-dd27e49780c9"
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::mask_epi_extents+tlrc",
+ "bids::pb03.$subj.r$run.blur+tlrc",
+ "bids::rm.mean_r$run+tlrc"
]
},
{
- "@id": "urn:5b1e5792-a7c3-4fd3-a40e-1f56638ead1c",
+ "@id": "urn:regress-tLkm9uCW",
"Label": "regress",
- "AssociatedWith": "urn:bf062820-dfad-4ff5-a794-14bfe43fd48b",
+ "AssociatedWith": "urn:afni-Azo4OHIC",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}; 3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj; 1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt; 3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD; 3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"; 3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"; 3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj; 3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc; 3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D; 3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D; 3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP; 3dTstat -sum -prefix corr_brain rm.DP+tlrc; 1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D; 1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D; 3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"; 1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D; ",
"Used": [
- "urn:7d4825ae-8174-4ca0-9365-17e45a88294e",
- "urn:7d4825ae-8174-4ca0-9365-17e45a88294e",
- "urn:7d4825ae-8174-4ca0-9365-17e45a88294e",
- "urn:62bdae8b-6b1c-4858-b2cf-d5c2ff2cb091",
- "urn:62bdae8b-6b1c-4858-b2cf-d5c2ff2cb091",
- "urn:3d0a295f-b783-4a04-94ac-2699c42f2e93",
- "urn:3f564b93-39c7-43e8-90e2-d000e316cec7",
- "urn:60b5705b-787c-4add-88b8-b6bd346e3b8b",
- "urn:9cfed3d2-3adb-4e38-8d3e-24dda4043257",
- "urn:b948ef91-aa46-4140-b8b7-c6abf40b9022",
- "urn:7cf8fd89-8821-4bcf-92fa-c25c5e3b5bcb",
- "urn:6f970a8c-d670-4c0e-8b97-41839e3c3c90",
- "urn:62ffd710-b951-4dcd-b02a-998f4f6c013a",
- "urn:26ec0d70-3f21-4bfe-be83-27f9b8eda5f9",
- "urn:2efbc0e7-5b73-40dc-aab5-ba4b75054202",
- "urn:2f09814e-eede-4696-bec8-1ffdf054d5e3",
- "urn:f03a6b50-e568-43a5-b8d2-7f9a7461a358",
- "urn:f03a6b50-e568-43a5-b8d2-7f9a7461a358"
+ "bids::dfile_rall.1D",
+ "bids::dfile_rall.1D",
+ "bids::dfile_rall.1D",
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD",
+ "bids::pb04.$subj.r*.scale+tlrc.HEAD",
+ "bids::all_runs.$subj+tlrc%22[$ktrs]%22",
+ "bids::errts.$%7Bsubj%7D+tlrc%22[$ktrs]%22",
+ "bids::full_mask.$subj+tlrc",
+ "bids::rm.noise.all+tlrc",
+ "bids::rm.signal.all+tlrc",
+ "bids::errts.$%7Bsubj%7D+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::out.gcor.1D",
+ "bids::rm.errts.unit+tlrc",
+ "bids::rm.DP+tlrc",
+ "bids::X.nocensor.xmat.1D'[3]'",
+ "bids::X.nocensor.xmat.1D'[4]'",
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22",
+ "bids::X.nocensor.xmat.1D%22[$reg_cols]%22"
]
},
{
- "@id": "urn:2afece4b-1134-467c-b01a-33d391048b34",
+ "@id": "urn:bluresti-u8JJjV7y",
"Label": "blur estimation",
- "AssociatedWith": "urn:bf062820-dfad-4ff5-a794-14bfe43fd48b",
+ "AssociatedWith": "urn:afni-Azo4OHIC",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D; 3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D; 3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim; ",
"Used": [
- "urn:9cfed3d2-3adb-4e38-8d3e-24dda4043257",
- "urn:9cfed3d2-3adb-4e38-8d3e-24dda4043257",
- "urn:9cfed3d2-3adb-4e38-8d3e-24dda4043257"
+ "bids::full_mask.$subj+tlrc",
+ "bids::full_mask.$subj+tlrc",
+ "bids::full_mask.$subj+tlrc"
]
},
{
- "@id": "urn:d111a15e-cff5-49f9-b84e-91a2cd55e718",
+ "@id": "urn:autobloc-cE18tebx",
"Label": "auto block: generate review scripts",
- "AssociatedWith": "urn:bf062820-dfad-4ff5-a794-14bfe43fd48b",
+ "AssociatedWith": "urn:afni-Azo4OHIC",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD; gen_ss_review_scripts.py -mot_limit 0.3 -exit0; ",
"Used": [
- "urn:42bc83c0-9238-41c5-8515-b2952bf77312"
+ "bids::pb00.$subj.r*.tcat+orig.HEAD"
]
}
],
"Entities": [
{
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+ "@id": "bids::afni_voxelwise_t4/tone_counting_onset_times.txt",
"Label": "tone_counting_onset_times.txt",
"AtLocation": "./afni_voxelwise_t4/tone_counting_onset_times.txt",
"digest": {
@@ -192,7 +194,7 @@
}
},
{
- "@id": "urn:a1eac4c0-76c2-4aaa-b595-fd3b0fe7292b",
+ "@id": "bids::afni_voxelwise_t4/tone_counting_probe_duration.txt",
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"AtLocation": "./afni_voxelwise_t4/tone_counting_probe_duration.txt",
"digest": {
@@ -200,7 +202,7 @@
}
},
{
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"AtLocation": "sub-01_T1w.nii.gz",
"digest": {
@@ -208,34 +210,34 @@
}
},
{
- "@id": "urn:259849bd-cf05-4538-84d0-59b5540fffdd",
+ "@id": "bids::$output_dir",
"Label": "$output_dir",
"AtLocation": "$output_dir",
- "GeneratedBy": "urn:5ab4d3ac-a283-4eb9-a6fe-522e161c6524",
+ "GeneratedBy": "urn:autobloc-XPw5Ibf6",
"digest": {
"sha256": "9fa4c635e6533ddf2fed54295920052818d948c3ffe97bc753bd7336b453f8cb"
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{
- "@id": "urn:42705fbf-bd87-439a-89a0-6f4a24e459e3",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:5ab4d3ac-a283-4eb9-a6fe-522e161c6524"
+ "GeneratedBy": "urn:autobloc-XPw5Ibf6"
},
{
- "@id": "urn:ee53297a-5ce2-4932-92b8-8550b3b89d1c",
+ "@id": "bids::$output_dir/stimuli",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:5ab4d3ac-a283-4eb9-a6fe-522e161c6524"
+ "GeneratedBy": "urn:autobloc-XPw5Ibf6"
},
{
- "@id": "urn:a8f99aa2-3c57-4b7e-a166-10298ab6e2bd",
+ "@id": "bids::$output_dir/sub-01_T1w",
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"AtLocation": "$output_dir/sub-01_T1w",
- "GeneratedBy": "urn:5ab4d3ac-a283-4eb9-a6fe-522e161c6524"
+ "GeneratedBy": "urn:autobloc-XPw5Ibf6"
},
{
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+ "@id": "bids::sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Label": "sub-01_task-tonecounting_bold.nii.gz",
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@@ -243,13 +245,13 @@
}
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{
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"AtLocation": "$output_dir/pb00.$subj.r01.tcat",
- "GeneratedBy": "urn:879c60d0-7bda-4e04-ad3c-36641b548b96"
+ "GeneratedBy": "urn:autobloc-Xsbsvk4k"
},
{
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@@ -257,7 +259,7 @@
}
},
{
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@@ -265,25 +267,25 @@
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},
{
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"AtLocation": "outcount.r$run.1D",
- "GeneratedBy": "urn:c9d55f80-276d-4292-ac96-5869007a076f",
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{
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"AtLocation": "outcount_rall.1D",
- "GeneratedBy": "urn:c9d55f80-276d-4292-ac96-5869007a076f",
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{
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"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -291,16 +293,16 @@
}
},
{
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"AtLocation": "pb01.$subj.r$run.tshift",
- "GeneratedBy": "urn:58710505-ae1c-4e15-8b8d-49eb446c14c6",
+ "GeneratedBy": "urn:tshift-4PWunAHR",
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{
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"digest": {
@@ -308,7 +310,7 @@
}
},
{
- "@id": "urn:18e33185-877f-4a53-a606-a91ceab1b3ca",
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"digest": {
@@ -316,16 +318,16 @@
}
},
{
- "@id": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "@id": "bids::_al_junk",
"Label": "_al_junk",
"AtLocation": "_al_junk",
- "GeneratedBy": "urn:f99457e7-83a1-4e36-9139-6343f87a9a6b",
+ "GeneratedBy": "urn:align-H9dKW59q",
"digest": {
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{
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+ "@id": "bids::TT_N27+tlrc",
"Label": "TT_N27",
"AtLocation": "TT_N27+tlrc",
"digest": {
@@ -333,7 +335,7 @@
}
},
{
- "@id": "urn:07c230b3-a6ca-4c45-9fb4-593e85fba620",
+ "@id": "bids::sub-01_T1w_ns+orig",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+orig",
"digest": {
@@ -341,7 +343,7 @@
}
},
{
- "@id": "urn:623eb35c-21fa-4b31-8073-dfdba666871f",
+ "@id": "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc::WARP_DATA",
"digest": {
@@ -349,16 +351,16 @@
}
},
{
- "@id": "urn:e4344175-20ec-4b1d-b49f-7542d37e6caa",
+ "@id": "bids::warp.anat.Xat.1D",
"Label": "warp.anat.Xat.1D",
"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:763b7462-e409-4572-ab59-5401b92a5da6",
+ "GeneratedBy": "urn:tlrc-8Ob4ZRGu",
"digest": {
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{
- "@id": "urn:623eb35c-21fa-4b31-8073-dfdba666871f",
+ "@id": "bids::sub-01_T1w_ns+tlrc::WARP_DATA",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc::WARP_DATA",
"digest": {
@@ -366,16 +368,16 @@
}
},
{
- "@id": "urn:e4344175-20ec-4b1d-b49f-7542d37e6caa",
+ "@id": "bids::warp.anat.Xat.1D",
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"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:763b7462-e409-4572-ab59-5401b92a5da6",
+ "GeneratedBy": "urn:tlrc-8Ob4ZRGu",
"digest": {
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{
- "@id": "urn:5620cc29-8198-4896-98b0-1649f1f44ded",
+ "@id": "bids::pb01.$subj.r$run.tshift+orig",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift+orig",
"digest": {
@@ -383,7 +385,7 @@
}
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{
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+ "@id": "bids::sub-01_T1w_ns+tlrc",
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@@ -391,7 +393,7 @@
}
},
{
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+ "@id": "bids::rm.epi.all1+orig",
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@@ -399,7 +401,7 @@
}
},
{
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"digest": {
@@ -407,7 +409,7 @@
}
},
{
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"digest": {
@@ -415,7 +417,7 @@
}
},
{
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+ "@id": "bids::rm.epi.min.r01+tlrc",
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"AtLocation": "rm.epi.min.r01+tlrc",
"digest": {
@@ -423,7 +425,7 @@
}
},
{
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+ "@id": "bids::rm.epi.nomask.r$run+tlrc",
"Label": "rm.epi.nomask.r$run",
"AtLocation": "rm.epi.nomask.r$run+tlrc",
"digest": {
@@ -431,7 +433,7 @@
}
},
{
- "@id": "urn:ef0a17e7-2410-459e-aa85-dd27e49780c9",
+ "@id": "bids::mask_epi_extents+tlrc",
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"AtLocation": "mask_epi_extents+tlrc",
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@@ -439,97 +441,105 @@
}
},
{
- "@id": "urn:e9dcd1ce-f9a5-4c85-8831-8e2118f3e436",
+ "@id": "bids::anat_final.$subj+tlrc",
+ "Label": "anat_final.$subj",
+ "AtLocation": "anat_final.$subj+tlrc",
+ "digest": {
+ "sha256": "94eb1853614cc085b22772c011f119f6a0ad7ec06cba2850587762e7f1a6eae6"
+ }
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+ {
+ "@id": "bids::mat.r$run.vr.aff12.1D",
"Label": "mat.r$run.vr.aff12.1D",
"AtLocation": "mat.r$run.vr.aff12.1D",
- "GeneratedBy": "urn:20835fc2-3de2-4f26-a384-721971a8011c",
+ "GeneratedBy": "urn:volreg-XniyBbVH",
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{
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+ "@id": "bids::rm.epi.all1",
"Label": "rm.epi.all1",
"AtLocation": "rm.epi.all1",
- "GeneratedBy": "urn:20835fc2-3de2-4f26-a384-721971a8011c",
+ "GeneratedBy": "urn:volreg-XniyBbVH",
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{
- "@id": "urn:19f7f936-05fb-4194-a6d8-10d878641d10",
+ "@id": "bids::rm.epi.nomask.r$run",
"Label": "rm.epi.nomask.r$run",
"AtLocation": "rm.epi.nomask.r$run",
- "GeneratedBy": "urn:20835fc2-3de2-4f26-a384-721971a8011c",
+ "GeneratedBy": "urn:volreg-XniyBbVH",
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{
- "@id": "urn:d124a1ec-ede9-4c55-9f3b-5534ba2d4bf1",
+ "@id": "bids::rm.epi.1.r$run",
"Label": "rm.epi.1.r$run",
"AtLocation": "rm.epi.1.r$run",
- "GeneratedBy": "urn:20835fc2-3de2-4f26-a384-721971a8011c",
+ "GeneratedBy": "urn:volreg-XniyBbVH",
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{
- "@id": "urn:5a483cd7-a169-420c-b682-fe81b2fb4411",
+ "@id": "bids::rm.epi.min.r$run",
"Label": "rm.epi.min.r$run",
"AtLocation": "rm.epi.min.r$run",
- "GeneratedBy": "urn:20835fc2-3de2-4f26-a384-721971a8011c",
+ "GeneratedBy": "urn:volreg-XniyBbVH",
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}
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{
- "@id": "urn:7d4825ae-8174-4ca0-9365-17e45a88294e",
+ "@id": "bids::dfile_rall.1D",
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"AtLocation": "dfile_rall.1D",
- "GeneratedBy": "urn:20835fc2-3de2-4f26-a384-721971a8011c",
+ "GeneratedBy": "urn:volreg-XniyBbVH",
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},
{
- "@id": "urn:8a10bc3b-8f5a-48c0-86e4-74a908ff2dff",
+ "@id": "bids::mask_epi_extents",
"Label": "mask_epi_extents",
"AtLocation": "mask_epi_extents",
- "GeneratedBy": "urn:20835fc2-3de2-4f26-a384-721971a8011c",
+ "GeneratedBy": "urn:volreg-XniyBbVH",
"digest": {
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}
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{
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+ "@id": "bids::pb02.$subj.r$run.volreg",
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"AtLocation": "pb02.$subj.r$run.volreg",
- "GeneratedBy": "urn:20835fc2-3de2-4f26-a384-721971a8011c",
+ "GeneratedBy": "urn:volreg-XniyBbVH",
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{
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+ "@id": "bids::anat_final.$subj",
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"AtLocation": "anat_final.$subj",
- "GeneratedBy": "urn:20835fc2-3de2-4f26-a384-721971a8011c",
+ "GeneratedBy": "urn:volreg-XniyBbVH",
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{
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+ "@id": "bids::anat_w_skull_warped",
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"AtLocation": "anat_w_skull_warped",
- "GeneratedBy": "urn:20835fc2-3de2-4f26-a384-721971a8011c",
+ "GeneratedBy": "urn:volreg-XniyBbVH",
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{
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@@ -537,7 +547,7 @@
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},
{
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@@ -545,7 +555,7 @@
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{
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@@ -553,7 +563,7 @@
}
},
{
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@@ -561,7 +571,7 @@
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@@ -569,7 +579,7 @@
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{
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@@ -577,7 +587,7 @@
}
},
{
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+ "@id": "bids::mask_anat.$subj+tlrc",
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@@ -585,7 +595,7 @@
}
},
{
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+ "@id": "bids::tee",
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@@ -593,7 +603,7 @@
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},
{
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+ "@id": "bids::/Users/u1591557/abin/TT_N27+tlrc",
"Label": "TT_N27",
"AtLocation": "/Users/u1591557/abin/TT_N27+tlrc",
"digest": {
@@ -601,7 +611,7 @@
}
},
{
- "@id": "urn:b4ea6769-7f32-4487-8166-0a5c9640f230",
+ "@id": "bids::rm.resam.group+tlrc",
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"digest": {
@@ -609,61 +619,61 @@
}
},
{
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+ "@id": "bids::rm.mask_r$run",
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"AtLocation": "rm.mask_r$run",
- "GeneratedBy": "urn:7e5081e7-c009-4256-9c58-49b629cdadd5",
+ "GeneratedBy": "urn:mask-6s6g20Wz",
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},
{
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+ "@id": "bids::full_mask.$subj",
"Label": "full_mask.$subj",
"AtLocation": "full_mask.$subj",
- "GeneratedBy": "urn:7e5081e7-c009-4256-9c58-49b629cdadd5",
+ "GeneratedBy": "urn:mask-6s6g20Wz",
"digest": {
"sha256": "02da8c6ed741c00cb6ccb8da25bf6ca853afb9100b992c854209afde9e30918f"
}
},
{
- "@id": "urn:758ad9e2-7feb-4de4-928e-1f722e1209d0",
+ "@id": "bids::rm.resam.anat",
"Label": "rm.resam.anat",
"AtLocation": "rm.resam.anat",
- "GeneratedBy": "urn:7e5081e7-c009-4256-9c58-49b629cdadd5",
+ "GeneratedBy": "urn:mask-6s6g20Wz",
"digest": {
"sha256": "fe716d2bdbce773476ef264f2cd990f7114d7f2d7245c0cbeb10e8abc7feff9b"
}
},
{
- "@id": "urn:74469c27-c574-4f02-9288-00dcb5161c82",
+ "@id": "bids::mask_anat.$subj",
"Label": "mask_anat.$subj",
"AtLocation": "mask_anat.$subj",
- "GeneratedBy": "urn:7e5081e7-c009-4256-9c58-49b629cdadd5",
+ "GeneratedBy": "urn:mask-6s6g20Wz",
"digest": {
"sha256": "d3f1becfb7c7d234361e002cc34c3ca5b5333640259f572993b773f6973f0e98"
}
},
{
- "@id": "urn:9b02e101-35be-41fb-81cb-4ebd4c4fb7ad",
+ "@id": "bids::rm.resam.group",
"Label": "rm.resam.group",
"AtLocation": "./rm.resam.group",
- "GeneratedBy": "urn:7e5081e7-c009-4256-9c58-49b629cdadd5",
+ "GeneratedBy": "urn:mask-6s6g20Wz",
"digest": {
"sha256": "79e954aee237a244a2498f6f7811a10a1c4508563eebd38000c13f2c145942c9"
}
},
{
- "@id": "urn:3ab3463b-3e76-4459-b00c-557a44d4c9c9",
+ "@id": "bids::mask_group",
"Label": "mask_group",
"AtLocation": "mask_group",
- "GeneratedBy": "urn:7e5081e7-c009-4256-9c58-49b629cdadd5",
+ "GeneratedBy": "urn:mask-6s6g20Wz",
"digest": {
"sha256": "d7093b26470ded8d7e939359017b18d28a2da4c6bb702c1183df20bca614f949"
}
},
{
- "@id": "urn:ef0a17e7-2410-459e-aa85-dd27e49780c9",
+ "@id": "bids::mask_epi_extents+tlrc",
"Label": "mask_epi_extents",
"AtLocation": "mask_epi_extents+tlrc",
"digest": {
@@ -671,7 +681,7 @@
}
},
{
- "@id": "urn:d0c4406f-db80-4b51-8651-292b0bd35f81",
+ "@id": "bids::pb03.$subj.r$run.blur+tlrc",
"Label": "pb03.$subj.r$run.blur",
"AtLocation": "pb03.$subj.r$run.blur+tlrc",
"digest": {
@@ -679,7 +689,7 @@
}
},
{
- "@id": "urn:76cbe384-e9c5-4aee-a9eb-7366d46724c1",
+ "@id": "bids::rm.mean_r$run+tlrc",
"Label": "rm.mean_r$run",
"AtLocation": "rm.mean_r$run+tlrc",
"digest": {
@@ -687,34 +697,34 @@
}
},
{
- "@id": "urn:791a37dd-7139-4be3-8f65-6c9aeb2c26fc",
+ "@id": "bids::rm.mean_r$run",
"Label": "rm.mean_r$run",
"AtLocation": "rm.mean_r$run",
- "GeneratedBy": "urn:f6d1f866-f52d-40b0-a893-4ba09265a1ce",
+ "GeneratedBy": "urn:scale-CYGvfYfG",
"digest": {
"sha256": "17047aa0c91933cf57076e6ce78a48ebe5975d6881ca47c8357cbd66e0fde9fb"
}
},
{
- "@id": "urn:bf3a439e-808c-464e-9cd8-69074082b387",
+ "@id": "bids::pb04.$subj.r$run.scale",
"Label": "pb04.$subj.r$run.scale",
"AtLocation": "pb04.$subj.r$run.scale",
- "GeneratedBy": "urn:f6d1f866-f52d-40b0-a893-4ba09265a1ce",
+ "GeneratedBy": "urn:scale-CYGvfYfG",
"digest": {
"sha256": "1e6d4160b1a7b120e8201df43aabc22c6fe0e0b0788b12c76c8d63554897a790"
}
},
{
- "@id": "urn:7d4825ae-8174-4ca0-9365-17e45a88294e",
+ "@id": "bids::dfile_rall.1D",
"Label": "dfile_rall.1D",
"AtLocation": "dfile_rall.1D",
- "GeneratedBy": "urn:20835fc2-3de2-4f26-a384-721971a8011c",
+ "GeneratedBy": "urn:volreg-XniyBbVH",
"digest": {
"sha256": "011e7296870a1ac7e15377fb0d529ed68710bb16b138bef6aeb6c645f437dcf2"
}
},
{
- "@id": "urn:9cfed3d2-3adb-4e38-8d3e-24dda4043257",
+ "@id": "bids::full_mask.$subj+tlrc",
"Label": "full_mask.$subj",
"AtLocation": "full_mask.$subj+tlrc",
"digest": {
@@ -722,7 +732,7 @@
}
},
{
- "@id": "urn:62bdae8b-6b1c-4858-b2cf-d5c2ff2cb091",
+ "@id": "bids::pb04.$subj.r*.scale+tlrc.HEAD",
"Label": "pb04.$subj.r*.scale",
"AtLocation": "pb04.$subj.r*.scale+tlrc.HEAD",
"digest": {
@@ -730,7 +740,7 @@
}
},
{
- "@id": "urn:3d0a295f-b783-4a04-94ac-2699c42f2e93",
+ "@id": "bids::all_runs.$subj+tlrc%22[$ktrs]%22",
"Label": "all_runs.$subj",
"AtLocation": "all_runs.$subj+tlrc\"[$ktrs]\"",
"digest": {
@@ -738,7 +748,7 @@
}
},
{
- "@id": "urn:3f564b93-39c7-43e8-90e2-d000e316cec7",
+ "@id": "bids::errts.$%7Bsubj%7D+tlrc%22[$ktrs]%22",
"Label": "errts.${subj}",
"AtLocation": "errts.${subj}+tlrc\"[$ktrs]\"",
"digest": {
@@ -746,7 +756,7 @@
}
},
{
- "@id": "urn:60b5705b-787c-4add-88b8-b6bd346e3b8b",
+ "@id": "bids::rm.signal.all+tlrc",
"Label": "rm.signal.all",
"AtLocation": "rm.signal.all+tlrc",
"digest": {
@@ -754,7 +764,7 @@
}
},
{
- "@id": "urn:b948ef91-aa46-4140-b8b7-c6abf40b9022",
+ "@id": "bids::rm.noise.all+tlrc",
"Label": "rm.noise.all",
"AtLocation": "rm.noise.all+tlrc",
"digest": {
@@ -762,7 +772,7 @@
}
},
{
- "@id": "urn:7cf8fd89-8821-4bcf-92fa-c25c5e3b5bcb",
+ "@id": "bids::errts.$%7Bsubj%7D+tlrc",
"Label": "errts.${subj}",
"AtLocation": "errts.${subj}+tlrc",
"digest": {
@@ -770,7 +780,7 @@
}
},
{
- "@id": "urn:6f970a8c-d670-4c0e-8b97-41839e3c3c90",
+ "@id": "bids::out.gcor.1D",
"Label": "out.gcor.1D",
"AtLocation": "out.gcor.1D",
"digest": {
@@ -778,7 +788,7 @@
}
},
{
- "@id": "urn:62ffd710-b951-4dcd-b02a-998f4f6c013a",
+ "@id": "bids::rm.errts.unit+tlrc",
"Label": "rm.errts.unit",
"AtLocation": "rm.errts.unit+tlrc",
"digest": {
@@ -786,7 +796,7 @@
}
},
{
- "@id": "urn:26ec0d70-3f21-4bfe-be83-27f9b8eda5f9",
+ "@id": "bids::rm.DP+tlrc",
"Label": "rm.DP",
"AtLocation": "rm.DP+tlrc",
"digest": {
@@ -794,7 +804,7 @@
}
},
{
- "@id": "urn:2efbc0e7-5b73-40dc-aab5-ba4b75054202",
+ "@id": "bids::X.nocensor.xmat.1D'[3]'",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D'[3]'",
"digest": {
@@ -802,7 +812,7 @@
}
},
{
- "@id": "urn:2f09814e-eede-4696-bec8-1ffdf054d5e3",
+ "@id": "bids::X.nocensor.xmat.1D'[4]'",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D'[4]'",
"digest": {
@@ -810,7 +820,7 @@
}
},
{
- "@id": "urn:f03a6b50-e568-43a5-b8d2-7f9a7461a358",
+ "@id": "bids::X.nocensor.xmat.1D%22[$reg_cols]%22",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D\"[$reg_cols]\"",
"digest": {
@@ -818,133 +828,133 @@
}
},
{
- "@id": "urn:0dd56933-46e0-4b97-a391-60e35d8c4844",
+ "@id": "bids::motion_demean.1D",
"Label": "motion_demean.1D",
"AtLocation": "motion_demean.1D",
- "GeneratedBy": "urn:5b1e5792-a7c3-4fd3-a40e-1f56638ead1c",
+ "GeneratedBy": "urn:regress-tLkm9uCW",
"digest": {
"sha256": "1de1e10c0120caa7b6cf441bd141a5a76716e458676ae56ce693039eecb79c85"
}
},
{
- "@id": "urn:1f43f5ac-38dd-42ab-b4b0-784a8d398c24",
+ "@id": "bids::motion_deriv.1D",
"Label": "motion_deriv.1D",
"AtLocation": "motion_deriv.1D",
- "GeneratedBy": "urn:5b1e5792-a7c3-4fd3-a40e-1f56638ead1c",
+ "GeneratedBy": "urn:regress-tLkm9uCW",
"digest": {
"sha256": "47185bf319e91642ad6f2a396a43fc9f8db7b82f2a9aef326bfe4a955120038b"
}
},
{
- "@id": "urn:7044196c-bcff-499e-976d-e8a4ec668bd8",
+ "@id": "bids::all_runs.$subj",
"Label": "all_runs.$subj",
"AtLocation": "all_runs.$subj",
- "GeneratedBy": "urn:5b1e5792-a7c3-4fd3-a40e-1f56638ead1c",
+ "GeneratedBy": "urn:regress-tLkm9uCW",
"digest": {
"sha256": "bcf27fc2e339e751d0ea9bba931674c21fd9d434ff411330f4df55f872a8cc7e"
}
},
{
- "@id": "urn:d187304a-f963-4ca1-9da5-8a9e7f1d6728",
+ "@id": "bids::rm.signal.all",
"Label": "rm.signal.all",
"AtLocation": "rm.signal.all",
- "GeneratedBy": "urn:5b1e5792-a7c3-4fd3-a40e-1f56638ead1c",
+ "GeneratedBy": "urn:regress-tLkm9uCW",
"digest": {
"sha256": "bda68a16c0afd5e55d4d7415c8c959e61a9aad7898dd456b0f3bb597363dde31"
}
},
{
- "@id": "urn:64057351-a13d-45e8-a43f-489a5e911597",
+ "@id": "bids::rm.noise.all",
"Label": "rm.noise.all",
"AtLocation": "rm.noise.all",
- "GeneratedBy": "urn:5b1e5792-a7c3-4fd3-a40e-1f56638ead1c",
+ "GeneratedBy": "urn:regress-tLkm9uCW",
"digest": {
"sha256": "431314eb75d086ce08373b3a374427969e89414c4a2d607e449c1f6485c547af"
}
},
{
- "@id": "urn:b5098ff2-a4c4-41d9-9478-fb6768535e96",
+ "@id": "bids::TSNR.$subj",
"Label": "TSNR.$subj",
"AtLocation": "TSNR.$subj",
- "GeneratedBy": "urn:5b1e5792-a7c3-4fd3-a40e-1f56638ead1c",
+ "GeneratedBy": "urn:regress-tLkm9uCW",
"digest": {
"sha256": "303f183145a1e295686c08335d3b70753777cf0fa0b3f9628cf8de5471359a00"
}
},
{
- "@id": "urn:ecd695c7-b43b-46a3-a180-749b4a38ee78",
+ "@id": "bids::rm.errts.unit",
"Label": "rm.errts.unit",
"AtLocation": "rm.errts.unit",
- "GeneratedBy": "urn:5b1e5792-a7c3-4fd3-a40e-1f56638ead1c",
+ "GeneratedBy": "urn:regress-tLkm9uCW",
"digest": {
"sha256": "03b570ad773a00f51ab7e6cdedfebdeca45f5356de0c25f9e3be44d7bf2c7151"
}
},
{
- "@id": "urn:9532b0c0-6fa7-4053-af9f-67025ce5ef0d",
+ "@id": "urn:uuid:15bedf62-df23-49b6-bbc8-1aa1713a09ea",
"Label": "-",
"AtLocation": "-",
- "GeneratedBy": "urn:5b1e5792-a7c3-4fd3-a40e-1f56638ead1c",
+ "GeneratedBy": "urn:regress-tLkm9uCW",
"digest": {
"sha256": "dac304c9f20899ca1ef5aa403e565345fd0ff4ed80c35f82007c9b03a68292b3"
}
},
{
- "@id": "urn:24abf5de-fe14-4a83-8d3c-5e3a723811fc",
+ "@id": "bids::rm.DP",
"Label": "rm.DP",
"AtLocation": "rm.DP",
- "GeneratedBy": "urn:5b1e5792-a7c3-4fd3-a40e-1f56638ead1c",
+ "GeneratedBy": "urn:regress-tLkm9uCW",
"digest": {
"sha256": "06a0bfbc609c1a06ecf93c479a3288d2911c7f5f3e93cf49c5d26f721c2035ed"
}
},
{
- "@id": "urn:2a391bc4-ee62-4540-9f9a-d4416041bae9",
+ "@id": "bids::corr_brain",
"Label": "corr_brain",
"AtLocation": "corr_brain",
- "GeneratedBy": "urn:5b1e5792-a7c3-4fd3-a40e-1f56638ead1c",
+ "GeneratedBy": "urn:regress-tLkm9uCW",
"digest": {
"sha256": "74e3aeae0da338b871ab5dc9e8859a4e81fcf1b3c0042cd22fe337eb7baf5eae"
}
},
{
- "@id": "urn:f9da1d1c-0b53-4cf6-8ce5-8d37378b9b39",
+ "@id": "bids::ideal_tone_counting.1D",
"Label": "ideal_tone_counting.1D",
"AtLocation": "ideal_tone_counting.1D",
- "GeneratedBy": "urn:5b1e5792-a7c3-4fd3-a40e-1f56638ead1c",
+ "GeneratedBy": "urn:regress-tLkm9uCW",
"digest": {
"sha256": "9bb1cabac5ce7ca19dffa5cd6336a9bf82d362fea2ce9341978406e421b5333c"
}
},
{
- "@id": "urn:9c40682e-36d5-484f-a9ff-c5cfe101b371",
+ "@id": "bids::ideal_probe.1D",
"Label": "ideal_probe.1D",
"AtLocation": "ideal_probe.1D",
- "GeneratedBy": "urn:5b1e5792-a7c3-4fd3-a40e-1f56638ead1c",
+ "GeneratedBy": "urn:regress-tLkm9uCW",
"digest": {
"sha256": "705d93afa8b6ded9f4f572db3f967b54e9906942669af51dd8287a9863bb4288"
}
},
{
- "@id": "urn:aec70b1e-a52a-4c34-afbe-58bab274e85c",
+ "@id": "bids::sum_ideal.1D",
"Label": "sum_ideal.1D",
"AtLocation": "sum_ideal.1D",
- "GeneratedBy": "urn:5b1e5792-a7c3-4fd3-a40e-1f56638ead1c",
+ "GeneratedBy": "urn:regress-tLkm9uCW",
"digest": {
"sha256": "b2dccadcd84b2d26ec9685c4d1846baf2f11b867f31c36a08748d1c85467b01a"
}
},
{
- "@id": "urn:32cd4f20-3d7d-4bf9-a487-f030afb3c263",
+ "@id": "bids::X.stim.xmat.1D",
"Label": "X.stim.xmat.1D",
"AtLocation": "X.stim.xmat.1D",
- "GeneratedBy": "urn:5b1e5792-a7c3-4fd3-a40e-1f56638ead1c",
+ "GeneratedBy": "urn:regress-tLkm9uCW",
"digest": {
"sha256": "7c61b2f4bbb9eb0cecb19f81faa3a79b94d547b7fb4087ed18e368619e0004e6"
}
},
{
- "@id": "urn:9cfed3d2-3adb-4e38-8d3e-24dda4043257",
+ "@id": "bids::full_mask.$subj+tlrc",
"Label": "full_mask.$subj",
"AtLocation": "full_mask.$subj+tlrc",
"digest": {
@@ -952,34 +962,34 @@
}
},
{
- "@id": "urn:d2014ac4-41ea-4cdd-aa27-1b61904eb214",
+ "@id": "bids::blur.epits.1D",
"Label": "blur.epits.1D",
"AtLocation": "blur.epits.1D",
- "GeneratedBy": "urn:2afece4b-1134-467c-b01a-33d391048b34",
+ "GeneratedBy": "urn:bluresti-u8JJjV7y",
"digest": {
"sha256": "623e70a42214e56babc1f1dca156e0b11ba09865dbd6ca9549d54ca2fc601515"
}
},
{
- "@id": "urn:f07ae6c3-d6bc-42a7-861b-015c6da45356",
+ "@id": "bids::blur.errts.1D",
"Label": "blur.errts.1D",
"AtLocation": "blur.errts.1D",
- "GeneratedBy": "urn:2afece4b-1134-467c-b01a-33d391048b34",
+ "GeneratedBy": "urn:bluresti-u8JJjV7y",
"digest": {
"sha256": "73969700079b5d3275536ac7eaf0e17571d7e74ec49553b6940f90d5718fc800"
}
},
{
- "@id": "urn:4aeeec3d-c0c4-41b2-9b59-e75fc2b134e9",
+ "@id": "bids::ClustSim",
"Label": "ClustSim",
"AtLocation": "ClustSim",
- "GeneratedBy": "urn:2afece4b-1134-467c-b01a-33d391048b34",
+ "GeneratedBy": "urn:bluresti-u8JJjV7y",
"digest": {
"sha256": "2e0cdba2c91902ba12d742a39cb20df66cfd705ba8de767fbf68aae8eb65c6f0"
}
},
{
- "@id": "urn:42bc83c0-9238-41c5-8515-b2952bf77312",
+ "@id": "bids::pb00.$subj.r*.tcat+orig.HEAD",
"Label": "pb00.$subj.r*.tcat",
"AtLocation": "pb00.$subj.r*.tcat+orig.HEAD",
"digest": {
@@ -987,10 +997,10 @@
}
},
{
- "@id": "urn:97a7a594-07de-445f-a94a-6a1132660219",
+ "@id": "bids::-exit0",
"Label": "-exit0",
"AtLocation": "-exit0",
- "GeneratedBy": "urn:d111a15e-cff5-49f9-b84e-91a2cd55e718",
+ "GeneratedBy": "urn:autobloc-cE18tebx",
"digest": {
"sha256": "871a4d3513ed2924cbb10c1c15a196eac4a46a05bdcc248e3bcdb23327b3ad90"
}
diff --git a/examples/from_parsers/afni/afni_thr_voxelunct4_proc_block.png b/examples/from_parsers/afni/afni_thr_voxelunct4_proc_block.png
index 89577cb58..d13519b84 100644
Binary files a/examples/from_parsers/afni/afni_thr_voxelunct4_proc_block.png and b/examples/from_parsers/afni/afni_thr_voxelunct4_proc_block.png differ
diff --git a/examples/from_parsers/afni/narps_do_02_pc_with_sign0.jsonld b/examples/from_parsers/afni/narps_do_02_pc_with_sign0.jsonld
index faf5444d0..b568809a2 100644
--- a/examples/from_parsers/afni/narps_do_02_pc_with_sign0.jsonld
+++ b/examples/from_parsers/afni/narps_do_02_pc_with_sign0.jsonld
@@ -4,62 +4,62 @@
"Records": {
"Software": [
{
- "@id": "urn:333734aa-0214-4c5f-b7e9-f648101328da",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:afni-ZvsAtHNd",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
- "Version": "afni24"
+ "Version": "afni24",
+ "AltIdentifier": "RRID:SCR_005927"
}
],
"Activities": [
{
- "@id": "urn:9565c071-19d4-4502-8f50-acf69e458431",
+ "@id": "urn:3dpc-zSEKMSc5",
"Label": "3dpc",
- "AssociatedWith": "urn:333734aa-0214-4c5f-b7e9-f648101328da",
+ "AssociatedWith": "urn:afni-ZvsAtHNd",
"Command": "3dpc -overwrite -mask ${dset_mask} -pcsave 5 -prefix ${dir_hyp}/PC_hyp${num} ${grp_dset}",
"Parameters": {},
"Used": [
- "urn:242c05a1-10e3-45a9-aa34-8e4799bf79d6",
- "urn:bd0e45d1-072d-4eb7-bf69-3fda63ddfba9"
+ "bids::$%7Bdset_mask%7D",
+ "bids::$%7Bgrp_dset%7D"
]
},
{
- "@id": "urn:f2905fa3-7c8d-4629-bc94-3108b1af34f2",
+ "@id": "urn:3dresamp-xAJr0qAP",
"Label": "3dresample",
- "AssociatedWith": "urn:333734aa-0214-4c5f-b7e9-f648101328da",
+ "AssociatedWith": "urn:afni-ZvsAtHNd",
"Command": "3dresample -overwrite -prefix tmp_REF_DSET.nii.gz -master ${dset_mask} -input \"${ref_dset}\"",
"Parameters": {},
"Used": [
- "urn:5deae2c5-d728-4f5b-9d1e-3ac865f0e162",
- "urn:bd0e45d1-072d-4eb7-bf69-3fda63ddfba9"
+ "bids::$%7Bdset_mask%7D",
+ "bids::%22$%7Bref_dset%7D%22"
]
},
{
- "@id": "urn:b281ae59-f7ca-40e4-a206-7c9fc41d6a24",
+ "@id": "urn:3dmatch-0E3O84FA",
"Label": "3dMatch",
- "AssociatedWith": "urn:333734aa-0214-4c5f-b7e9-f648101328da",
+ "AssociatedWith": "urn:afni-ZvsAtHNd",
"Command": "3dMatch -echo_edu -overwrite -mask ${dset_mask} -refset ${dir_hyp}/PC_hyp${num}+tlrc -inset tmp_REF_DSET.nii.gz -prefix tmp_MATCHED",
"Parameters": {},
"Used": [
- "urn:643c3f61-e81e-440d-9d0a-da03147eb483",
- "urn:a02c3dfa-efee-4642-a8db-093fed35d380",
- "urn:bd0e45d1-072d-4eb7-bf69-3fda63ddfba9"
+ "bids::$%7Bdir_hyp%7D/PC_hyp$%7Bnum%7D+tlrc",
+ "bids::$%7Bdset_mask%7D",
+ "bids::tmp_REF_DSET.nii.gz"
]
},
{
- "@id": "urn:71b7fd66-39e5-4104-bec8-598dafdea9cc",
+ "@id": "urn:3dcalc-NJBuzmnS",
"Label": "3dcalc",
- "AssociatedWith": "urn:333734aa-0214-4c5f-b7e9-f648101328da",
+ "AssociatedWith": "urn:afni-ZvsAtHNd",
"Command": "3dcalc -echo_edu -overwrite -a ${dir_hyp}/PC_hyp${num}+tlrc -expr \"${signum}*a\" -prefix ${dir_hyp}/PC_hyp${num}_sign0.nii.gz",
"Parameters": {},
"Used": [
- "urn:643c3f61-e81e-440d-9d0a-da03147eb483"
+ "bids::$%7Bdir_hyp%7D/PC_hyp$%7Bnum%7D+tlrc"
]
}
],
"Entities": [
{
- "@id": "urn:bd0e45d1-072d-4eb7-bf69-3fda63ddfba9",
+ "@id": "bids::$%7Bdset_mask%7D",
"Label": "${dset_mask}",
"AtLocation": "${dset_mask}",
"digest": {
@@ -67,7 +67,7 @@
}
},
{
- "@id": "urn:242c05a1-10e3-45a9-aa34-8e4799bf79d6",
+ "@id": "bids::$%7Bgrp_dset%7D",
"Label": "${grp_dset}",
"AtLocation": "${grp_dset}",
"digest": {
@@ -75,16 +75,16 @@
}
},
{
- "@id": "urn:ef481cba-a841-48ab-91a2-700b3b045a3e",
+ "@id": "bids::$%7Bdir_hyp%7D/PC_hyp$%7Bnum%7D",
"Label": "PC_hyp${num}",
"AtLocation": "${dir_hyp}/PC_hyp${num}",
- "GeneratedBy": "urn:9565c071-19d4-4502-8f50-acf69e458431",
+ "GeneratedBy": "urn:3dpc-zSEKMSc5",
"digest": {
"sha256": "915832134c7f76c64fd48179b53dfb05de128b50ef451380b440cff2ec1990fb"
}
},
{
- "@id": "urn:5deae2c5-d728-4f5b-9d1e-3ac865f0e162",
+ "@id": "bids::%22$%7Bref_dset%7D%22",
"Label": "\"${ref_dset}\"",
"AtLocation": "\"${ref_dset}\"",
"digest": {
@@ -92,16 +92,16 @@
}
},
{
- "@id": "urn:a02c3dfa-efee-4642-a8db-093fed35d380",
+ "@id": "bids::tmp_REF_DSET.nii.gz",
"Label": "tmp_REF_DSET.nii.gz",
"AtLocation": "tmp_REF_DSET.nii.gz",
- "GeneratedBy": "urn:f2905fa3-7c8d-4629-bc94-3108b1af34f2",
+ "GeneratedBy": "urn:3dresamp-xAJr0qAP",
"digest": {
"sha256": "e943c60b478a75e89c043bc4a7a6e6c629c3f075007ff501f7b2ab3a253e8d3d"
}
},
{
- "@id": "urn:643c3f61-e81e-440d-9d0a-da03147eb483",
+ "@id": "bids::$%7Bdir_hyp%7D/PC_hyp$%7Bnum%7D+tlrc",
"Label": "PC_hyp${num}",
"AtLocation": "${dir_hyp}/PC_hyp${num}+tlrc",
"digest": {
@@ -109,19 +109,19 @@
}
},
{
- "@id": "urn:0fc01c72-be31-41da-8050-498c6fc2f72d",
+ "@id": "bids::tmp_MATCHED",
"Label": "tmp_MATCHED",
"AtLocation": "tmp_MATCHED",
- "GeneratedBy": "urn:b281ae59-f7ca-40e4-a206-7c9fc41d6a24",
+ "GeneratedBy": "urn:3dmatch-0E3O84FA",
"digest": {
"sha256": "a251065c7203a21b76c1fb6acd1edb6da1c29896ad2df1f5479c71e16a29c302"
}
},
{
- "@id": "urn:e3486423-f966-4ef5-be39-ed9946ed911d",
+ "@id": "bids::$%7Bdir_hyp%7D/PC_hyp$%7Bnum%7D_sign0.nii.gz",
"Label": "PC_hyp${num}_sign0.nii.gz",
"AtLocation": "${dir_hyp}/PC_hyp${num}_sign0.nii.gz",
- "GeneratedBy": "urn:71b7fd66-39e5-4104-bec8-598dafdea9cc",
+ "GeneratedBy": "urn:3dcalc-NJBuzmnS",
"digest": {
"sha256": "5f0818d820edebe892295ffc1dd6f69823f2fb843bc2c3b0b5304054fa227af0"
}
diff --git a/examples/from_parsers/afni/narps_do_02_pc_with_sign0.png b/examples/from_parsers/afni/narps_do_02_pc_with_sign0.png
index 2f4d691e7..1e47294a0 100644
Binary files a/examples/from_parsers/afni/narps_do_02_pc_with_sign0.png and b/examples/from_parsers/afni/narps_do_02_pc_with_sign0.png differ
diff --git a/examples/from_parsers/afni/narps_do_02_pc_with_sign0_block.jsonld b/examples/from_parsers/afni/narps_do_02_pc_with_sign0_block.jsonld
index a827332ba..ae34d788e 100644
--- a/examples/from_parsers/afni/narps_do_02_pc_with_sign0_block.jsonld
+++ b/examples/from_parsers/afni/narps_do_02_pc_with_sign0_block.jsonld
@@ -4,41 +4,41 @@
"Records": {
"Software": [
{
- "@id": "urn:c9c41032-a75b-4535-84cd-acb432b3d541",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:afni-oHzJ5GRz",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
- "Version": "afni24"
+ "Version": "afni24",
+ "AltIdentifier": "RRID:SCR_005927"
}
],
"Activities": [
{
- "@id": "urn:1a4cacfc-6c2f-4960-8b86-7bcda40db9b3",
+ "@id": "urn:-2wgEiing",
"Label": "",
- "AssociatedWith": "urn:c9c41032-a75b-4535-84cd-acb432b3d541",
+ "AssociatedWith": "urn:afni-oHzJ5GRz",
"Command": "3dpc -overwrite -mask ${dset_mask} -pcsave 5 -prefix ${dir_hyp}/PC_hyp${num} ${grp_dset}; ",
"Used": [
- "urn:4349b024-08f7-4723-831a-77a19b4c1144",
- "urn:f40d24fd-8ee7-4822-b98b-3e889411760e"
+ "bids::$%7Bdset_mask%7D",
+ "bids::$%7Bgrp_dset%7D"
]
},
{
- "@id": "urn:51b6566c-ac9f-4514-a29a-2047f479b665",
+ "@id": "urn:block-qU0Fey8I",
"Label": "block ...",
- "AssociatedWith": "urn:c9c41032-a75b-4535-84cd-acb432b3d541",
+ "AssociatedWith": "urn:afni-oHzJ5GRz",
"Command": "3dresample -overwrite -prefix tmp_REF_DSET.nii.gz -master ${dset_mask} -input \"${ref_dset}\"; 3dMatch -echo_edu -overwrite -mask ${dset_mask} -refset ${dir_hyp}/PC_hyp${num}+tlrc -inset tmp_REF_DSET.nii.gz -prefix tmp_MATCHED; 3dcalc -echo_edu -overwrite -a ${dir_hyp}/PC_hyp${num}+tlrc -expr \"${signum}*a\" -prefix ${dir_hyp}/PC_hyp${num}_sign0.nii.gz; ",
"Used": [
- "urn:05fbe4f8-2e63-4f9b-8d24-0b6839d69dc6",
- "urn:f40d24fd-8ee7-4822-b98b-3e889411760e",
- "urn:6fb270cb-246a-489a-9655-358899756167",
- "urn:f40d24fd-8ee7-4822-b98b-3e889411760e",
- "urn:6fb270cb-246a-489a-9655-358899756167"
+ "bids::$%7Bdset_mask%7D",
+ "bids::%22$%7Bref_dset%7D%22",
+ "bids::$%7Bdir_hyp%7D/PC_hyp$%7Bnum%7D+tlrc",
+ "bids::$%7Bdset_mask%7D",
+ "bids::$%7Bdir_hyp%7D/PC_hyp$%7Bnum%7D+tlrc"
]
}
],
"Entities": [
{
- "@id": "urn:f40d24fd-8ee7-4822-b98b-3e889411760e",
+ "@id": "bids::$%7Bdset_mask%7D",
"Label": "${dset_mask}",
"AtLocation": "${dset_mask}",
"digest": {
@@ -46,7 +46,7 @@
}
},
{
- "@id": "urn:4349b024-08f7-4723-831a-77a19b4c1144",
+ "@id": "bids::$%7Bgrp_dset%7D",
"Label": "${grp_dset}",
"AtLocation": "${grp_dset}",
"digest": {
@@ -54,16 +54,16 @@
}
},
{
- "@id": "urn:d7653c13-bc89-4e81-99a2-e4f6cc895c5b",
+ "@id": "bids::$%7Bdir_hyp%7D/PC_hyp$%7Bnum%7D",
"Label": "PC_hyp${num}",
"AtLocation": "${dir_hyp}/PC_hyp${num}",
- "GeneratedBy": "urn:1a4cacfc-6c2f-4960-8b86-7bcda40db9b3",
+ "GeneratedBy": "urn:-2wgEiing",
"digest": {
"sha256": "915832134c7f76c64fd48179b53dfb05de128b50ef451380b440cff2ec1990fb"
}
},
{
- "@id": "urn:f40d24fd-8ee7-4822-b98b-3e889411760e",
+ "@id": "bids::$%7Bdset_mask%7D",
"Label": "${dset_mask}",
"AtLocation": "${dset_mask}",
"digest": {
@@ -71,7 +71,7 @@
}
},
{
- "@id": "urn:05fbe4f8-2e63-4f9b-8d24-0b6839d69dc6",
+ "@id": "bids::%22$%7Bref_dset%7D%22",
"Label": "\"${ref_dset}\"",
"AtLocation": "\"${ref_dset}\"",
"digest": {
@@ -79,7 +79,7 @@
}
},
{
- "@id": "urn:6fb270cb-246a-489a-9655-358899756167",
+ "@id": "bids::$%7Bdir_hyp%7D/PC_hyp$%7Bnum%7D+tlrc",
"Label": "PC_hyp${num}",
"AtLocation": "${dir_hyp}/PC_hyp${num}+tlrc",
"digest": {
@@ -87,19 +87,19 @@
}
},
{
- "@id": "urn:b13a8837-4e83-4ffe-8583-44ad77c778bf",
+ "@id": "bids::tmp_MATCHED",
"Label": "tmp_MATCHED",
"AtLocation": "tmp_MATCHED",
- "GeneratedBy": "urn:51b6566c-ac9f-4514-a29a-2047f479b665",
+ "GeneratedBy": "urn:block-qU0Fey8I",
"digest": {
"sha256": "a251065c7203a21b76c1fb6acd1edb6da1c29896ad2df1f5479c71e16a29c302"
}
},
{
- "@id": "urn:d8969622-62e2-4899-b5bc-b94a3a671e93",
+ "@id": "bids::$%7Bdir_hyp%7D/PC_hyp$%7Bnum%7D_sign0.nii.gz",
"Label": "PC_hyp${num}_sign0.nii.gz",
"AtLocation": "${dir_hyp}/PC_hyp${num}_sign0.nii.gz",
- "GeneratedBy": "urn:51b6566c-ac9f-4514-a29a-2047f479b665",
+ "GeneratedBy": "urn:block-qU0Fey8I",
"digest": {
"sha256": "5f0818d820edebe892295ffc1dd6f69823f2fb843bc2c3b0b5304054fa227af0"
}
diff --git a/examples/from_parsers/afni/narps_do_02_pc_with_sign0_block.png b/examples/from_parsers/afni/narps_do_02_pc_with_sign0_block.png
index 8613f0d1a..56f1d1d15 100644
Binary files a/examples/from_parsers/afni/narps_do_02_pc_with_sign0_block.png and b/examples/from_parsers/afni/narps_do_02_pc_with_sign0_block.png differ
diff --git a/examples/from_parsers/afni/narps_do_04_make_imgs_A.jsonld b/examples/from_parsers/afni/narps_do_04_make_imgs_A.jsonld
index 44729ca68..7043e2f1d 100644
--- a/examples/from_parsers/afni/narps_do_04_make_imgs_A.jsonld
+++ b/examples/from_parsers/afni/narps_do_04_make_imgs_A.jsonld
@@ -4,76 +4,76 @@
"Records": {
"Software": [
{
- "@id": "urn:330d4fc2-a9cb-4bec-a07d-d6330eba562c",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:afni-jIIjAQ4i",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
- "Version": "afni24"
+ "Version": "afni24",
+ "AltIdentifier": "RRID:SCR_005927"
}
],
"Activities": [
{
- "@id": "urn:86081194-0636-47f1-9e3b-b68114def1d2",
+ "@id": "urn:makedire-yn1TxmnM",
"Label": "Make directory",
- "AssociatedWith": "urn:330d4fc2-a9cb-4bec-a07d-d6330eba562c",
+ "AssociatedWith": "urn:afni-jIIjAQ4i",
"Command": "\\mkdir ${odir}",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:7c985012-41b6-48aa-8ae4-c809eb06bb31",
+ "@id": "urn:chauffeu-vqfOC3c7",
"Label": "@chauffeur_afni",
- "AssociatedWith": "urn:330d4fc2-a9cb-4bec-a07d-d6330eba562c",
+ "AssociatedWith": "urn:afni-jIIjAQ4i",
"Command": "@chauffeur_afni -ulay ${ref} -ulay_range \"2%\" \"110%\" -olay ${ff} -set_subbricks -1 0 0 -func_range 5 -thr_olay 3 -cbar Reds_and_Blues_Inv -olay_alpha Linear -olay_boxed Yes -opacity 7 -prefix ${odir}/img_${nnn}_alpha_${iid} -montx 1 -monty 1 -set_dicom_xyz 5 18 18 -set_xhairs OFF -label_string \"::${iid}\" -label_mode 1 -label_size 3 -do_clean",
"Parameters": {},
"Used": [
- "urn:b211929c-39f5-4ff2-a860-a505763c0865"
+ "bids::$%7Bref%7D"
]
},
{
- "@id": "urn:9649d954-d3f8-4d7f-9749-43c44cfb4870",
+ "@id": "urn:chauffeu-oq80JGUT",
"Label": "@chauffeur_afni",
- "AssociatedWith": "urn:330d4fc2-a9cb-4bec-a07d-d6330eba562c",
+ "AssociatedWith": "urn:afni-jIIjAQ4i",
"Command": "@chauffeur_afni -ulay ${ref} -ulay_range \"2%\" \"110%\" -olay ${ff} -set_subbricks -1 0 0 -func_range 5 -thr_olay 3 -cbar Reds_and_Blues_Inv -olay_alpha No -olay_boxed No -opacity 7 -prefix ${odir}/img_${nnn}_psi_${iid} -montx 1 -monty 1 -set_dicom_xyz 5 18 18 -set_xhairs OFF -label_string \"::${iid}\" -label_mode 1 -label_size 3 -do_clean",
"Parameters": {},
"Used": [
- "urn:b211929c-39f5-4ff2-a860-a505763c0865"
+ "bids::$%7Bref%7D"
]
},
{
- "@id": "urn:6e541d60-0c94-438b-954e-9eb5ef2f3afd",
+ "@id": "urn:adjunctc-i20W9Yge",
"Label": "adjunct_calc_mont_dims.py",
- "AssociatedWith": "urn:330d4fc2-a9cb-4bec-a07d-d6330eba562c",
+ "AssociatedWith": "urn:afni-jIIjAQ4i",
"Command": "adjunct_calc_mont_dims.py ${nallbase} __tmp_${hyp}",
"Parameters": {},
"Used": [
- "urn:6e9ff6ba-9946-4100-b10d-48c131fe1e8d"
+ "bids::nallbase"
]
},
{
- "@id": "urn:eb232e1e-58ae-4077-b3ad-87d1feb35b6c",
+ "@id": "urn:2dcat-OgarwyZa",
"Label": "2dcat",
- "AssociatedWith": "urn:330d4fc2-a9cb-4bec-a07d-d6330eba562c",
+ "AssociatedWith": "urn:afni-jIIjAQ4i",
"Command": "2dcat -echo_edu -gap 5 -gap_col ${lcol} -ny ${dims[4]} -nx ${dims[3]} -zero_wrap -prefix ${odir}/ALL_alpha_${hyp}_sview_${ss}.jpg ${odir}/img_*_alpha*${ss}*",
"Parameters": {},
"Used": [
- "urn:8273d1cf-36af-4d5a-b308-a5d717a67b33"
+ "bids::$%7Bodir%7D/img_*_alpha*$%7Bss%7D*"
]
},
{
- "@id": "urn:df9d2191-8a3a-45c5-9650-403521b23e4d",
+ "@id": "urn:2dcat-9kS1gW3n",
"Label": "2dcat",
- "AssociatedWith": "urn:330d4fc2-a9cb-4bec-a07d-d6330eba562c",
+ "AssociatedWith": "urn:afni-jIIjAQ4i",
"Command": "2dcat -echo_edu -gap 5 -gap_col ${lcol} -ny ${dims[4]} -nx ${dims[3]} -zero_wrap -prefix ${odir}/ALL_psi_${hyp}_sview_${ss}.jpg ${odir}/img_*_psi*${ss}*",
"Parameters": {},
"Used": [
- "urn:830c7ba4-21c4-4cb8-a251-90cd2636a179"
+ "bids::$%7Bodir%7D/img_*_psi*$%7Bss%7D*"
]
}
],
"Entities": [
{
- "@id": "urn:b211929c-39f5-4ff2-a860-a505763c0865",
+ "@id": "bids::$%7Bref%7D",
"Label": "${ref}",
"AtLocation": "${ref}",
"digest": {
@@ -81,25 +81,25 @@
}
},
{
- "@id": "urn:f71aba7e-cfbf-475d-a938-f89e03affa34",
+ "@id": "bids::$%7Bodir%7D/img_$%7Bnnn%7D_alpha_$%7Biid%7D",
"Label": "img_${nnn}_alpha_${iid}",
"AtLocation": "${odir}/img_${nnn}_alpha_${iid}",
- "GeneratedBy": "urn:7c985012-41b6-48aa-8ae4-c809eb06bb31",
+ "GeneratedBy": "urn:chauffeu-vqfOC3c7",
"digest": {
"sha256": "a0e5cbd9fe17cb80fe572ff230c1433b6f007d58746205bc6cf4747a1da48d1e"
}
},
{
- "@id": "urn:6bb2f2da-6e50-4376-958c-d807ba9130f4",
+ "@id": "bids::$%7Bodir%7D/img_$%7Bnnn%7D_psi_$%7Biid%7D",
"Label": "img_${nnn}_psi_${iid}",
"AtLocation": "${odir}/img_${nnn}_psi_${iid}",
- "GeneratedBy": "urn:9649d954-d3f8-4d7f-9749-43c44cfb4870",
+ "GeneratedBy": "urn:chauffeu-oq80JGUT",
"digest": {
"sha256": "7c339c3ad32d56d3fd94128ff49e2bd3d109fddaaaa46451e0a8d646ae23cfe3"
}
},
{
- "@id": "urn:6e9ff6ba-9946-4100-b10d-48c131fe1e8d",
+ "@id": "bids::nallbase",
"Label": "nallbase",
"AtLocation": "nallbase",
"digest": {
@@ -107,16 +107,16 @@
}
},
{
- "@id": "urn:d351d30f-a4e9-40b2-9de0-e697ad8f4e22",
+ "@id": "bids::__tmp_",
"Label": "__tmp_",
"AtLocation": "__tmp_",
- "GeneratedBy": "urn:6e541d60-0c94-438b-954e-9eb5ef2f3afd",
+ "GeneratedBy": "urn:adjunctc-i20W9Yge",
"digest": {
"sha256": "cdd06e3421f1953c55722187ed4a54d26fbbdabf2b77d6ba9abce36f2a9a8bbb"
}
},
{
- "@id": "urn:8273d1cf-36af-4d5a-b308-a5d717a67b33",
+ "@id": "bids::$%7Bodir%7D/img_*_alpha*$%7Bss%7D*",
"Label": "img_*_alpha*${ss}*",
"AtLocation": "${odir}/img_*_alpha*${ss}*",
"digest": {
@@ -124,16 +124,16 @@
}
},
{
- "@id": "urn:968c32d6-2eb2-4c77-9682-582fcb20b7b3",
+ "@id": "bids::$%7Bodir%7D/ALL_alpha_$%7Bhyp%7D_sview_$%7Bss%7D.jpg",
"Label": "ALL_alpha_${hyp}_sview_${ss}.jpg",
"AtLocation": "${odir}/ALL_alpha_${hyp}_sview_${ss}.jpg",
- "GeneratedBy": "urn:eb232e1e-58ae-4077-b3ad-87d1feb35b6c",
+ "GeneratedBy": "urn:2dcat-OgarwyZa",
"digest": {
"sha256": "b30960ff9bf2be10473ab3cdd82775a150362f0b714db8b55d263d0d94078ecf"
}
},
{
- "@id": "urn:830c7ba4-21c4-4cb8-a251-90cd2636a179",
+ "@id": "bids::$%7Bodir%7D/img_*_psi*$%7Bss%7D*",
"Label": "img_*_psi*${ss}*",
"AtLocation": "${odir}/img_*_psi*${ss}*",
"digest": {
@@ -141,10 +141,10 @@
}
},
{
- "@id": "urn:556ef24d-95ef-4bd6-9ece-befd90da3730",
+ "@id": "bids::$%7Bodir%7D/ALL_psi_$%7Bhyp%7D_sview_$%7Bss%7D.jpg",
"Label": "ALL_psi_${hyp}_sview_${ss}.jpg",
"AtLocation": "${odir}/ALL_psi_${hyp}_sview_${ss}.jpg",
- "GeneratedBy": "urn:df9d2191-8a3a-45c5-9650-403521b23e4d",
+ "GeneratedBy": "urn:2dcat-9kS1gW3n",
"digest": {
"sha256": "c9b97ba53a4832ccd96c2802949fe72dc1e3718be9fc91d8fd85375a99c4d290"
}
diff --git a/examples/from_parsers/afni/narps_do_04_make_imgs_A.png b/examples/from_parsers/afni/narps_do_04_make_imgs_A.png
index 1fa3bfbcf..cff9094e6 100644
Binary files a/examples/from_parsers/afni/narps_do_04_make_imgs_A.png and b/examples/from_parsers/afni/narps_do_04_make_imgs_A.png differ
diff --git a/examples/from_parsers/afni/narps_do_04_make_imgs_A_block.jsonld b/examples/from_parsers/afni/narps_do_04_make_imgs_A_block.jsonld
index 0e1af9b35..cf6a8d0eb 100644
--- a/examples/from_parsers/afni/narps_do_04_make_imgs_A_block.jsonld
+++ b/examples/from_parsers/afni/narps_do_04_make_imgs_A_block.jsonld
@@ -4,38 +4,38 @@
"Records": {
"Software": [
{
- "@id": "urn:d6a0021f-3b10-4fdc-9081-b66a5c08bfe9",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:afni-VLZIevJh",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
- "Version": "afni24"
+ "Version": "afni24",
+ "AltIdentifier": "RRID:SCR_005927"
}
],
"Activities": [
{
- "@id": "urn:a6d1d7d9-e39a-449b-b19f-74c4fdb27448",
+ "@id": "urn:-NU4cG5f8",
"Label": "",
- "AssociatedWith": "urn:d6a0021f-3b10-4fdc-9081-b66a5c08bfe9",
+ "AssociatedWith": "urn:afni-VLZIevJh",
"Command": "\\mkdir ${odir}; ",
"Used": []
},
{
- "@id": "urn:02936a64-481f-4382-8b6b-948a05e2ee63",
+ "@id": "urn:block-jBYVWSxh",
"Label": "block ...",
- "AssociatedWith": "urn:d6a0021f-3b10-4fdc-9081-b66a5c08bfe9",
+ "AssociatedWith": "urn:afni-VLZIevJh",
"Command": "@chauffeur_afni -ulay ${ref} -ulay_range \"2%\" \"110%\" -olay ${ff} -set_subbricks -1 0 0 -func_range 5 -thr_olay 3 -cbar Reds_and_Blues_Inv -olay_alpha Linear -olay_boxed Yes -opacity 7 -prefix ${odir}/img_${nnn}_alpha_${iid} -montx 1 -monty 1 -set_dicom_xyz 5 18 18 -set_xhairs OFF -label_string \"::${iid}\" -label_mode 1 -label_size 3 -do_clean; @chauffeur_afni -ulay ${ref} -ulay_range \"2%\" \"110%\" -olay ${ff} -set_subbricks -1 0 0 -func_range 5 -thr_olay 3 -cbar Reds_and_Blues_Inv -olay_alpha No -olay_boxed No -opacity 7 -prefix ${odir}/img_${nnn}_psi_${iid} -montx 1 -monty 1 -set_dicom_xyz 5 18 18 -set_xhairs OFF -label_string \"::${iid}\" -label_mode 1 -label_size 3 -do_clean; adjunct_calc_mont_dims.py ${nallbase} __tmp_${hyp}; 2dcat -echo_edu -gap 5 -gap_col ${lcol} -ny ${dims[4]} -nx ${dims[3]} -zero_wrap -prefix ${odir}/ALL_alpha_${hyp}_sview_${ss}.jpg ${odir}/img_*_alpha*${ss}*; 2dcat -echo_edu -gap 5 -gap_col ${lcol} -ny ${dims[4]} -nx ${dims[3]} -zero_wrap -prefix ${odir}/ALL_psi_${hyp}_sview_${ss}.jpg ${odir}/img_*_psi*${ss}*; ",
"Used": [
- "urn:cf470468-8935-47d3-9691-08ad68075642",
- "urn:cf470468-8935-47d3-9691-08ad68075642",
- "urn:f3d3c8eb-359a-40e9-8d1b-d12c2819bbfe",
- "urn:0ca738f1-7ffe-4315-ab71-a82a810cfb9c",
- "urn:85c3ce0a-f7b8-45ed-91e7-a7a671050994"
+ "bids::$%7Bref%7D",
+ "bids::$%7Bref%7D",
+ "bids::nallbase",
+ "bids::$%7Bodir%7D/img_*_alpha*$%7Bss%7D*",
+ "bids::$%7Bodir%7D/img_*_psi*$%7Bss%7D*"
]
}
],
"Entities": [
{
- "@id": "urn:cf470468-8935-47d3-9691-08ad68075642",
+ "@id": "bids::$%7Bref%7D",
"Label": "${ref}",
"AtLocation": "${ref}",
"digest": {
@@ -43,7 +43,7 @@
}
},
{
- "@id": "urn:f3d3c8eb-359a-40e9-8d1b-d12c2819bbfe",
+ "@id": "bids::nallbase",
"Label": "nallbase",
"AtLocation": "nallbase",
"digest": {
@@ -51,7 +51,7 @@
}
},
{
- "@id": "urn:0ca738f1-7ffe-4315-ab71-a82a810cfb9c",
+ "@id": "bids::$%7Bodir%7D/img_*_alpha*$%7Bss%7D*",
"Label": "img_*_alpha*${ss}*",
"AtLocation": "${odir}/img_*_alpha*${ss}*",
"digest": {
@@ -59,7 +59,7 @@
}
},
{
- "@id": "urn:85c3ce0a-f7b8-45ed-91e7-a7a671050994",
+ "@id": "bids::$%7Bodir%7D/img_*_psi*$%7Bss%7D*",
"Label": "img_*_psi*${ss}*",
"AtLocation": "${odir}/img_*_psi*${ss}*",
"digest": {
@@ -67,46 +67,46 @@
}
},
{
- "@id": "urn:c9c0d4d9-bd85-425e-b9c7-bb4537311f58",
+ "@id": "bids::$%7Bodir%7D/img_$%7Bnnn%7D_alpha_$%7Biid%7D",
"Label": "img_${nnn}_alpha_${iid}",
"AtLocation": "${odir}/img_${nnn}_alpha_${iid}",
- "GeneratedBy": "urn:02936a64-481f-4382-8b6b-948a05e2ee63",
+ "GeneratedBy": "urn:block-jBYVWSxh",
"digest": {
"sha256": "a0e5cbd9fe17cb80fe572ff230c1433b6f007d58746205bc6cf4747a1da48d1e"
}
},
{
- "@id": "urn:afd73d9e-98e4-49e9-bb72-38124a2423c9",
+ "@id": "bids::$%7Bodir%7D/img_$%7Bnnn%7D_psi_$%7Biid%7D",
"Label": "img_${nnn}_psi_${iid}",
"AtLocation": "${odir}/img_${nnn}_psi_${iid}",
- "GeneratedBy": "urn:02936a64-481f-4382-8b6b-948a05e2ee63",
+ "GeneratedBy": "urn:block-jBYVWSxh",
"digest": {
"sha256": "7c339c3ad32d56d3fd94128ff49e2bd3d109fddaaaa46451e0a8d646ae23cfe3"
}
},
{
- "@id": "urn:861e89e6-1845-4582-a116-5e03e9fcc252",
+ "@id": "bids::__tmp_",
"Label": "__tmp_",
"AtLocation": "__tmp_",
- "GeneratedBy": "urn:02936a64-481f-4382-8b6b-948a05e2ee63",
+ "GeneratedBy": "urn:block-jBYVWSxh",
"digest": {
"sha256": "cdd06e3421f1953c55722187ed4a54d26fbbdabf2b77d6ba9abce36f2a9a8bbb"
}
},
{
- "@id": "urn:7810aa9d-85e0-453b-abae-a626eabca20e",
+ "@id": "bids::$%7Bodir%7D/ALL_alpha_$%7Bhyp%7D_sview_$%7Bss%7D.jpg",
"Label": "ALL_alpha_${hyp}_sview_${ss}.jpg",
"AtLocation": "${odir}/ALL_alpha_${hyp}_sview_${ss}.jpg",
- "GeneratedBy": "urn:02936a64-481f-4382-8b6b-948a05e2ee63",
+ "GeneratedBy": "urn:block-jBYVWSxh",
"digest": {
"sha256": "b30960ff9bf2be10473ab3cdd82775a150362f0b714db8b55d263d0d94078ecf"
}
},
{
- "@id": "urn:5066b42d-c30f-4ef9-bcd0-3a0d0fe6ad41",
+ "@id": "bids::$%7Bodir%7D/ALL_psi_$%7Bhyp%7D_sview_$%7Bss%7D.jpg",
"Label": "ALL_psi_${hyp}_sview_${ss}.jpg",
"AtLocation": "${odir}/ALL_psi_${hyp}_sview_${ss}.jpg",
- "GeneratedBy": "urn:02936a64-481f-4382-8b6b-948a05e2ee63",
+ "GeneratedBy": "urn:block-jBYVWSxh",
"digest": {
"sha256": "c9b97ba53a4832ccd96c2802949fe72dc1e3718be9fc91d8fd85375a99c4d290"
}
diff --git a/examples/from_parsers/afni/narps_do_04_make_imgs_A_block.png b/examples/from_parsers/afni/narps_do_04_make_imgs_A_block.png
index 46aac5b21..712563c1d 100644
Binary files a/examples/from_parsers/afni/narps_do_04_make_imgs_A_block.png and b/examples/from_parsers/afni/narps_do_04_make_imgs_A_block.png differ
diff --git a/examples/from_parsers/afni/narps_do_13_view_zoom.jsonld b/examples/from_parsers/afni/narps_do_13_view_zoom.jsonld
index f787854e5..ee5ddeb5c 100644
--- a/examples/from_parsers/afni/narps_do_13_view_zoom.jsonld
+++ b/examples/from_parsers/afni/narps_do_13_view_zoom.jsonld
@@ -4,44 +4,44 @@
"Records": {
"Software": [
{
- "@id": "urn:f5e4ae76-a5a0-4b3d-876d-4183e80d5a95",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:afni-wiCVuDES",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
- "Version": "afni24"
+ "Version": "afni24",
+ "AltIdentifier": "RRID:SCR_005927"
}
],
"Activities": [
{
- "@id": "urn:a2172ef5-7a19-4922-a6b7-0a36a1766ded",
+ "@id": "urn:makedire-zyl0QmyL",
"Label": "Make directory",
- "AssociatedWith": "urn:f5e4ae76-a5a0-4b3d-876d-4183e80d5a95",
+ "AssociatedWith": "urn:afni-wiCVuDES",
"Command": "mkdir -p ${odir}",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:befe22ef-add6-4ad8-b093-fe79bd549d51",
+ "@id": "urn:isosurfa-6HaOfiy0",
"Label": "IsoSurface",
- "AssociatedWith": "urn:f5e4ae76-a5a0-4b3d-876d-4183e80d5a95",
+ "AssociatedWith": "urn:afni-wiCVuDES",
"Command": "IsoSurface -overwrite -isorois+dsets -input ${ivol} -o_gii cc_${pref_surf} -Tsmooth 0 0 -remesh 1",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:26c558ba-8b6d-4b5c-bf5b-936db5ea9a5f",
+ "@id": "urn:1dtoolpy-duovL16A",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:f5e4ae76-a5a0-4b3d-876d-4183e80d5a95",
+ "AssociatedWith": "urn:afni-wiCVuDES",
"Command": "1d_tool.py -csim_pthr ${pthr} -csim_alpha ${alpha} -infile ${file_1D}",
"Parameters": {},
"Used": [
- "urn:ee0f5301-e428-4406-9bbe-45eb8e1fe8da"
+ "bids::$%7Bfile_1D%7D"
]
},
{
- "@id": "urn:b7b77d81-1384-436c-80a5-7f0f62115948",
+ "@id": "urn:plugoutd-Mi2Op0t1",
"Label": "plugout_drive",
- "AssociatedWith": "urn:f5e4ae76-a5a0-4b3d-876d-4183e80d5a95",
+ "AssociatedWith": "urn:afni-wiCVuDES",
"Command": "plugout_drive -echo_edu -npb $portnum -com \"SWITCH_UNDERLAY ${dset_ref:t}\" -com \"SWITCH_OVERLAY ${dset_ttest:t}\" -com \"SET_XHAIRS OFF\" -com \"SET_SUBBRICKS ${subbb}\" -com \"SET_PBAR_ALL -99 1.0 ${cbar}\" -com \"SET_FUNC_ALPHA ${olay_alpha}\" -com \"SET_FUNC_BOXED ${olay_boxed}\" -com \"$coor_type $coors\" -com \"SET_THRESHNEW ${thr}\" -com \"SET_FUNC_VISIBLE +\" -com \"SET_FUNC_RANGE $frange\" -com \"$OW sagittalimage ifrac=${ifrac} opacity=${opac} mont=${mx}x${my}:${gapord[1]}:${mgap}:${mcolor}\" -com \"$OW coronalimage ifrac=${ifrac} opacity=${opac} mont=${mx}x${my}:${gapord[2]}:${mgap}:${mcolor}\" -com \"$OW axialimage ifrac=${ifrac} opacity=${opac} mont=${mx}x${my}:${gapord[3]}:${mgap}:${mcolor}\" &",
"Parameters": {
"-echo_edu": true,
@@ -50,23 +50,23 @@
"-99": "1.0"
},
"Used": [
- "urn:5b8c4638-771b-45cf-843f-eed11904b166"
+ "bids::portnum"
]
},
{
- "@id": "urn:52b5a16d-e063-4b0b-828e-c4143d18e14d",
+ "@id": "urn:suma-l1dTtGBm",
"Label": "suma",
- "AssociatedWith": "urn:f5e4ae76-a5a0-4b3d-876d-4183e80d5a95",
+ "AssociatedWith": "urn:afni-wiCVuDES",
"Command": "suma -echo_edu -npb $portnum -onestate -niml -i cc*.k*.gii -vol ${dset_ref} -sv ${dset_ref} &",
"Parameters": {},
"Used": [
- "urn:e1ae001c-ae9b-4f3a-93c6-0c1645cc0cc6"
+ "bids::cc*.k*.gii"
]
},
{
- "@id": "urn:e5cde463-e48d-484b-b743-a9a652b0f3bb",
+ "@id": "urn:drivesum-urGoHOyw",
"Label": "DriveSuma",
- "AssociatedWith": "urn:f5e4ae76-a5a0-4b3d-876d-4183e80d5a95",
+ "AssociatedWith": "urn:afni-wiCVuDES",
"Command": "DriveSuma -npb $portnum -com viewer_cont -key \"t\" -key \".\" &",
"Parameters": {
"-npb": "$portnum",
@@ -78,25 +78,25 @@
],
"Entities": [
{
- "@id": "urn:2486fe67-6767-4b41-ad86-0d8b7dd40624",
+ "@id": "bids::$%7Bodir%7D",
"Label": "${odir}",
"AtLocation": "${odir}",
- "GeneratedBy": "urn:a2172ef5-7a19-4922-a6b7-0a36a1766ded",
+ "GeneratedBy": "urn:makedire-zyl0QmyL",
"digest": {
"sha256": "b1fc5ec0acec0bf1a5d6697b7f63ed3b4c8e33adcb77445bc544e124ade50c60"
}
},
{
- "@id": "urn:69edfdc1-cb09-4f41-8510-b0ac07b3c949",
+ "@id": "bids::cc_$%7Bpref_surf%7D",
"Label": "cc_${pref_surf}",
"AtLocation": "cc_${pref_surf}",
- "GeneratedBy": "urn:befe22ef-add6-4ad8-b093-fe79bd549d51",
+ "GeneratedBy": "urn:isosurfa-6HaOfiy0",
"digest": {
"sha256": "5e02dacb1f0d92310532c03d04b14d6bdc19634a71800752df6d2e4f1adadf06"
}
},
{
- "@id": "urn:ee0f5301-e428-4406-9bbe-45eb8e1fe8da",
+ "@id": "bids::$%7Bfile_1D%7D",
"Label": "${file_1D}",
"AtLocation": "${file_1D}",
"digest": {
@@ -104,7 +104,7 @@
}
},
{
- "@id": "urn:5b8c4638-771b-45cf-843f-eed11904b166",
+ "@id": "bids::portnum",
"Label": "portnum",
"AtLocation": "portnum",
"digest": {
@@ -112,16 +112,16 @@
}
},
{
- "@id": "urn:b0bca173-59eb-49c7-845a-74d5b96dfc0a",
+ "@id": "bids::mcolor",
"Label": "mcolor",
"AtLocation": "mcolor",
- "GeneratedBy": "urn:b7b77d81-1384-436c-80a5-7f0f62115948",
+ "GeneratedBy": "urn:plugoutd-Mi2Op0t1",
"digest": {
"sha256": "a757facd6497c040401a26469144a2df7ad28984bf0e7688a2f32d607fcd6797"
}
},
{
- "@id": "urn:e1ae001c-ae9b-4f3a-93c6-0c1645cc0cc6",
+ "@id": "bids::cc*.k*.gii",
"Label": "cc*.k*.gii",
"AtLocation": "cc*.k*.gii",
"digest": {
diff --git a/examples/from_parsers/afni/narps_do_13_view_zoom.png b/examples/from_parsers/afni/narps_do_13_view_zoom.png
index 41c1c1ad6..9c6a266b2 100644
Binary files a/examples/from_parsers/afni/narps_do_13_view_zoom.png and b/examples/from_parsers/afni/narps_do_13_view_zoom.png differ
diff --git a/examples/from_parsers/afni/narps_do_13_view_zoom_block.jsonld b/examples/from_parsers/afni/narps_do_13_view_zoom_block.jsonld
index 498a2b788..96d855600 100644
--- a/examples/from_parsers/afni/narps_do_13_view_zoom_block.jsonld
+++ b/examples/from_parsers/afni/narps_do_13_view_zoom_block.jsonld
@@ -4,45 +4,45 @@
"Records": {
"Software": [
{
- "@id": "urn:7891b04d-79c7-490c-b5ae-53a2d9225899",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:afni-UTYTzyNw",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
- "Version": "afni24"
+ "Version": "afni24",
+ "AltIdentifier": "RRID:SCR_005927"
}
],
"Activities": [
{
- "@id": "urn:ee9fc801-0cec-47c2-b99d-60a01df64f52",
+ "@id": "urn:-XCHU0CSU",
"Label": "",
- "AssociatedWith": "urn:7891b04d-79c7-490c-b5ae-53a2d9225899",
+ "AssociatedWith": "urn:afni-UTYTzyNw",
"Command": "mkdir -p ${odir}; ",
"Used": []
},
{
- "@id": "urn:59855331-85db-49d2-b637-e7f573189444",
+ "@id": "urn:block-8SCS9Ax3",
"Label": "block ...",
- "AssociatedWith": "urn:7891b04d-79c7-490c-b5ae-53a2d9225899",
+ "AssociatedWith": "urn:afni-UTYTzyNw",
"Command": "IsoSurface -overwrite -isorois+dsets -input ${ivol} -o_gii cc_${pref_surf} -Tsmooth 0 0 -remesh 1; 1d_tool.py -csim_pthr ${pthr} -csim_alpha ${alpha} -infile ${file_1D}; plugout_drive -echo_edu -npb $portnum -com \"SWITCH_UNDERLAY ${dset_ref:t}\" -com \"SWITCH_OVERLAY ${dset_ttest:t}\" -com \"SET_XHAIRS OFF\" -com \"SET_SUBBRICKS ${subbb}\" -com \"SET_PBAR_ALL -99 1.0 ${cbar}\" -com \"SET_FUNC_ALPHA ${olay_alpha}\" -com \"SET_FUNC_BOXED ${olay_boxed}\" -com \"$coor_type $coors\" -com \"SET_THRESHNEW ${thr}\" -com \"SET_FUNC_VISIBLE +\" -com \"SET_FUNC_RANGE $frange\" -com \"$OW sagittalimage ifrac=${ifrac} opacity=${opac} mont=${mx}x${my}:${gapord[1]}:${mgap}:${mcolor}\" -com \"$OW coronalimage ifrac=${ifrac} opacity=${opac} mont=${mx}x${my}:${gapord[2]}:${mgap}:${mcolor}\" -com \"$OW axialimage ifrac=${ifrac} opacity=${opac} mont=${mx}x${my}:${gapord[3]}:${mgap}:${mcolor}\" &; suma -echo_edu -npb $portnum -onestate -niml -i cc*.k*.gii -vol ${dset_ref} -sv ${dset_ref} &; DriveSuma -npb $portnum -com viewer_cont -key \"t\" -key \".\" &; ",
"Used": [
- "urn:ec3fde1b-e382-4f29-a2ba-e04bbd8c559b",
- "urn:ada01202-ea7b-4b88-b337-d7350ee0a693",
- "urn:da3d5f91-9e99-4368-8202-f07e1a5015c0"
+ "bids::$%7Bfile_1D%7D",
+ "bids::portnum",
+ "bids::cc*.k*.gii"
]
}
],
"Entities": [
{
- "@id": "urn:3dd604e1-8ae3-4359-bff8-ca1746af6d4f",
+ "@id": "bids::$%7Bodir%7D",
"Label": "${odir}",
"AtLocation": "${odir}",
- "GeneratedBy": "urn:ee9fc801-0cec-47c2-b99d-60a01df64f52",
+ "GeneratedBy": "urn:-XCHU0CSU",
"digest": {
"sha256": "b1fc5ec0acec0bf1a5d6697b7f63ed3b4c8e33adcb77445bc544e124ade50c60"
}
},
{
- "@id": "urn:ec3fde1b-e382-4f29-a2ba-e04bbd8c559b",
+ "@id": "bids::$%7Bfile_1D%7D",
"Label": "${file_1D}",
"AtLocation": "${file_1D}",
"digest": {
@@ -50,7 +50,7 @@
}
},
{
- "@id": "urn:ada01202-ea7b-4b88-b337-d7350ee0a693",
+ "@id": "bids::portnum",
"Label": "portnum",
"AtLocation": "portnum",
"digest": {
@@ -58,7 +58,7 @@
}
},
{
- "@id": "urn:da3d5f91-9e99-4368-8202-f07e1a5015c0",
+ "@id": "bids::cc*.k*.gii",
"Label": "cc*.k*.gii",
"AtLocation": "cc*.k*.gii",
"digest": {
@@ -66,19 +66,19 @@
}
},
{
- "@id": "urn:c91f3941-0dd2-459c-978d-8e8c2226af18",
+ "@id": "bids::cc_$%7Bpref_surf%7D",
"Label": "cc_${pref_surf}",
"AtLocation": "cc_${pref_surf}",
- "GeneratedBy": "urn:59855331-85db-49d2-b637-e7f573189444",
+ "GeneratedBy": "urn:block-8SCS9Ax3",
"digest": {
"sha256": "5e02dacb1f0d92310532c03d04b14d6bdc19634a71800752df6d2e4f1adadf06"
}
},
{
- "@id": "urn:f4c23dd9-74c7-4efe-9d1e-3d547ac64d81",
+ "@id": "bids::mcolor",
"Label": "mcolor",
"AtLocation": "mcolor",
- "GeneratedBy": "urn:59855331-85db-49d2-b637-e7f573189444",
+ "GeneratedBy": "urn:block-8SCS9Ax3",
"digest": {
"sha256": "a757facd6497c040401a26469144a2df7ad28984bf0e7688a2f32d607fcd6797"
}
diff --git a/examples/from_parsers/afni/narps_do_13_view_zoom_block.png b/examples/from_parsers/afni/narps_do_13_view_zoom_block.png
index f0392df5c..d27ec2b7d 100644
Binary files a/examples/from_parsers/afni/narps_do_13_view_zoom_block.png and b/examples/from_parsers/afni/narps_do_13_view_zoom_block.png differ
diff --git a/examples/from_parsers/context_2024_06_13_07h55m05s.txt b/examples/from_parsers/context_2024_10_04_12h28m38s.txt
similarity index 98%
rename from examples/from_parsers/context_2024_06_13_07h55m05s.txt
rename to examples/from_parsers/context_2024_10_04_12h28m38s.txt
index 0c0d575b3..d1bda5cc8 100644
--- a/examples/from_parsers/context_2024_06_13_07h55m05s.txt
+++ b/examples/from_parsers/context_2024_10_04_12h28m38s.txt
@@ -1,4 +1,4 @@
-Date : 2024_06_13_07h55m05s
+Date : 2024_10_04_12h28m38s
Processing files...
file= nidmresults-examples/afni_alt_onesided_proc.sub_001
file= nidmresults-examples/afni_alt_onesided_proc.sub_001
@@ -69,4 +69,4 @@ Processing files...
file= nidmresults-examples/spm_thr_voxelfdrp05_batch.m
file= nidmresults-examples/spm_thr_voxelfwep05_batch.m
file= nidmresults-examples/spm_thr_voxelunct4_batch.m
-End of processed files. Results in dir : 'examples/from_parsers'. Time required: 0:00:02.365113
+End of processed files. Results in dir : 'examples/from_parsers'. Time required: 0:01:09.558909
diff --git a/examples/from_parsers/fsl/fsl_con_f_multiple_report_log.html b/examples/from_parsers/fsl/fsl_con_f_multiple_report_log.html
index 9c688d675..d79bee5e9 100644
--- a/examples/from_parsers/fsl/fsl_con_f_multiple_report_log.html
+++ b/examples/from_parsers/fsl/fsl_con_f_multiple_report_log.html
@@ -35,14 +35,14 @@ Progress Report / Log
/usr/local/packages/fsl-5.0.8/bin/fslroi prefiltered_func_data example_func 52 1
Preprocessing:Stage 1
-/usr/local/packages/fsl-5.0.8/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90
+/usr/local/packages/fsl-5.0.8/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/example_func.nii.gz -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90
Option -F ( FEAT version parameter ) selected with argument "6.00"
Option -d ( output directory ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat"
Option -l ( logfile )input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/logs/feat2_pre"
Option -R ( html unwarping report ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/report_unwarp.html"
Option -r ( html registration report ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/report_reg.html"
Option -i ( main input ) input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/example_func.nii.gz"
-Option -h ( high-res structural image ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
+Option -h ( high-res structural image ) selected with argument "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
Option -w ( highres dof ) selected with argument "BBR"
Option -x ( highres search ) selected with argument "90"
Option -s ( standard image ) selected with argument "/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain"
@@ -53,10 +53,10 @@ Progress Report / Log
/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/reg
-/usr/local/packages/fsl-5.0.8/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
+/usr/local/packages/fsl-5.0.8/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
-/usr/local/packages/fsl-5.0.8/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres_head
+/usr/local/packages/fsl-5.0.8/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres_head
/usr/local/packages/fsl-5.0.8/bin/fslmaths /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain standard
@@ -151,9 +151,9 @@ Progress Report / Log
/bin/rm -rf prefiltered_func_data*
Stats
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.8/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.8/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.8/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.8/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
/usr/local/packages/fsl-5.0.8/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con --fcon=design.fts
Log directory is: stats
diff --git a/examples/from_parsers/fsl/fsl_con_f_multiple_report_log.jsonld b/examples/from_parsers/fsl/fsl_con_f_multiple_report_log.jsonld
index 28af90fdb..d25d87e28 100644
--- a/examples/from_parsers/fsl/fsl_con_f_multiple_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_con_f_multiple_report_log.jsonld
@@ -4,1143 +4,1153 @@
"Records": {
"Software": [
{
- "@id": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:fsl-RWQkET6j",
"@type": "prov:SoftwareAgent",
"Label": "FSL",
- "Version": "xxx"
+ "Version": "xxx",
+ "AltIdentifier": "RRID:SCR_002823"
}
],
"Activities": [
{
- "@id": "urn:39f1ca8b-66d3-4d02-b1e6-5af2de7b426a",
+ "@id": "urn:fslmaths-X40sMWOm",
"Label": "fslmaths",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths /home/tommaullin/Documents/Data/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
"Used": [
- "urn:2d8d1329-479a-44e0-9894-05aabc7d7877"
+ "bids::/home/tommaullin/Documents/Data/ds011/sub-01/func/sub-01_task-tonecounting_bold"
]
},
{
- "@id": "urn:19fb39c5-b85c-4be4-8f4a-c8be81315b19",
+ "@id": "urn:fslroi-oh19ScPe",
"Label": "fslroi",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslroi prefiltered_func_data example_func 52 1",
"Used": [
- "urn:6bbcef9d-c59c-420e-af06-7b51ccae0169"
+ "bids::prefiltered_func_data"
]
},
{
- "@id": "urn:60e714fe-8ee1-42e7-a6da-d0bd9dde8c93",
+ "@id": "urn:mainfeat-aTrcG3Fx",
"Label": "mainfeatreg",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
- "Command": "/usr/local/packages/fsl-5.0.8/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
+ "Command": "/usr/local/packages/fsl-5.0.8/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/example_func.nii.gz -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
"Used": [
- "urn:06b049a4-fd81-489d-b3c8-ce116f153f26",
- "urn:164dec41-95f0-4393-bd4e-a73b5b698322",
- "urn:cbc9d9a1-d1a6-44f4-a551-6a3c652bccbc"
+ "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/example_func.nii.gz",
+ "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain",
+ "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
]
},
{
- "@id": "urn:608b662d-4757-4c39-94d5-44c28ff93938",
+ "@id": "urn:makedire-3zzI0Agw",
"Label": "Make directory",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/reg",
"Used": []
},
{
- "@id": "urn:3e1a6330-6d27-41ed-b2d7-f50b8348f477",
+ "@id": "urn:fslmaths-w3sXEcK0",
"Label": "fslmaths",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
- "Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
+ "Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
"Used": [
- "urn:164dec41-95f0-4393-bd4e-a73b5b698322"
+ "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
]
},
{
- "@id": "urn:e7e28ef4-f1eb-482b-8d94-6a0f1f9ef566",
+ "@id": "urn:fslmaths-QEpXdgnq",
"Label": "fslmaths",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
- "Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres_head",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
+ "Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres_head",
"Used": [
- "urn:164dec41-95f0-4393-bd4e-a73b5b698322"
+ "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
]
},
{
- "@id": "urn:9b581ae8-7368-4411-84c6-4d66165bd5c4",
+ "@id": "urn:fslmaths-pZHZsQhS",
"Label": "fslmaths",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain standard",
"Used": [
- "urn:cbc9d9a1-d1a6-44f4-a551-6a3c652bccbc"
+ "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain"
]
},
{
- "@id": "urn:331e2b4a-aba9-414d-b93d-abc5a7b6ed3b",
+ "@id": "urn:epireg-fHxZonCr",
"Label": "epi_reg",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres",
- "Used": []
+ "Used": [
+ "bids::example_func",
+ "bids::highres",
+ "bids::highres_head"
+ ]
},
{
- "@id": "urn:4d350b62-1091-4725-af58-4f40d3f08a39",
+ "@id": "urn:convertx-hYXi1Bs2",
"Label": "convert_xfm",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat",
"Used": [
- "urn:ab16f273-2c0a-4821-ba88-1636745d121a"
+ "bids::example_func2highres.mat"
]
},
{
- "@id": "urn:20ea2776-872a-45b1-a331-31916a8cedd1",
+ "@id": "urn:slicer-sVwU0TQP",
"Label": "slicer",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:335ec760-8131-4706-84e5-ec26bcbb76aa",
- "urn:cb238dbf-75c3-47f0-a085-fd84a05307a3"
+ "bids::example_func2highres",
+ "bids::highres"
]
},
{
- "@id": "urn:a480128c-f2e7-4ae8-8701-3b370caca2e4",
+ "@id": "urn:pngappen-3fyJh6cv",
"Label": "pngappend",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres1.png",
"Used": [
- "urn:30d22fd1-b991-44ff-a846-4cd67a2ceebf",
- "urn:3140a577-2df8-4acd-aa3b-9982b5902b0b",
- "urn:3a9ac2c0-6d83-46a5-9337-3e2a7dd912ec",
- "urn:47b36bbc-f1ff-4bbd-8c90-6f05275ec35f",
- "urn:4da92ba7-72e4-4de2-aee1-4c5bcac55b24",
- "urn:4de0ea67-369a-452f-9771-14224cec49ca",
- "urn:61c386a1-698a-46a2-a770-18e5ec43fcf8",
- "urn:bc5744d3-5449-453a-ae20-bbc6e990f4b4",
- "urn:bcc2a705-8e18-420a-976a-0a7618110f5f",
- "urn:bcc8aaac-4310-4786-8364-ddfe40fd5712",
- "urn:bd9ba12f-ca5a-4b94-b3ef-b1630faf29b2",
- "urn:e169e92d-af0e-44de-9e28-1903bc99ef94"
+ "bids::sla.png",
+ "bids::slb.png",
+ "bids::slc.png",
+ "bids::sld.png",
+ "bids::sle.png",
+ "bids::slf.png",
+ "bids::slg.png",
+ "bids::slh.png",
+ "bids::sli.png",
+ "bids::slj.png",
+ "bids::slk.png",
+ "bids::sll.png"
]
},
{
- "@id": "urn:d2e6341a-2c4e-4dfd-a507-10d4a06328cb",
+ "@id": "urn:slicer-IZBDalQP",
"Label": "slicer",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:335ec760-8131-4706-84e5-ec26bcbb76aa",
- "urn:cb238dbf-75c3-47f0-a085-fd84a05307a3"
+ "bids::example_func2highres",
+ "bids::highres"
]
},
{
- "@id": "urn:d1faa8a8-b3c1-4927-9969-0cff951f9d13",
+ "@id": "urn:pngappen-zkTzwqDN",
"Label": "pngappend",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres2.png",
"Used": [
- "urn:30d22fd1-b991-44ff-a846-4cd67a2ceebf",
- "urn:3140a577-2df8-4acd-aa3b-9982b5902b0b",
- "urn:3a9ac2c0-6d83-46a5-9337-3e2a7dd912ec",
- "urn:47b36bbc-f1ff-4bbd-8c90-6f05275ec35f",
- "urn:4da92ba7-72e4-4de2-aee1-4c5bcac55b24",
- "urn:4de0ea67-369a-452f-9771-14224cec49ca",
- "urn:61c386a1-698a-46a2-a770-18e5ec43fcf8",
- "urn:bc5744d3-5449-453a-ae20-bbc6e990f4b4",
- "urn:bcc2a705-8e18-420a-976a-0a7618110f5f",
- "urn:bcc8aaac-4310-4786-8364-ddfe40fd5712",
- "urn:bd9ba12f-ca5a-4b94-b3ef-b1630faf29b2",
- "urn:e169e92d-af0e-44de-9e28-1903bc99ef94"
+ "bids::sla.png",
+ "bids::slb.png",
+ "bids::slc.png",
+ "bids::sld.png",
+ "bids::sle.png",
+ "bids::slf.png",
+ "bids::slg.png",
+ "bids::slh.png",
+ "bids::sli.png",
+ "bids::slj.png",
+ "bids::slk.png",
+ "bids::sll.png"
]
},
{
- "@id": "urn:1b7d2ad3-8d29-4aef-a8fa-f9fb4bbb9a40",
+ "@id": "urn:pngappen-vIamPDjN",
"Label": "pngappend",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/pngappend example_func2highres1.png example_func2highres2.png example_func2highres.png",
"Used": [
- "urn:50d48bd5-727e-4b5c-85d0-84a98ef98fa2",
- "urn:8f3ed102-329d-4e15-ae8d-d8487158a7e8"
+ "bids::example_func2highres1.png",
+ "bids::example_func2highres2.png"
]
},
{
- "@id": "urn:3b2b28ba-ed52-4d32-bd20-a000c0400aab",
+ "@id": "urn:rm-OKQx0V46",
"Label": "rm",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/bin/rm -f sl?.png example_func2highres2.png",
"Used": [
- "urn:07c0c668-0989-448b-bf80-146e799b0890",
- "urn:50d48bd5-727e-4b5c-85d0-84a98ef98fa2"
+ "bids::example_func2highres2.png",
+ "bids::sl?.png"
]
},
{
- "@id": "urn:49b0f0fb-21e2-4832-8ca3-db889a5448e9",
+ "@id": "urn:rm-YNr6d9hV",
"Label": "rm",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/bin/rm example_func2highres1.png",
"Used": [
- "urn:8f3ed102-329d-4e15-ae8d-d8487158a7e8"
+ "bids::example_func2highres1.png"
]
},
{
- "@id": "urn:4d9601c7-6917-4b90-93c0-4d87f3eddf11",
+ "@id": "urn:flirt-3JDHmTy3",
"Label": "flirt",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/flirt -in highres -ref standard -out highres2standard -omat highres2standard.mat -cost corratio -dof 12 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear",
"Used": [
- "urn:71da4817-5c97-4d51-ac51-760d380d635b",
- "urn:cb238dbf-75c3-47f0-a085-fd84a05307a3"
+ "bids::highres",
+ "bids::standard"
]
},
{
- "@id": "urn:38c17bbc-be12-48da-8ba9-ce5a9511513a",
+ "@id": "urn:convertx-4mENLjfA",
"Label": "convert_xfm",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/convert_xfm -inverse -omat standard2highres.mat highres2standard.mat",
"Used": [
- "urn:5a3b604b-22dc-4710-981b-3474bb824324"
+ "bids::highres2standard.mat"
]
},
{
- "@id": "urn:91ea8032-3aff-4df0-aa5c-1437dda477f2",
+ "@id": "urn:slicer-9X1OkKJ1",
"Label": "slicer",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/slicer highres2standard standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:592f88cc-114e-41ab-9d6a-e95cfddb13f4",
- "urn:71da4817-5c97-4d51-ac51-760d380d635b"
+ "bids::highres2standard",
+ "bids::standard"
]
},
{
- "@id": "urn:821222ba-cb2f-47a8-bc1b-6bb24d814509",
+ "@id": "urn:pngappen-dBq2Zzk0",
"Label": "pngappend",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png highres2standard1.png",
"Used": [
- "urn:30d22fd1-b991-44ff-a846-4cd67a2ceebf",
- "urn:3140a577-2df8-4acd-aa3b-9982b5902b0b",
- "urn:3a9ac2c0-6d83-46a5-9337-3e2a7dd912ec",
- "urn:47b36bbc-f1ff-4bbd-8c90-6f05275ec35f",
- "urn:4da92ba7-72e4-4de2-aee1-4c5bcac55b24",
- "urn:4de0ea67-369a-452f-9771-14224cec49ca",
- "urn:61c386a1-698a-46a2-a770-18e5ec43fcf8",
- "urn:bc5744d3-5449-453a-ae20-bbc6e990f4b4",
- "urn:bcc2a705-8e18-420a-976a-0a7618110f5f",
- "urn:bcc8aaac-4310-4786-8364-ddfe40fd5712",
- "urn:bd9ba12f-ca5a-4b94-b3ef-b1630faf29b2",
- "urn:e169e92d-af0e-44de-9e28-1903bc99ef94"
+ "bids::sla.png",
+ "bids::slb.png",
+ "bids::slc.png",
+ "bids::sld.png",
+ "bids::sle.png",
+ "bids::slf.png",
+ "bids::slg.png",
+ "bids::slh.png",
+ "bids::sli.png",
+ "bids::slj.png",
+ "bids::slk.png",
+ "bids::sll.png"
]
},
{
- "@id": "urn:62eb0889-4f7f-4b45-afa7-be2f445b4d65",
+ "@id": "urn:slicer-Ll7VbI1E",
"Label": "slicer",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/slicer standard highres2standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:592f88cc-114e-41ab-9d6a-e95cfddb13f4",
- "urn:71da4817-5c97-4d51-ac51-760d380d635b"
+ "bids::highres2standard",
+ "bids::standard"
]
},
{
- "@id": "urn:d7134c48-220f-433f-b3b7-c18b5b63915d",
+ "@id": "urn:pngappen-smb7ArFx",
"Label": "pngappend",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png highres2standard2.png",
"Used": [
- "urn:30d22fd1-b991-44ff-a846-4cd67a2ceebf",
- "urn:3140a577-2df8-4acd-aa3b-9982b5902b0b",
- "urn:3a9ac2c0-6d83-46a5-9337-3e2a7dd912ec",
- "urn:47b36bbc-f1ff-4bbd-8c90-6f05275ec35f",
- "urn:4da92ba7-72e4-4de2-aee1-4c5bcac55b24",
- "urn:4de0ea67-369a-452f-9771-14224cec49ca",
- "urn:61c386a1-698a-46a2-a770-18e5ec43fcf8",
- "urn:bc5744d3-5449-453a-ae20-bbc6e990f4b4",
- "urn:bcc2a705-8e18-420a-976a-0a7618110f5f",
- "urn:bcc8aaac-4310-4786-8364-ddfe40fd5712",
- "urn:bd9ba12f-ca5a-4b94-b3ef-b1630faf29b2",
- "urn:e169e92d-af0e-44de-9e28-1903bc99ef94"
+ "bids::sla.png",
+ "bids::slb.png",
+ "bids::slc.png",
+ "bids::sld.png",
+ "bids::sle.png",
+ "bids::slf.png",
+ "bids::slg.png",
+ "bids::slh.png",
+ "bids::sli.png",
+ "bids::slj.png",
+ "bids::slk.png",
+ "bids::sll.png"
]
},
{
- "@id": "urn:7453b882-53de-488b-b771-4e68323e3bed",
+ "@id": "urn:pngappen-JKK6GHt6",
"Label": "pngappend",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/pngappend highres2standard1.png highres2standard2.png highres2standard.png",
"Used": [
- "urn:798f3557-326c-4903-9e80-4880b5cd5bfc",
- "urn:e83f84e5-d148-4623-98a6-51db60ece79a"
+ "bids::highres2standard1.png",
+ "bids::highres2standard2.png"
]
},
{
- "@id": "urn:fa4a5008-018c-454b-9399-c24a2febe47b",
+ "@id": "urn:rm-MB1AOON1",
"Label": "rm",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/bin/rm -f sl?.png highres2standard2.png",
"Used": [
- "urn:07c0c668-0989-448b-bf80-146e799b0890",
- "urn:e83f84e5-d148-4623-98a6-51db60ece79a"
+ "bids::highres2standard2.png",
+ "bids::sl?.png"
]
},
{
- "@id": "urn:99167c56-bdb8-4082-ad8a-6393fa210af1",
+ "@id": "urn:rm-GgsgGxnu",
"Label": "rm",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/bin/rm highres2standard1.png",
"Used": [
- "urn:798f3557-326c-4903-9e80-4880b5cd5bfc"
+ "bids::highres2standard1.png"
]
},
{
- "@id": "urn:bbd72fc4-3902-4871-9552-bf7438111b8a",
+ "@id": "urn:convertx-SQmLkvOL",
"Label": "convert_xfm",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/convert_xfm -omat example_func2standard.mat -concat highres2standard.mat example_func2highres.mat",
"Used": [
- "urn:ab16f273-2c0a-4821-ba88-1636745d121a"
+ "bids::example_func2highres.mat"
]
},
{
- "@id": "urn:a1c61c00-791a-4ea7-8b70-db69ded7d388",
+ "@id": "urn:flirt-Mfdaj8tY",
"Label": "flirt",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/flirt -ref standard -in example_func -out example_func2standard -applyxfm -init example_func2standard.mat -interp trilinear",
"Used": [
- "urn:053adfcf-45e4-4b25-a9cd-5da93c03211d",
- "urn:0e149e1c-0eb6-4f8d-8f47-1499c7fbfda6",
- "urn:71da4817-5c97-4d51-ac51-760d380d635b"
+ "bids::example_func",
+ "bids::example_func2standard.mat",
+ "bids::standard"
]
},
{
- "@id": "urn:8a97f971-0af2-41df-93c6-908c373e914c",
+ "@id": "urn:convertx-a3Wz3MSn",
"Label": "convert_xfm",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/convert_xfm -inverse -omat standard2example_func.mat example_func2standard.mat",
"Used": [
- "urn:0e149e1c-0eb6-4f8d-8f47-1499c7fbfda6"
+ "bids::example_func2standard.mat"
]
},
{
- "@id": "urn:75ec118a-dd30-4341-9849-6145a99eb6a3",
+ "@id": "urn:slicer-Nj4PlX7k",
"Label": "slicer",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/slicer example_func2standard standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:51addcfb-fda4-4e4e-a15f-391edfcdd750",
- "urn:71da4817-5c97-4d51-ac51-760d380d635b"
+ "bids::example_func2standard",
+ "bids::standard"
]
},
{
- "@id": "urn:49f8bfd0-d9cf-49ab-a537-461a68af5ebd",
+ "@id": "urn:pngappen-ZTsccGHu",
"Label": "pngappend",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2standard1.png",
"Used": [
- "urn:30d22fd1-b991-44ff-a846-4cd67a2ceebf",
- "urn:3140a577-2df8-4acd-aa3b-9982b5902b0b",
- "urn:3a9ac2c0-6d83-46a5-9337-3e2a7dd912ec",
- "urn:47b36bbc-f1ff-4bbd-8c90-6f05275ec35f",
- "urn:4da92ba7-72e4-4de2-aee1-4c5bcac55b24",
- "urn:4de0ea67-369a-452f-9771-14224cec49ca",
- "urn:61c386a1-698a-46a2-a770-18e5ec43fcf8",
- "urn:bc5744d3-5449-453a-ae20-bbc6e990f4b4",
- "urn:bcc2a705-8e18-420a-976a-0a7618110f5f",
- "urn:bcc8aaac-4310-4786-8364-ddfe40fd5712",
- "urn:bd9ba12f-ca5a-4b94-b3ef-b1630faf29b2",
- "urn:e169e92d-af0e-44de-9e28-1903bc99ef94"
+ "bids::sla.png",
+ "bids::slb.png",
+ "bids::slc.png",
+ "bids::sld.png",
+ "bids::sle.png",
+ "bids::slf.png",
+ "bids::slg.png",
+ "bids::slh.png",
+ "bids::sli.png",
+ "bids::slj.png",
+ "bids::slk.png",
+ "bids::sll.png"
]
},
{
- "@id": "urn:437944b7-da8d-4fe2-9606-45329b04b990",
+ "@id": "urn:slicer-XFKi41kx",
"Label": "slicer",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/slicer standard example_func2standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:51addcfb-fda4-4e4e-a15f-391edfcdd750",
- "urn:71da4817-5c97-4d51-ac51-760d380d635b"
+ "bids::example_func2standard",
+ "bids::standard"
]
},
{
- "@id": "urn:4de6638c-23f0-4324-bc91-5f022edec878",
+ "@id": "urn:pngappen-95KxztEE",
"Label": "pngappend",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2standard2.png",
"Used": [
- "urn:30d22fd1-b991-44ff-a846-4cd67a2ceebf",
- "urn:3140a577-2df8-4acd-aa3b-9982b5902b0b",
- "urn:3a9ac2c0-6d83-46a5-9337-3e2a7dd912ec",
- "urn:47b36bbc-f1ff-4bbd-8c90-6f05275ec35f",
- "urn:4da92ba7-72e4-4de2-aee1-4c5bcac55b24",
- "urn:4de0ea67-369a-452f-9771-14224cec49ca",
- "urn:61c386a1-698a-46a2-a770-18e5ec43fcf8",
- "urn:bc5744d3-5449-453a-ae20-bbc6e990f4b4",
- "urn:bcc2a705-8e18-420a-976a-0a7618110f5f",
- "urn:bcc8aaac-4310-4786-8364-ddfe40fd5712",
- "urn:bd9ba12f-ca5a-4b94-b3ef-b1630faf29b2",
- "urn:e169e92d-af0e-44de-9e28-1903bc99ef94"
+ "bids::sla.png",
+ "bids::slb.png",
+ "bids::slc.png",
+ "bids::sld.png",
+ "bids::sle.png",
+ "bids::slf.png",
+ "bids::slg.png",
+ "bids::slh.png",
+ "bids::sli.png",
+ "bids::slj.png",
+ "bids::slk.png",
+ "bids::sll.png"
]
},
{
- "@id": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "@id": "urn:pngappen-Emkbpxnn",
"Label": "pngappend",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/pngappend example_func2standard1.png example_func2standard2.png example_func2standard.png",
"Used": [
- "urn:56952d52-4563-43f3-b14e-5428f5aaef2d",
- "urn:bf4ed4ca-115c-4320-bbfa-cf160080113d"
+ "bids::example_func2standard1.png",
+ "bids::example_func2standard2.png"
]
},
{
- "@id": "urn:0c1f173a-a1e8-43ad-942f-d3231383ed70",
+ "@id": "urn:rm-PwA8gtun",
"Label": "rm",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/bin/rm -f sl?.png example_func2standard2.png",
"Used": [
- "urn:07c0c668-0989-448b-bf80-146e799b0890",
- "urn:bf4ed4ca-115c-4320-bbfa-cf160080113d"
+ "bids::example_func2standard2.png",
+ "bids::sl?.png"
]
},
{
- "@id": "urn:957b2a43-07df-4b2e-942d-783862b74031",
+ "@id": "urn:mcflirt-RhkfkZU8",
"Label": "mcflirt",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs -spline_final",
"Used": [
- "urn:6bbcef9d-c59c-420e-af06-7b51ccae0169"
+ "bids::prefiltered_func_data"
]
},
{
- "@id": "urn:f55c118c-56ab-4383-a123-3704c2418a98",
+ "@id": "urn:makedire-L9bykLV3",
"Label": "Make directory",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/bin/mkdir -p mc",
"Used": []
},
{
- "@id": "urn:1e0b939a-7f03-4ce5-94d3-ec2db95d67b5",
+ "@id": "urn:mv-Dezd134K",
"Label": "mv",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc",
"Used": [
- "urn:2bfd1d18-9f2e-4320-aaef-09ce4964eab6",
- "urn:7d15df61-0c90-47a2-b901-a49fb72542ad",
- "urn:886a634a-92ae-4b6a-a202-50de6c793825",
- "urn:940bcdf8-e7cf-4cb8-8c23-a54d80cac020",
- "urn:958a9af3-d67a-49c5-be0f-f910d982040b",
- "urn:e987b7b3-5351-425a-80bd-1c18f436aa05"
+ "bids::prefiltered_func_data_mcf.mat",
+ "bids::prefiltered_func_data_mcf.par",
+ "bids::prefiltered_func_data_mcf_abs.rms",
+ "bids::prefiltered_func_data_mcf_abs_mean.rms",
+ "bids::prefiltered_func_data_mcf_rel.rms",
+ "bids::prefiltered_func_data_mcf_rel_mean.rms"
]
},
{
- "@id": "urn:65b22365-2211-4d46-bfc4-975be5c60659",
+ "@id": "urn:fsltsplo-GHWIXd10",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png",
"Used": [
- "urn:e987b7b3-5351-425a-80bd-1c18f436aa05"
+ "bids::prefiltered_func_data_mcf.par"
]
},
{
- "@id": "urn:6f21e13d-7fd5-41e1-bb1b-8fe9651d57b1",
+ "@id": "urn:fsltsplo-FjkHHTOt",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png",
"Used": [
- "urn:e987b7b3-5351-425a-80bd-1c18f436aa05"
+ "bids::prefiltered_func_data_mcf.par"
]
},
{
- "@id": "urn:ef409fbf-d2a1-4f68-a1ea-d7f905983286",
+ "@id": "urn:fsltsplo-1AOZD9Ii",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png",
"Used": [
- "urn:97719e5d-4229-4ff2-8310-05340e8ce878"
+ "bids::prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms"
]
},
{
- "@id": "urn:9b687564-6599-4fc2-a127-ba19d5e56934",
+ "@id": "urn:fslmaths-hWzoSr4S",
"Label": "fslmaths",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func",
"Used": [
- "urn:7772020d-ac05-4d0e-aa6b-ba7c6516fb74"
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:0ca14c7d-bdca-4c21-8942-3567d6212845",
+ "@id": "urn:bet2-cTeUPlvL",
"Label": "bet2",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/bet2 mean_func mask -f 0.3 -n -m",
"Used": [
- "urn:c82e7fa3-80eb-4169-978d-93ec72026c55"
+ "bids::mean_func"
]
},
{
- "@id": "urn:3f293e77-c0ee-4d38-8aad-1c5aa4760477",
+ "@id": "urn:immv-XjUkbn2U",
"Label": "immv",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/immv mask_mask mask",
"Used": [
- "urn:c774d4f0-4ad3-44d8-b9c5-7775c0dc9776"
+ "bids::mask_mask"
]
},
{
- "@id": "urn:ad20686e-7a8c-4964-a10e-799a1c8761c9",
+ "@id": "urn:fslmaths-EV2GCd4j",
"Label": "fslmaths",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet",
"Used": [
- "urn:3beb9088-e8a6-44f2-b869-189fa7e32181",
- "urn:7772020d-ac05-4d0e-aa6b-ba7c6516fb74"
+ "bids::mask",
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:7b98fe35-6185-46c1-b6ab-218cd580fb53",
+ "@id": "urn:fslstats-WuQ9EvLs",
"Label": "fslstats",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslstats prefiltered_func_data_bet -p 2 -p 98",
"Used": [
- "urn:ca644e16-bc8f-4cb8-a310-fb2005b8f3d8"
+ "bids::prefiltered_func_data_bet"
]
},
{
- "@id": "urn:cc89346d-5c53-4652-84d4-847a29ab7c7c",
+ "@id": "urn:fslmaths-HQvvGkr3",
"Label": "fslmaths",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths prefiltered_func_data_bet -thr 74.4585571 -Tmin -bin mask -odt char",
"Used": [
- "urn:ca644e16-bc8f-4cb8-a310-fb2005b8f3d8"
+ "bids::prefiltered_func_data_bet"
]
},
{
- "@id": "urn:2c4629c9-90fd-4777-a252-2d2d739ff1ee",
+ "@id": "urn:fslstats-X9E18DJd",
"Label": "fslstats",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslstats prefiltered_func_data_mcf -k mask -p 50",
"Used": [
- "urn:7772020d-ac05-4d0e-aa6b-ba7c6516fb74"
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:5b90ef67-d464-423c-9769-46fed7afde85",
+ "@id": "urn:fslmaths-6dbK2akr",
"Label": "fslmaths",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths mask -dilF mask",
"Used": [
- "urn:3beb9088-e8a6-44f2-b869-189fa7e32181"
+ "bids::mask"
]
},
{
- "@id": "urn:b850c3bb-c708-4927-a081-f0f6462076a0",
+ "@id": "urn:fslmaths-LhcU1kaU",
"Label": "fslmaths",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh",
"Used": [
- "urn:3beb9088-e8a6-44f2-b869-189fa7e32181",
- "urn:7772020d-ac05-4d0e-aa6b-ba7c6516fb74"
+ "bids::mask",
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:0ea248cd-0b5c-47e6-86ab-b81edcdad19f",
+ "@id": "urn:fslmaths-8vlKApk2",
"Label": "fslmaths",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func",
"Used": [
- "urn:73706964-2ab5-4dbc-8f4a-edc7d81fe7eb"
+ "bids::prefiltered_func_data_thresh"
]
},
{
- "@id": "urn:fe9f2e68-5450-4466-b842-ccc9dd39f6f7",
+ "@id": "urn:susan-UxYIP1lX",
"Label": "susan",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/susan prefiltered_func_data_thresh 445.8289035 2.54777070064 3 1 1 mean_func 445.8289035 prefiltered_func_data_smooth",
"Used": [
- "urn:73706964-2ab5-4dbc-8f4a-edc7d81fe7eb"
+ "bids::prefiltered_func_data_thresh"
]
},
{
- "@id": "urn:61509192-5cb3-441a-8c1d-ad52d092302a",
+ "@id": "urn:fslmaths-iFvYKT4p",
"Label": "fslmaths",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth",
"Used": [
- "urn:32f9bfaf-ad74-42f3-9703-e946cb2ec370",
- "urn:3beb9088-e8a6-44f2-b869-189fa7e32181"
+ "bids::mask",
+ "bids::prefiltered_func_data_smooth"
]
},
{
- "@id": "urn:8ae31d5e-a3ad-42bd-ad51-5124acc6a71f",
+ "@id": "urn:fslmaths-4pYyDrcL",
"Label": "fslmaths",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths prefiltered_func_data_smooth -mul 16.8225970571 prefiltered_func_data_intnorm",
"Used": [
- "urn:32f9bfaf-ad74-42f3-9703-e946cb2ec370"
+ "bids::prefiltered_func_data_smooth"
]
},
{
- "@id": "urn:ee2408cc-c449-4e10-93d3-7c11e0a58e0f",
+ "@id": "urn:fslmaths-wLkyGtTj",
"Label": "fslmaths",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean",
"Used": [
- "urn:431edd12-cde6-4811-9006-d6fed017d3c5"
+ "bids::prefiltered_func_data_intnorm"
]
},
{
- "@id": "urn:e70dd1e8-a92b-4729-967d-c0dbcba46a21",
+ "@id": "urn:fslmaths-kSriC40g",
"Label": "fslmaths",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths prefiltered_func_data_intnorm -bptf 15.0 -1 -add tempMean prefiltered_func_data_tempfilt",
"Used": [
- "urn:3508e8e8-f0c1-4ffd-8dfe-464026c65a88",
- "urn:431edd12-cde6-4811-9006-d6fed017d3c5"
+ "bids::prefiltered_func_data_intnorm",
+ "bids::tempMean"
]
},
{
- "@id": "urn:6fa21350-0c53-4a84-a153-14a2afab1044",
+ "@id": "urn:imrm-PJYzYkv0",
"Label": "imrm",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/imrm tempMean",
"Used": [
- "urn:3508e8e8-f0c1-4ffd-8dfe-464026c65a88"
+ "bids::tempMean"
]
},
{
- "@id": "urn:b7120cae-1b38-4812-9aa4-8123b3e36f0c",
+ "@id": "urn:fslmaths-x2Mvt4OA",
"Label": "fslmaths",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data",
"Used": [
- "urn:d4a98127-8091-4ed0-9db3-ec2724d0dbcd"
+ "bids::prefiltered_func_data_tempfilt"
]
},
{
- "@id": "urn:64faf72a-c81a-4277-ad7b-95ef6daef451",
+ "@id": "urn:fslmaths-o6vpI5Id",
"Label": "fslmaths",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths filtered_func_data -Tmean mean_func",
"Used": [
- "urn:9220cdcc-449f-4185-b7fd-f95b6f48368b"
+ "bids::filtered_func_data"
]
},
{
- "@id": "urn:9c6d0647-4ef8-47d7-9883-9cc78c976689",
+ "@id": "urn:rm-Hj8YxGgj",
"Label": "rm",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/bin/rm -rf prefiltered_func_data*",
"Used": [
- "urn:7e4155c0-c82a-4288-9c97-0d282d04ea98"
+ "bids::prefiltered_func_data*"
]
},
{
- "@id": "urn:f39e533d-15dd-40d0-b151-cf39c441c721",
+ "@id": "urn:makedire-RDOOlycE",
"Label": "Make directory",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
- "@id": "urn:7962f1b9-fbcc-4216-999d-a029e8e92124",
+ "@id": "urn:fslfixte-3PXP67h4",
"Label": "fslFixText",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
- "Command": "/usr/local/packages/fsl-5.0.8/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
+ "Command": "/usr/local/packages/fsl-5.0.8/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
"Used": [
- "urn:0cf78e42-8032-409c-949c-c52da8f63be7"
+ "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt"
]
},
{
- "@id": "urn:09759f75-f271-429a-ae59-0a44f00dd289",
+ "@id": "urn:makedire-RrxzWAED",
"Label": "Make directory",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
- "@id": "urn:7dedc9bb-8c86-4990-a6b8-648da3100168",
+ "@id": "urn:fslfixte-f9DuphuI",
"Label": "fslFixText",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
- "Command": "/usr/local/packages/fsl-5.0.8/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
+ "Command": "/usr/local/packages/fsl-5.0.8/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
"Used": [
- "urn:694de773-9fb6-4d11-9f94-7d4464c1040d"
+ "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt"
]
},
{
- "@id": "urn:5387229e-d088-4ba4-884e-34bc3ff43df0",
+ "@id": "urn:filmgls-xpjNuWUs",
"Label": "film_gls",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con --fcon=design.fts",
- "Used": []
+ "Used": [
+ "bids::design.con",
+ "bids::design.fts",
+ "bids::design.mat",
+ "bids::filtered_func_data",
+ "bids::stats"
+ ]
},
{
- "@id": "urn:cdecbeaf-18f4-4a48-8375-8486e681054a",
+ "@id": "urn:smoothes-VTT9rn8N",
"Label": "smoothest",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
- "Command": "/usr/local/packages/fsl-5.0.8/bin/smoothest -d 102 -m mask -r stats/res4d > stats/smoothness",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
+ "Command": "/usr/local/packages/fsl-5.0.8/bin/smoothest -d 102 -m mask -r stats/res4d > stats/smoothness",
"Used": [
- "urn:3beb9088-e8a6-44f2-b869-189fa7e32181",
- "urn:453f2339-e213-4b5e-ab94-4573425a181a"
+ "bids::mask",
+ "bids::stats/res4d"
]
},
{
- "@id": "urn:7a3ae6ca-12a9-4b93-af1d-4e77a0ecd4ec",
+ "@id": "urn:fslmaths-wxrzYlhL",
"Label": "fslmaths",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1",
"Used": [
- "urn:3beb9088-e8a6-44f2-b869-189fa7e32181",
- "urn:3ca7ac59-c231-4f0c-87ae-b1e12cd7e06a"
+ "bids::mask",
+ "bids::stats/zstat1"
]
},
{
- "@id": "urn:00b4805d-d286-4d84-b9df-5106175197bf",
+ "@id": "urn:echo-IbMksC8P",
"Label": "echo",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "echo 38352 > thresh_zstat1.vol",
"Used": []
},
{
- "@id": "urn:e0ccf79c-c0c8-4648-9c87-5d2049923838",
+ "@id": "urn:fslmaths-2YQYb7ln",
"Label": "fslmaths",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths stats/zstat2 -mas mask thresh_zstat2",
"Used": [
- "urn:3beb9088-e8a6-44f2-b869-189fa7e32181",
- "urn:c7f540ab-8cca-4a10-bb24-c709b962b774"
+ "bids::mask",
+ "bids::stats/zstat2"
]
},
{
- "@id": "urn:a3c105fb-3a60-46d9-8d40-3788d08530ea",
+ "@id": "urn:echo-OIwar3Jw",
"Label": "echo",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "echo 38352 > thresh_zstat2.vol",
"Used": []
},
{
- "@id": "urn:753d9758-36e4-406a-b40f-4d8ec0e5d9dc",
+ "@id": "urn:fslmaths-mUk1TnwY",
"Label": "fslmaths",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths stats/zfstat1 -mas mask thresh_zfstat1",
"Used": [
- "urn:3beb9088-e8a6-44f2-b869-189fa7e32181",
- "urn:c0e1b9d1-bc9a-4e5d-ba92-b530ccf740e2"
+ "bids::mask",
+ "bids::stats/zfstat1"
]
},
{
- "@id": "urn:acbe48d2-2243-4d5d-87be-c86b1864707e",
+ "@id": "urn:echo-yGvpKaqD",
"Label": "echo",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "echo 38352 > thresh_zfstat1.vol",
"Used": []
},
{
- "@id": "urn:b6bd7923-5f95-4de9-b336-d38e1ef54915",
+ "@id": "urn:fslmaths-VTzvv2bx",
"Label": "fslmaths",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths stats/zfstat2 -mas mask thresh_zfstat2",
"Used": [
- "urn:3beb9088-e8a6-44f2-b869-189fa7e32181",
- "urn:58ff1f1c-76ec-4363-a1d2-038927e2825b"
+ "bids::mask",
+ "bids::stats/zfstat2"
]
},
{
- "@id": "urn:b6e36cc4-2772-48cd-b50f-e50e29ac1c74",
+ "@id": "urn:echo-u8ZXMJhB",
"Label": "echo",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "echo 38352 > thresh_zfstat2.vol",
"Used": []
},
{
- "@id": "urn:e8fc634a-717b-4e72-a852-cd4cef0e4447",
+ "@id": "urn:fslmaths-OZbfjxwh",
"Label": "fslmaths",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths stats/zfstat3 -mas mask thresh_zfstat3",
"Used": [
- "urn:3beb9088-e8a6-44f2-b869-189fa7e32181",
- "urn:c9ee2495-5b57-4aaa-81c9-e342553d373a"
+ "bids::mask",
+ "bids::stats/zfstat3"
]
},
{
- "@id": "urn:7c06248d-d806-4e4e-944e-78d2a6556e52",
+ "@id": "urn:echo-W1LSESgK",
"Label": "echo",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "echo 38352 > thresh_zfstat3.vol",
"Used": []
},
{
- "@id": "urn:573aaa5d-6d96-4cd2-9b87-153f522da1da",
+ "@id": "urn:ptoz-C9rpj6iK",
"Label": "ptoz",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:11a104fa-e66b-41e8-b818-75667e809a71",
+ "@id": "urn:cluster-6EgN0K4y",
"Label": "cluster",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
- "Command": "/usr/local/packages/fsl-5.0.8/bin/cluster -i thresh_zstat1 -t 3.090232 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z --voxuncthresh -c stats/cope1 > cluster_zstat1.txt",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
+ "Command": "/usr/local/packages/fsl-5.0.8/bin/cluster -i thresh_zstat1 -t 3.090232 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z --voxuncthresh -c stats/cope1 > cluster_zstat1.txt",
"Used": [
- "urn:18bc1e51-3fac-487f-b249-7bd9ce9b56fc",
- "urn:4e9a3e8d-ff8b-4cf9-a37d-f3a39fb6c160"
+ "bids::stats/cope1",
+ "bids::thresh_zstat1"
]
},
{
- "@id": "urn:bf4a6373-4547-42e7-a6f6-db7f2f907ea5",
+ "@id": "urn:cluster2-1Slnt5f5",
"Label": "cluster2html",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/cluster2html . cluster_zstat1",
"Used": [
- "urn:48d9754b-4a40-49db-a0de-65552667fd1b"
+ "bids::cluster_zstat1"
]
},
{
- "@id": "urn:6ce3dbc9-b7ef-4e84-8cfa-fb2f54ada26d",
+ "@id": "urn:ptoz-pdPBHfty",
"Label": "ptoz",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:454caa2e-6cdb-40f4-acf7-786cfbbda286",
+ "@id": "urn:cluster-3VvOdnac",
"Label": "cluster",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
- "Command": "/usr/local/packages/fsl-5.0.8/bin/cluster -i thresh_zstat2 -t 3.090232 --othresh=thresh_zstat2 -o cluster_mask_zstat2 --connectivity=26 --olmax=lmax_zstat2.txt --scalarname=Z --voxuncthresh -c stats/cope2 > cluster_zstat2.txt",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
+ "Command": "/usr/local/packages/fsl-5.0.8/bin/cluster -i thresh_zstat2 -t 3.090232 --othresh=thresh_zstat2 -o cluster_mask_zstat2 --connectivity=26 --olmax=lmax_zstat2.txt --scalarname=Z --voxuncthresh -c stats/cope2 > cluster_zstat2.txt",
"Used": [
- "urn:13988305-f114-4572-a248-552704d0eece",
- "urn:56b37ee0-3fb0-4a62-820c-76bcdcb90b46"
+ "bids::stats/cope2",
+ "bids::thresh_zstat2"
]
},
{
- "@id": "urn:0fe9750e-e253-4ce3-9501-6f9b5be5612c",
+ "@id": "urn:cluster2-SUXY6x29",
"Label": "cluster2html",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/cluster2html . cluster_zstat2",
"Used": [
- "urn:3e2d0b3c-a9d8-459a-a5b6-1c442573c6a9"
+ "bids::cluster_zstat2"
]
},
{
- "@id": "urn:216f85ed-b590-4747-8b5b-0ef17c869cbf",
+ "@id": "urn:ptoz-nAQkKuoV",
"Label": "ptoz",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:6a4f28e4-2599-49cd-a360-89709dc67815",
+ "@id": "urn:cluster-se2emGpz",
"Label": "cluster",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
- "Command": "/usr/local/packages/fsl-5.0.8/bin/cluster -i thresh_zfstat1 -t 3.090232 --othresh=thresh_zfstat1 -o cluster_mask_zfstat1 --connectivity=26 --olmax=lmax_zfstat1.txt --scalarname=Z --voxuncthresh > cluster_zfstat1.txt",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
+ "Command": "/usr/local/packages/fsl-5.0.8/bin/cluster -i thresh_zfstat1 -t 3.090232 --othresh=thresh_zfstat1 -o cluster_mask_zfstat1 --connectivity=26 --olmax=lmax_zfstat1.txt --scalarname=Z --voxuncthresh > cluster_zfstat1.txt",
"Used": [
- "urn:62fe3bcd-2595-4d45-8f19-0e45a205fed2"
+ "bids::thresh_zfstat1"
]
},
{
- "@id": "urn:ceee4051-d07c-4b5d-bfb1-174f111ea5c2",
+ "@id": "urn:cluster2-isaWHcwc",
"Label": "cluster2html",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/cluster2html . cluster_zfstat1",
"Used": [
- "urn:b4b22bb5-74c5-4bc1-a775-35f180100e22"
+ "bids::cluster_zfstat1"
]
},
{
- "@id": "urn:7e0c56eb-958e-44b5-be14-a6d366612be8",
+ "@id": "urn:ptoz-GMJ6r1Ua",
"Label": "ptoz",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:5538393a-0e9e-4399-a092-fabfef6b5282",
+ "@id": "urn:cluster-0M7QqJvZ",
"Label": "cluster",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
- "Command": "/usr/local/packages/fsl-5.0.8/bin/cluster -i thresh_zfstat2 -t 3.090232 --othresh=thresh_zfstat2 -o cluster_mask_zfstat2 --connectivity=26 --olmax=lmax_zfstat2.txt --scalarname=Z --voxuncthresh > cluster_zfstat2.txt",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
+ "Command": "/usr/local/packages/fsl-5.0.8/bin/cluster -i thresh_zfstat2 -t 3.090232 --othresh=thresh_zfstat2 -o cluster_mask_zfstat2 --connectivity=26 --olmax=lmax_zfstat2.txt --scalarname=Z --voxuncthresh > cluster_zfstat2.txt",
"Used": [
- "urn:addaa522-7bef-42e3-a6ac-aef2fa1b260b"
+ "bids::thresh_zfstat2"
]
},
{
- "@id": "urn:407a0dcc-199e-43d1-820c-6c4488d6b491",
+ "@id": "urn:cluster2-89Uqgluc",
"Label": "cluster2html",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/cluster2html . cluster_zfstat2",
"Used": [
- "urn:be62d30a-74c7-4d75-8b5e-a9279b6f18b9"
+ "bids::cluster_zfstat2"
]
},
{
- "@id": "urn:dcbb9a26-c93b-4b31-bcd1-59dacb0383d6",
+ "@id": "urn:ptoz-HswgvjMt",
"Label": "ptoz",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:7c1874c9-f93c-4559-9f77-77113ffc2a9f",
+ "@id": "urn:cluster-OF94q1Q7",
"Label": "cluster",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
- "Command": "/usr/local/packages/fsl-5.0.8/bin/cluster -i thresh_zfstat3 -t 3.090232 --othresh=thresh_zfstat3 -o cluster_mask_zfstat3 --connectivity=26 --olmax=lmax_zfstat3.txt --scalarname=Z --voxuncthresh > cluster_zfstat3.txt",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
+ "Command": "/usr/local/packages/fsl-5.0.8/bin/cluster -i thresh_zfstat3 -t 3.090232 --othresh=thresh_zfstat3 -o cluster_mask_zfstat3 --connectivity=26 --olmax=lmax_zfstat3.txt --scalarname=Z --voxuncthresh > cluster_zfstat3.txt",
"Used": [
- "urn:c0aa7d2f-c91b-4291-987b-f3293bd8bc35"
+ "bids::thresh_zfstat3"
]
},
{
- "@id": "urn:1e49c15c-14eb-4d2a-91f1-2b6617511ba6",
+ "@id": "urn:cluster2-NX555VWz",
"Label": "cluster2html",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/cluster2html . cluster_zfstat3",
"Used": [
- "urn:4a906933-51a2-44bc-b703-d09459da47ac"
+ "bids::cluster_zfstat3"
]
},
{
- "@id": "urn:78c69982-04a2-404f-afba-2445db0955dc",
+ "@id": "urn:ptoz-Vl4IyDA0",
"Label": "ptoz",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:35384b90-2956-47b9-856a-48728b487eb5",
+ "@id": "urn:cluster-iGFpF9oV",
"Label": "cluster",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
- "Command": "/usr/local/packages/fsl-5.0.8/bin/cluster -i thresh_zstat1 -c stats/cope1 -t 3.090232 -d 0.70114 --volume=38352 -x reg/example_func2standard.mat --stdvol=reg/standard --mm --connectivity=26 --olmax=lmax_zstat1_std.txt --scalarname=Z --voxuncthresh > cluster_zstat1_std.txt",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
+ "Command": "/usr/local/packages/fsl-5.0.8/bin/cluster -i thresh_zstat1 -c stats/cope1 -t 3.090232 -d 0.70114 --volume=38352 -x reg/example_func2standard.mat --stdvol=reg/standard --mm --connectivity=26 --olmax=lmax_zstat1_std.txt --scalarname=Z --voxuncthresh > cluster_zstat1_std.txt",
"Used": [
- "urn:18bc1e51-3fac-487f-b249-7bd9ce9b56fc",
- "urn:4e9a3e8d-ff8b-4cf9-a37d-f3a39fb6c160"
+ "bids::stats/cope1",
+ "bids::thresh_zstat1"
]
},
{
- "@id": "urn:8733e18f-ec50-4e5a-a166-7f730cc55d6b",
+ "@id": "urn:cluster2-aPqs0IQH",
"Label": "cluster2html",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/cluster2html . cluster_zstat1 -std",
"Used": [
- "urn:48d9754b-4a40-49db-a0de-65552667fd1b"
+ "bids::cluster_zstat1"
]
},
{
- "@id": "urn:d6a4f09c-fd94-4b7e-8d73-f3144c571e1d",
+ "@id": "urn:cluster-CUsyPhtO",
"Label": "cluster",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
- "Command": "/usr/local/packages/fsl-5.0.8/bin/cluster -i thresh_zstat2 -c stats/cope2 -t 3.090232 -d 0.70114 --volume=38352 -x reg/example_func2standard.mat --stdvol=reg/standard --mm --connectivity=26 --olmax=lmax_zstat2_std.txt --scalarname=Z --voxuncthresh > cluster_zstat2_std.txt",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
+ "Command": "/usr/local/packages/fsl-5.0.8/bin/cluster -i thresh_zstat2 -c stats/cope2 -t 3.090232 -d 0.70114 --volume=38352 -x reg/example_func2standard.mat --stdvol=reg/standard --mm --connectivity=26 --olmax=lmax_zstat2_std.txt --scalarname=Z --voxuncthresh > cluster_zstat2_std.txt",
"Used": [
- "urn:13988305-f114-4572-a248-552704d0eece",
- "urn:56b37ee0-3fb0-4a62-820c-76bcdcb90b46"
+ "bids::stats/cope2",
+ "bids::thresh_zstat2"
]
},
{
- "@id": "urn:a5e01309-a083-4d4d-8aef-4a5e487731b8",
+ "@id": "urn:cluster2-1MwzcECw",
"Label": "cluster2html",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/cluster2html . cluster_zstat2 -std",
"Used": [
- "urn:3e2d0b3c-a9d8-459a-a5b6-1c442573c6a9"
+ "bids::cluster_zstat2"
]
},
{
- "@id": "urn:b17a6347-3a64-4991-8693-5df741284ef9",
+ "@id": "urn:cluster-PFSC1Nv3",
"Label": "cluster",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
- "Command": "/usr/local/packages/fsl-5.0.8/bin/cluster -i thresh_zfstat1 -t 3.090232 -d 0.70114 --volume=38352 -x reg/example_func2standard.mat --stdvol=reg/standard --mm --connectivity=26 --olmax=lmax_zfstat1_std.txt --scalarname=Z --voxuncthresh > cluster_zfstat1_std.txt",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
+ "Command": "/usr/local/packages/fsl-5.0.8/bin/cluster -i thresh_zfstat1 -t 3.090232 -d 0.70114 --volume=38352 -x reg/example_func2standard.mat --stdvol=reg/standard --mm --connectivity=26 --olmax=lmax_zfstat1_std.txt --scalarname=Z --voxuncthresh > cluster_zfstat1_std.txt",
"Used": [
- "urn:62fe3bcd-2595-4d45-8f19-0e45a205fed2"
+ "bids::thresh_zfstat1"
]
},
{
- "@id": "urn:3131df81-13b1-4303-b080-c1762e3f6c2c",
+ "@id": "urn:cluster2-ioZKXTRb",
"Label": "cluster2html",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/cluster2html . cluster_zfstat1 -std",
"Used": [
- "urn:b4b22bb5-74c5-4bc1-a775-35f180100e22"
+ "bids::cluster_zfstat1"
]
},
{
- "@id": "urn:bfb154e5-1622-4d36-8847-391e988e8f0a",
+ "@id": "urn:cluster-Gzi0hcGl",
"Label": "cluster",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
- "Command": "/usr/local/packages/fsl-5.0.8/bin/cluster -i thresh_zfstat2 -t 3.090232 -d 0.70114 --volume=38352 -x reg/example_func2standard.mat --stdvol=reg/standard --mm --connectivity=26 --olmax=lmax_zfstat2_std.txt --scalarname=Z --voxuncthresh > cluster_zfstat2_std.txt",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
+ "Command": "/usr/local/packages/fsl-5.0.8/bin/cluster -i thresh_zfstat2 -t 3.090232 -d 0.70114 --volume=38352 -x reg/example_func2standard.mat --stdvol=reg/standard --mm --connectivity=26 --olmax=lmax_zfstat2_std.txt --scalarname=Z --voxuncthresh > cluster_zfstat2_std.txt",
"Used": [
- "urn:addaa522-7bef-42e3-a6ac-aef2fa1b260b"
+ "bids::thresh_zfstat2"
]
},
{
- "@id": "urn:fe7bab3b-b788-4ff1-8203-71c218ac9e44",
+ "@id": "urn:cluster2-YswmVVvl",
"Label": "cluster2html",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/cluster2html . cluster_zfstat2 -std",
"Used": [
- "urn:be62d30a-74c7-4d75-8b5e-a9279b6f18b9"
+ "bids::cluster_zfstat2"
]
},
{
- "@id": "urn:c38e0853-4b73-4883-a114-f777cb6214ea",
+ "@id": "urn:cluster-AbETZMSV",
"Label": "cluster",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
- "Command": "/usr/local/packages/fsl-5.0.8/bin/cluster -i thresh_zfstat3 -t 3.090232 -d 0.70114 --volume=38352 -x reg/example_func2standard.mat --stdvol=reg/standard --mm --connectivity=26 --olmax=lmax_zfstat3_std.txt --scalarname=Z --voxuncthresh > cluster_zfstat3_std.txt",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
+ "Command": "/usr/local/packages/fsl-5.0.8/bin/cluster -i thresh_zfstat3 -t 3.090232 -d 0.70114 --volume=38352 -x reg/example_func2standard.mat --stdvol=reg/standard --mm --connectivity=26 --olmax=lmax_zfstat3_std.txt --scalarname=Z --voxuncthresh > cluster_zfstat3_std.txt",
"Used": [
- "urn:c0aa7d2f-c91b-4291-987b-f3293bd8bc35"
+ "bids::thresh_zfstat3"
]
},
{
- "@id": "urn:729f3dff-159d-402a-9f36-28921892046e",
+ "@id": "urn:cluster2-NoOJS8aG",
"Label": "cluster2html",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/cluster2html . cluster_zfstat3 -std",
"Used": [
- "urn:4a906933-51a2-44bc-b703-d09459da47ac"
+ "bids::cluster_zfstat3"
]
},
{
- "@id": "urn:715ce524-ccc2-47f4-8b72-9f73e454133c",
+ "@id": "urn:fslstats-P85DXb3S",
"Label": "fslstats",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslstats thresh_zstat1 -l 0.0001 -R 2>/dev/null",
"Used": [
- "urn:4e9a3e8d-ff8b-4cf9-a37d-f3a39fb6c160"
+ "bids::thresh_zstat1"
]
},
{
- "@id": "urn:1317c367-ccd7-439e-ae8c-571e7c06b9d2",
+ "@id": "urn:fslstats-MzAH9rNz",
"Label": "fslstats",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslstats thresh_zstat2 -l 0.0001 -R 2>/dev/null",
"Used": [
- "urn:13988305-f114-4572-a248-552704d0eece"
+ "bids::thresh_zstat2"
]
},
{
- "@id": "urn:9864dc9e-f672-4ec3-a9a7-9dc4d63f271c",
+ "@id": "urn:fslstats-1niR35ux",
"Label": "fslstats",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslstats thresh_zfstat1 -l 0.0001 -R 2>/dev/null",
"Used": [
- "urn:62fe3bcd-2595-4d45-8f19-0e45a205fed2"
+ "bids::thresh_zfstat1"
]
},
{
- "@id": "urn:2febfdbd-7e9f-4c1b-9664-02ee79368854",
+ "@id": "urn:fslstats-iwrasjHL",
"Label": "fslstats",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslstats thresh_zfstat2 -l 0.0001 -R 2>/dev/null",
"Used": [
- "urn:addaa522-7bef-42e3-a6ac-aef2fa1b260b"
+ "bids::thresh_zfstat2"
]
},
{
- "@id": "urn:212ecd81-c3bd-40f1-9f18-e77aafbf6c1c",
+ "@id": "urn:fslstats-yZ4wfefH",
"Label": "fslstats",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslstats thresh_zfstat3 -l 0.0001 -R 2>/dev/null",
"Used": [
- "urn:c0aa7d2f-c91b-4291-987b-f3293bd8bc35"
+ "bids::thresh_zfstat3"
]
},
{
- "@id": "urn:2e4b5df1-9dc5-4228-9bfe-aa3e957bb791",
+ "@id": "urn:overlay-AEeSiJRN",
"Label": "overlay",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/overlay 1 0 example_func -a thresh_zstat1 3.090250 7.488793 rendered_thresh_zstat1",
"Used": []
},
{
- "@id": "urn:937b139f-5ca7-42f5-8f3d-ac6cfbb528d9",
+ "@id": "urn:slicer-gUWrtCQu",
"Label": "slicer",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/slicer rendered_thresh_zstat1 -A 750 rendered_thresh_zstat1.png",
"Used": [
- "urn:82a4e9c0-dbe6-455d-bcd3-b26b934765fa"
+ "bids::rendered_thresh_zstat1"
]
},
{
- "@id": "urn:a1e86077-4609-41a2-8ca5-782d4d26bfc4",
+ "@id": "urn:cp-XWedD4a4",
"Label": "cp",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/bin/cp /usr/local/packages/fsl-5.0.8/etc/luts/ramp.gif .ramp.gif",
"Used": [
- "urn:3778da3b-49b0-4064-a214-69d1eb951d03"
+ "bids::/usr/local/packages/fsl-5.0.8/etc/luts/ramp.gif"
]
},
{
- "@id": "urn:42562745-8ff4-4e2d-8775-7ac339c7d569",
+ "@id": "urn:overlay-CTlqYESD",
"Label": "overlay",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/overlay 1 0 example_func -a thresh_zstat2 3.090250 7.488793 rendered_thresh_zstat2",
"Used": []
},
{
- "@id": "urn:771ae86f-2170-4828-b748-e4319401099b",
+ "@id": "urn:slicer-fmz6vzFn",
"Label": "slicer",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/slicer rendered_thresh_zstat2 -A 750 rendered_thresh_zstat2.png",
"Used": [
- "urn:7bbdf8ac-0ffb-4bc1-895d-8861ec9ecfac"
+ "bids::rendered_thresh_zstat2"
]
},
{
- "@id": "urn:5cedd5b4-458c-4276-81ff-476367f5d9a4",
+ "@id": "urn:overlay-7HYmK5zG",
"Label": "overlay",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/overlay 1 0 example_func -a thresh_zfstat1 3.090250 7.488793 rendered_thresh_zfstat1",
"Used": []
},
{
- "@id": "urn:9bb3b3c7-d9e7-4990-b618-54e62cdb8449",
+ "@id": "urn:slicer-NyAy9pUv",
"Label": "slicer",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/slicer rendered_thresh_zfstat1 -A 750 rendered_thresh_zfstat1.png",
"Used": [
- "urn:1ed9b558-b314-4c4c-b751-1482a25a84f4"
+ "bids::rendered_thresh_zfstat1"
]
},
{
- "@id": "urn:ddfcf1f2-5254-4261-bbd2-ef03ed5bb814",
+ "@id": "urn:overlay-ilPFUrlv",
"Label": "overlay",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/overlay 1 0 example_func -a thresh_zfstat2 3.090250 7.488793 rendered_thresh_zfstat2",
"Used": []
},
{
- "@id": "urn:660e76f5-e52e-4958-ab9a-ca2aa5d72ee0",
+ "@id": "urn:slicer-zwdZ7Um5",
"Label": "slicer",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/slicer rendered_thresh_zfstat2 -A 750 rendered_thresh_zfstat2.png",
"Used": [
- "urn:191530b0-9eb9-46d7-8143-7d371359a1fc"
+ "bids::rendered_thresh_zfstat2"
]
},
{
- "@id": "urn:9706816c-e2a0-4428-a917-403ac5fdf50a",
+ "@id": "urn:overlay-8fyKCoI9",
"Label": "overlay",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/overlay 1 0 example_func -a thresh_zfstat3 3.090250 7.488793 rendered_thresh_zfstat3",
"Used": []
},
{
- "@id": "urn:0a5cfb70-7c38-4790-b0e2-bf22f32161b2",
+ "@id": "urn:slicer-mmdzsZLM",
"Label": "slicer",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/slicer rendered_thresh_zfstat3 -A 750 rendered_thresh_zfstat3.png",
"Used": [
- "urn:7564c2c2-a931-4c72-a838-570247b2b213"
+ "bids::rendered_thresh_zfstat3"
]
},
{
- "@id": "urn:7bd4ef46-e596-482c-9e4d-7c5154719873",
+ "@id": "urn:makedire-vZc4wsey",
"Label": "Make directory",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "mkdir -p tsplot",
"Used": []
},
{
- "@id": "urn:550ce33c-c8c6-470f-ad14-5f94187fffa6",
+ "@id": "urn:tsplot-qwfDtqRW",
"Label": "tsplot",
- "AssociatedWith": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "AssociatedWith": "urn:fsl-RWQkET6j",
"Command": "/usr/local/packages/fsl-5.0.8/bin/tsplot . -f filtered_func_data -o tsplot",
"Used": []
}
],
"Entities": [
{
- "@id": "urn:2d8d1329-479a-44e0-9894-05aabc7d7877",
+ "@id": "bids::/home/tommaullin/Documents/Data/ds011/sub-01/func/sub-01_task-tonecounting_bold",
"Label": "sub-01_task-tonecounting_bold",
"AtLocation": "/home/tommaullin/Documents/Data/ds011/sub-01/func/sub-01_task-tonecounting_bold",
"digest": {
@@ -1148,25 +1158,25 @@
}
},
{
- "@id": "urn:6bbcef9d-c59c-420e-af06-7b51ccae0169",
+ "@id": "bids::prefiltered_func_data",
"Label": "prefiltered_func_data",
"AtLocation": "prefiltered_func_data",
- "GeneratedBy": "urn:39f1ca8b-66d3-4d02-b1e6-5af2de7b426a",
+ "GeneratedBy": "urn:fslmaths-X40sMWOm",
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"sha256": "2bea6005bace2adbea3534588b8c1b0d1759aa1af85b703b7f5bd2959c961a29"
}
},
{
- "@id": "urn:053adfcf-45e4-4b25-a9cd-5da93c03211d",
+ "@id": "bids::example_func",
"Label": "example_func",
"AtLocation": "example_func",
- "GeneratedBy": "urn:19fb39c5-b85c-4be4-8f4a-c8be81315b19",
+ "GeneratedBy": "urn:fslroi-oh19ScPe",
"digest": {
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}
},
{
- "@id": "urn:06b049a4-fd81-489d-b3c8-ce116f153f26",
+ "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/example_func.nii.gz",
"Label": "example_func.nii.gz",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/example_func.nii.gz",
"digest": {
@@ -1174,15 +1184,15 @@
}
},
{
- "@id": "urn:164dec41-95f0-4393-bd4e-a73b5b698322",
+ "@id": "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
"Label": "sub-01_T1w_brain",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
+ "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
"digest": {
- "sha256": "ccb9a4d1def67002e358c45bd912034053ffc221ab52c2a19aa55f72c3236279"
+ "sha256": "8f1ae7ba69869c79b2cc5a83ce4ca24a7d666187256c2aa4d61a952b903b05b0"
}
},
{
- "@id": "urn:cbc9d9a1-d1a6-44f4-a551-6a3c652bccbc",
+ "@id": "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain",
"Label": "MNI152_T1_2mm_brain",
"AtLocation": "/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain",
"digest": {
@@ -1190,46 +1200,58 @@
}
},
{
- "@id": "urn:7875fa28-0d90-44a1-a518-b16af69727f1",
+ "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat",
"Label": "fsl_con_f_multiple_test.feat",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat",
- "GeneratedBy": "urn:60e714fe-8ee1-42e7-a6da-d0bd9dde8c93"
+ "GeneratedBy": "urn:mainfeat-aTrcG3Fx"
},
{
- "@id": "urn:0b5d9f6c-e4eb-4ece-a250-cd75da76911c",
+ "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/reg",
"Label": "reg",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/reg",
- "GeneratedBy": "urn:608b662d-4757-4c39-94d5-44c28ff93938",
+ "GeneratedBy": "urn:makedire-3zzI0Agw",
"digest": {
"sha256": "8fb9b2fd5755a86b25b1ab75f1e66181b2bb2ad667a0e08f5a9a608995216139"
}
},
{
- "@id": "urn:cb238dbf-75c3-47f0-a085-fd84a05307a3",
+ "@id": "bids::highres",
"Label": "highres",
"AtLocation": "highres",
- "GeneratedBy": "urn:3e1a6330-6d27-41ed-b2d7-f50b8348f477",
+ "GeneratedBy": "urn:fslmaths-w3sXEcK0",
"digest": {
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- "Label": "",
- "AtLocation": "",
- "GeneratedBy": "urn:e7e28ef4-f1eb-482b-8d94-6a0f1f9ef566"
+ "@id": "bids::highres_head",
+ "Label": "highres_head",
+ "AtLocation": "highres_head",
+ "GeneratedBy": "urn:fslmaths-QEpXdgnq",
+ "digest": {
+ "sha256": "590f180bade23162ef1567a5a61d86ee93155e4c7dc59c04c8ac5d6b7a20ea51"
+ }
},
{
- "@id": "urn:71da4817-5c97-4d51-ac51-760d380d635b",
+ "@id": "bids::standard",
"Label": "standard",
"AtLocation": "standard",
- "GeneratedBy": "urn:9b581ae8-7368-4411-84c6-4d66165bd5c4",
+ "GeneratedBy": "urn:fslmaths-pZHZsQhS",
"digest": {
"sha256": "ee560b20f733f620251717de588d9d32214065b3837bc49db52e0370911bbbdf"
}
},
{
- "@id": "urn:ab16f273-2c0a-4821-ba88-1636745d121a",
+ "@id": "bids::example_func2highres",
+ "Label": "example_func2highres",
+ "AtLocation": "example_func2highres",
+ "GeneratedBy": "urn:epireg-fHxZonCr",
+ "digest": {
+ "sha256": "00c021d82b83d2dc562c77f76528ece0f7425d4982f292f22021467afce1ba59"
+ }
+ },
+ {
+ "@id": "bids::example_func2highres.mat",
"Label": "example_func2highres.mat",
"AtLocation": "example_func2highres.mat",
"digest": {
@@ -1237,267 +1259,259 @@
}
},
{
- "@id": "urn:7ea2b784-f436-4f64-aefd-727e6575842d",
+ "@id": "bids::highres2example_func.mat",
"Label": "highres2example_func.mat",
"AtLocation": "highres2example_func.mat",
- "GeneratedBy": "urn:4d350b62-1091-4725-af58-4f40d3f08a39",
+ "GeneratedBy": "urn:convertx-hYXi1Bs2",
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{
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- "digest": {
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- }
- },
- {
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+ "@id": "bids::sla.png",
"Label": "sla.png",
"AtLocation": "sla.png",
- "GeneratedBy": "urn:20ea2776-872a-45b1-a331-31916a8cedd1",
+ "GeneratedBy": "urn:slicer-sVwU0TQP",
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}
},
{
- "@id": "urn:30d22fd1-b991-44ff-a846-4cd67a2ceebf",
+ "@id": "bids::slb.png",
"Label": "slb.png",
"AtLocation": "slb.png",
- "GeneratedBy": "urn:20ea2776-872a-45b1-a331-31916a8cedd1",
+ "GeneratedBy": "urn:slicer-sVwU0TQP",
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}
},
{
- "@id": "urn:3a9ac2c0-6d83-46a5-9337-3e2a7dd912ec",
+ "@id": "bids::slc.png",
"Label": "slc.png",
"AtLocation": "slc.png",
- "GeneratedBy": "urn:20ea2776-872a-45b1-a331-31916a8cedd1",
+ "GeneratedBy": "urn:slicer-sVwU0TQP",
"digest": {
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}
},
{
- "@id": "urn:47b36bbc-f1ff-4bbd-8c90-6f05275ec35f",
+ "@id": "bids::sld.png",
"Label": "sld.png",
"AtLocation": "sld.png",
- "GeneratedBy": "urn:20ea2776-872a-45b1-a331-31916a8cedd1",
+ "GeneratedBy": "urn:slicer-sVwU0TQP",
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{
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- "GeneratedBy": "urn:20ea2776-872a-45b1-a331-31916a8cedd1",
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{
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- "GeneratedBy": "urn:20ea2776-872a-45b1-a331-31916a8cedd1",
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{
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- "GeneratedBy": "urn:20ea2776-872a-45b1-a331-31916a8cedd1",
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- "GeneratedBy": "urn:20ea2776-872a-45b1-a331-31916a8cedd1",
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{
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- "GeneratedBy": "urn:20ea2776-872a-45b1-a331-31916a8cedd1",
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- "GeneratedBy": "urn:20ea2776-872a-45b1-a331-31916a8cedd1",
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{
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"AtLocation": "example_func2highres1.png",
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- "GeneratedBy": "urn:d2e6341a-2c4e-4dfd-a507-10d4a06328cb",
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- "GeneratedBy": "urn:d2e6341a-2c4e-4dfd-a507-10d4a06328cb",
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- "GeneratedBy": "urn:d2e6341a-2c4e-4dfd-a507-10d4a06328cb",
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- "GeneratedBy": "urn:d2e6341a-2c4e-4dfd-a507-10d4a06328cb",
+ "GeneratedBy": "urn:slicer-IZBDalQP",
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- "GeneratedBy": "urn:d2e6341a-2c4e-4dfd-a507-10d4a06328cb",
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- "GeneratedBy": "urn:d2e6341a-2c4e-4dfd-a507-10d4a06328cb",
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- "GeneratedBy": "urn:d2e6341a-2c4e-4dfd-a507-10d4a06328cb",
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- "GeneratedBy": "urn:d2e6341a-2c4e-4dfd-a507-10d4a06328cb",
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- "GeneratedBy": "urn:d2e6341a-2c4e-4dfd-a507-10d4a06328cb",
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{
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- "GeneratedBy": "urn:1b7d2ad3-8d29-4aef-a8fa-f9fb4bbb9a40",
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"digest": {
@@ -1505,565 +1519,565 @@
}
},
{
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{
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}
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- "GeneratedBy": "urn:91ea8032-3aff-4df0-aa5c-1437dda477f2",
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{
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- "GeneratedBy": "urn:91ea8032-3aff-4df0-aa5c-1437dda477f2",
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{
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"Label": "highres2standard1.png",
"AtLocation": "highres2standard1.png",
- "GeneratedBy": "urn:821222ba-cb2f-47a8-bc1b-6bb24d814509",
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"AtLocation": "sla.png",
- "GeneratedBy": "urn:62eb0889-4f7f-4b45-afa7-be2f445b4d65",
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{
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- "GeneratedBy": "urn:62eb0889-4f7f-4b45-afa7-be2f445b4d65",
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}
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{
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- "GeneratedBy": "urn:62eb0889-4f7f-4b45-afa7-be2f445b4d65",
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}
},
{
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+ "@id": "bids::prefiltered_func_data_mcf.mat",
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"AtLocation": "prefiltered_func_data_mcf.mat",
"digest": {
@@ -2071,7 +2085,7 @@
}
},
{
- "@id": "urn:e987b7b3-5351-425a-80bd-1c18f436aa05",
+ "@id": "bids::prefiltered_func_data_mcf.par",
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"AtLocation": "prefiltered_func_data_mcf.par",
"digest": {
@@ -2079,7 +2093,7 @@
}
},
{
- "@id": "urn:958a9af3-d67a-49c5-be0f-f910d982040b",
+ "@id": "bids::prefiltered_func_data_mcf_abs.rms",
"Label": "prefiltered_func_data_mcf_abs.rms",
"AtLocation": "prefiltered_func_data_mcf_abs.rms",
"digest": {
@@ -2087,7 +2101,7 @@
}
},
{
- "@id": "urn:7d15df61-0c90-47a2-b901-a49fb72542ad",
+ "@id": "bids::prefiltered_func_data_mcf_abs_mean.rms",
"Label": "prefiltered_func_data_mcf_abs_mean.rms",
"AtLocation": "prefiltered_func_data_mcf_abs_mean.rms",
"digest": {
@@ -2095,7 +2109,7 @@
}
},
{
- "@id": "urn:886a634a-92ae-4b6a-a202-50de6c793825",
+ "@id": "bids::prefiltered_func_data_mcf_rel.rms",
"Label": "prefiltered_func_data_mcf_rel.rms",
"AtLocation": "prefiltered_func_data_mcf_rel.rms",
"digest": {
@@ -2103,7 +2117,7 @@
}
},
{
- "@id": "urn:2bfd1d18-9f2e-4320-aaef-09ce4964eab6",
+ "@id": "bids::prefiltered_func_data_mcf_rel_mean.rms",
"Label": "prefiltered_func_data_mcf_rel_mean.rms",
"AtLocation": "prefiltered_func_data_mcf_rel_mean.rms",
"digest": {
@@ -2111,34 +2125,34 @@
}
},
{
- "@id": "urn:b90bda86-d4c6-4834-8a69-d115a75f5584",
+ "@id": "bids::mc",
"Label": "mc",
"AtLocation": "mc",
- "GeneratedBy": "urn:1e0b939a-7f03-4ce5-94d3-ec2db95d67b5",
+ "GeneratedBy": "urn:mv-Dezd134K",
"digest": {
"sha256": "a1a8fa7b1d2bf5bc0a263e95f926d3d9b656d2572455245d46edf48e93744ffa"
}
},
{
- "@id": "urn:0690a611-adcc-4f06-aa92-734143220e88",
+ "@id": "bids::rot.png",
"Label": "rot.png",
"AtLocation": "rot.png",
- "GeneratedBy": "urn:65b22365-2211-4d46-bfc4-975be5c60659",
+ "GeneratedBy": "urn:fsltsplo-GHWIXd10",
"digest": {
"sha256": "b8776603f8865a358b2273847d21e63491e7c2e10567fb640608dd47ba721f29"
}
},
{
- "@id": "urn:9ee22513-1fd7-4480-bc21-82a8cc9d6ab3",
+ "@id": "bids::trans.png",
"Label": "trans.png",
"AtLocation": "trans.png",
- "GeneratedBy": "urn:6f21e13d-7fd5-41e1-bb1b-8fe9651d57b1",
+ "GeneratedBy": "urn:fsltsplo-FjkHHTOt",
"digest": {
"sha256": "496eac1d0ac15e80928780c73766c7791a1707291b2b9a6d1781c2f6a38de3cd"
}
},
{
- "@id": "urn:97719e5d-4229-4ff2-8310-05340e8ce878",
+ "@id": "bids::prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"Label": "prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"AtLocation": "prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"digest": {
@@ -2146,34 +2160,34 @@
}
},
{
- "@id": "urn:5467cc52-e440-45eb-82e8-0c1218f65454",
+ "@id": "bids::disp.png",
"Label": "disp.png",
"AtLocation": "disp.png",
- "GeneratedBy": "urn:ef409fbf-d2a1-4f68-a1ea-d7f905983286",
+ "GeneratedBy": "urn:fsltsplo-1AOZD9Ii",
"digest": {
"sha256": "c4615e07e04f0c390d969482634cb62e81d47c818d2866ee866ec9c64a5350fd"
}
},
{
- "@id": "urn:c82e7fa3-80eb-4169-978d-93ec72026c55",
+ "@id": "bids::mean_func",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:9b687564-6599-4fc2-a127-ba19d5e56934",
+ "GeneratedBy": "urn:fslmaths-hWzoSr4S",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:3beb9088-e8a6-44f2-b869-189fa7e32181",
+ "@id": "bids::mask",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:0ca14c7d-bdca-4c21-8942-3567d6212845",
+ "GeneratedBy": "urn:bet2-cTeUPlvL",
"digest": {
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}
},
{
- "@id": "urn:c774d4f0-4ad3-44d8-b9c5-7775c0dc9776",
+ "@id": "bids::mask_mask",
"Label": "mask_mask",
"AtLocation": "mask_mask",
"digest": {
@@ -2181,132 +2195,124 @@
}
},
{
- "@id": "urn:b36e766f-aeb8-4515-aaf6-d76431c4f769",
+ "@id": "bids::mask",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:3f293e77-c0ee-4d38-8aad-1c5aa4760477",
+ "GeneratedBy": "urn:immv-XjUkbn2U",
"digest": {
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}
},
{
- "@id": "urn:ca644e16-bc8f-4cb8-a310-fb2005b8f3d8",
+ "@id": "bids::prefiltered_func_data_bet",
"Label": "prefiltered_func_data_bet",
"AtLocation": "prefiltered_func_data_bet",
- "GeneratedBy": "urn:ad20686e-7a8c-4964-a10e-799a1c8761c9",
+ "GeneratedBy": "urn:fslmaths-EV2GCd4j",
"digest": {
"sha256": "c01f21947b38d9886528dec14edf23dfb55304b7da67569fe93902472b286cf4"
}
},
{
- "@id": "urn:2db82d0b-3360-4127-ad60-d9505fc28fe6",
+ "@id": "bids::mask",
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"AtLocation": "mask",
- "GeneratedBy": "urn:cc89346d-5c53-4652-84d4-847a29ab7c7c",
+ "GeneratedBy": "urn:fslmaths-HQvvGkr3",
"digest": {
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}
},
{
- "@id": "urn:72a2adcf-06bd-47a9-82ed-2f7be937388c",
+ "@id": "bids::mask",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:5b90ef67-d464-423c-9769-46fed7afde85",
+ "GeneratedBy": "urn:fslmaths-6dbK2akr",
"digest": {
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}
},
{
- "@id": "urn:73706964-2ab5-4dbc-8f4a-edc7d81fe7eb",
+ "@id": "bids::prefiltered_func_data_thresh",
"Label": "prefiltered_func_data_thresh",
"AtLocation": "prefiltered_func_data_thresh",
- "GeneratedBy": "urn:b850c3bb-c708-4927-a081-f0f6462076a0",
+ "GeneratedBy": "urn:fslmaths-LhcU1kaU",
"digest": {
"sha256": "c5c015a8df079b497bbce596808cbbdc09fb39411f490244de192dfa72d33640"
}
},
{
- "@id": "urn:0bd5799e-da4c-488f-8427-4b14fb5557eb",
+ "@id": "bids::mean_func",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:0ea248cd-0b5c-47e6-86ab-b81edcdad19f",
+ "GeneratedBy": "urn:fslmaths-8vlKApk2",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:32f9bfaf-ad74-42f3-9703-e946cb2ec370",
+ "@id": "bids::prefiltered_func_data_smooth",
"Label": "prefiltered_func_data_smooth",
"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:fe9f2e68-5450-4466-b842-ccc9dd39f6f7",
+ "GeneratedBy": "urn:susan-UxYIP1lX",
"digest": {
"sha256": "2a4901d885fce0b083c9f99364da8dcff184635e74ab011f53a68cfc6827b429"
}
},
{
- "@id": "urn:e149b9d7-48c5-49ff-944c-c8358c8c58f6",
+ "@id": "bids::prefiltered_func_data_smooth",
"Label": "prefiltered_func_data_smooth",
"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:61509192-5cb3-441a-8c1d-ad52d092302a",
+ "GeneratedBy": "urn:fslmaths-iFvYKT4p",
"digest": {
"sha256": "2a4901d885fce0b083c9f99364da8dcff184635e74ab011f53a68cfc6827b429"
}
},
{
- "@id": "urn:431edd12-cde6-4811-9006-d6fed017d3c5",
+ "@id": "bids::prefiltered_func_data_intnorm",
"Label": "prefiltered_func_data_intnorm",
"AtLocation": "prefiltered_func_data_intnorm",
- "GeneratedBy": "urn:8ae31d5e-a3ad-42bd-ad51-5124acc6a71f",
+ "GeneratedBy": "urn:fslmaths-4pYyDrcL",
"digest": {
"sha256": "0698a276f6f0fdccfb06033926d333a176503a09aaa87b78384fbffbf1c54dee"
}
},
{
- "@id": "urn:3508e8e8-f0c1-4ffd-8dfe-464026c65a88",
+ "@id": "bids::tempMean",
"Label": "tempMean",
"AtLocation": "tempMean",
- "GeneratedBy": "urn:ee2408cc-c449-4e10-93d3-7c11e0a58e0f",
+ "GeneratedBy": "urn:fslmaths-wLkyGtTj",
"digest": {
"sha256": "1a01513c76bc17516b60df315a1922789ce79d72e66e105fbf2723df9cb1b038"
}
},
{
- "@id": "urn:9c0ba698-c0c5-4305-977c-d9e1c1862185",
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- "digest": {
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- }
- },
- {
- "@id": "urn:d4a98127-8091-4ed0-9db3-ec2724d0dbcd",
+ "@id": "bids::prefiltered_func_data_tempfilt",
"Label": "prefiltered_func_data_tempfilt",
"AtLocation": "prefiltered_func_data_tempfilt",
+ "GeneratedBy": "urn:fslmaths-kSriC40g",
"digest": {
"sha256": "a1836f4694e7ffdb50484626724602498c7b22b4f3cdd1e7d105efd336cbc8bd"
}
},
{
- "@id": "urn:9220cdcc-449f-4185-b7fd-f95b6f48368b",
+ "@id": "bids::filtered_func_data",
"Label": "filtered_func_data",
"AtLocation": "filtered_func_data",
- "GeneratedBy": "urn:b7120cae-1b38-4812-9aa4-8123b3e36f0c",
+ "GeneratedBy": "urn:fslmaths-x2Mvt4OA",
"digest": {
"sha256": "2a1854e3b48a54f88e063191e25159015a0afbd300d18a1cfda37b4b68a1ee69"
}
},
{
- "@id": "urn:7374f398-be8e-4534-9ce6-61d41763e8e6",
+ "@id": "bids::mean_func",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:64faf72a-c81a-4277-ad7b-95ef6daef451",
+ "GeneratedBy": "urn:fslmaths-o6vpI5Id",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:7e4155c0-c82a-4288-9c97-0d282d04ea98",
+ "@id": "bids::prefiltered_func_data*",
"Label": "prefiltered_func_data*",
"AtLocation": "prefiltered_func_data*",
"digest": {
@@ -2314,181 +2320,222 @@
}
},
{
- "@id": "urn:b0d9a9c0-05e2-46e5-aecc-eb834e7acba1",
+ "@id": "bids::custom_timing_files",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:f39e533d-15dd-40d0-b151-cf39c441c721",
+ "GeneratedBy": "urn:makedire-RDOOlycE",
"digest": {
"sha256": "1d7e19792328d5040f2f9fb3c15d59de90fc771785f81c67039a043bd5f2ed20"
}
},
{
- "@id": "urn:0cf78e42-8032-409c-949c-c52da8f63be7",
+ "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
"Label": "sub-01_tone_counting.txt",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
+ "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
"digest": {
- "sha256": "c120d27b9d5d81a91be0e55f5cb880b2cb7de6c655554d9c15c9c04c6232ea8e"
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}
},
{
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+ "@id": "bids::custom_timing_files/ev1.txt",
"Label": "ev1.txt",
"AtLocation": "custom_timing_files/ev1.txt",
- "GeneratedBy": "urn:7962f1b9-fbcc-4216-999d-a029e8e92124"
+ "GeneratedBy": "urn:fslfixte-3PXP67h4"
},
{
- "@id": "urn:7409e6c4-7e3c-41fc-8ade-752542f081ae",
+ "@id": "bids::custom_timing_files",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:09759f75-f271-429a-ae59-0a44f00dd289",
+ "GeneratedBy": "urn:makedire-RrxzWAED",
"digest": {
"sha256": "1d7e19792328d5040f2f9fb3c15d59de90fc771785f81c67039a043bd5f2ed20"
}
},
{
- "@id": "urn:694de773-9fb6-4d11-9f94-7d4464c1040d",
+ "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
"Label": "sub-01_tone_counting_probe.txt",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
+ "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
"digest": {
- "sha256": "f09eeb82fa0be8e8759a5269403f36ec2b7dbf2c5b6caba1f0f985cc6cb3f703"
+ "sha256": "8b912293767f1a5e082311f6aaf0c44fc91fe45b0f2ae7f80e368bc2f4c2918a"
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{
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+ "@id": "bids::custom_timing_files/ev2.txt",
"Label": "ev2.txt",
"AtLocation": "custom_timing_files/ev2.txt",
- "GeneratedBy": "urn:7dedc9bb-8c86-4990-a6b8-648da3100168"
+ "GeneratedBy": "urn:fslfixte-f9DuphuI"
},
{
- "@id": "urn:453f2339-e213-4b5e-ab94-4573425a181a",
- "Label": "res4d",
- "AtLocation": "stats/res4d",
+ "@id": "bids::stats",
+ "Label": "stats",
+ "AtLocation": "stats",
"digest": {
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{
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- "Label": "smoothness",
- "AtLocation": "stats/smoothness",
- "GeneratedBy": "urn:cdecbeaf-18f4-4a48-8375-8486e681054a",
+ "@id": "bids::design.mat",
+ "Label": "design.mat",
+ "AtLocation": "design.mat",
"digest": {
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{
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+ "@id": "bids::design.con",
+ "Label": "design.con",
+ "AtLocation": "design.con",
"digest": {
- "sha256": "70ae47cee1ea1d3f1f6f8aa7ac51f2641cb2fcb745dfd8cc54a389346e6fa094"
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{
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+ "@id": "bids::design.fts",
+ "Label": "design.fts",
+ "AtLocation": "design.fts",
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+ {
+ "@id": "bids::stats",
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+ "AtLocation": "stats",
+ "GeneratedBy": "urn:filmgls-xpjNuWUs",
+ "digest": {
+ "sha256": "a9f3e135372514a16d11a8038262b3eff94ccd69a9b35c4724b2759cfc944a07"
+ }
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+ {
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+ "AtLocation": "stats/res4d"
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+ {
+ "@id": "bids::stats/smoothness",
+ "Label": "smoothness",
+ "AtLocation": "stats/smoothness",
+ "GeneratedBy": "urn:smoothes-VTT9rn8N"
+ },
+ {
+ "@id": "bids::stats/zstat1",
+ "Label": "zstat1",
+ "AtLocation": "stats/zstat1"
+ },
+ {
+ "@id": "bids::thresh_zstat1",
"Label": "thresh_zstat1",
"AtLocation": "thresh_zstat1",
- "GeneratedBy": "urn:7a3ae6ca-12a9-4b93-af1d-4e77a0ecd4ec",
+ "GeneratedBy": "urn:fslmaths-wxrzYlhL",
"digest": {
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}
},
{
- "@id": "urn:c7f540ab-8cca-4a10-bb24-c709b962b774",
+ "@id": "bids::stats/zstat2",
"Label": "zstat2",
- "AtLocation": "stats/zstat2",
- "digest": {
- "sha256": "b6b265908257e91648f7007e172c3ba159d9231b0acfce7fbf48d754f8cfe52c"
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+ "AtLocation": "stats/zstat2"
},
{
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+ "@id": "bids::thresh_zstat2",
"Label": "thresh_zstat2",
"AtLocation": "thresh_zstat2",
- "GeneratedBy": "urn:e0ccf79c-c0c8-4648-9c87-5d2049923838",
+ "GeneratedBy": "urn:fslmaths-2YQYb7ln",
"digest": {
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},
{
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+ "@id": "bids::stats/zfstat1",
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- "digest": {
- "sha256": "7411c38cb93415865a53b21dc0427506ed7994230aca73062e72251f77549cb9"
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+ "AtLocation": "stats/zfstat1"
},
{
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+ "@id": "bids::thresh_zfstat1",
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"AtLocation": "thresh_zfstat1",
- "GeneratedBy": "urn:753d9758-36e4-406a-b40f-4d8ec0e5d9dc",
+ "GeneratedBy": "urn:fslmaths-mUk1TnwY",
"digest": {
"sha256": "e4e927e247bdf8ff3b58b41cbb9db7643b27df1f7578c506950eb4b1ca2d0031"
}
},
{
- "@id": "urn:58ff1f1c-76ec-4363-a1d2-038927e2825b",
+ "@id": "bids::stats/zfstat2",
"Label": "zfstat2",
- "AtLocation": "stats/zfstat2",
- "digest": {
- "sha256": "bb4ff282a5f3cb0f071d986283a23ffd3ec4aee0180437f0cceed465ca29c4ea"
- }
+ "AtLocation": "stats/zfstat2"
},
{
- "@id": "urn:addaa522-7bef-42e3-a6ac-aef2fa1b260b",
+ "@id": "bids::thresh_zfstat2",
"Label": "thresh_zfstat2",
"AtLocation": "thresh_zfstat2",
- "GeneratedBy": "urn:b6bd7923-5f95-4de9-b336-d38e1ef54915",
+ "GeneratedBy": "urn:fslmaths-VTzvv2bx",
"digest": {
"sha256": "c298297997e4640c4c2d803314ca8cee706d302781975cdc53946aa6ca0d69c1"
}
},
{
- "@id": "urn:c9ee2495-5b57-4aaa-81c9-e342553d373a",
+ "@id": "bids::stats/zfstat3",
"Label": "zfstat3",
- "AtLocation": "stats/zfstat3",
- "digest": {
- "sha256": "a453ac126db546809ffb260275a445bad91e8b9db0559b6aae86088d6843a923"
- }
+ "AtLocation": "stats/zfstat3"
},
{
- "@id": "urn:c0aa7d2f-c91b-4291-987b-f3293bd8bc35",
+ "@id": "bids::thresh_zfstat3",
"Label": "thresh_zfstat3",
"AtLocation": "thresh_zfstat3",
- "GeneratedBy": "urn:e8fc634a-717b-4e72-a852-cd4cef0e4447",
+ "GeneratedBy": "urn:fslmaths-OZbfjxwh",
"digest": {
"sha256": "d146fc312c5094abf2cb41add06d96d79e5f36d27a64adea95365e8776a3707d"
}
},
{
- "@id": "urn:18bc1e51-3fac-487f-b249-7bd9ce9b56fc",
+ "@id": "bids::stats/cope1",
"Label": "cope1",
- "AtLocation": "stats/cope1",
- "digest": {
- "sha256": "bf3b603569da6dbe3d6f0e8667d346f3ac943c9d01d2fc9743ce17abeb1547fb"
- }
+ "AtLocation": "stats/cope1"
},
{
- "@id": "urn:27c0b428-9b3c-4279-981d-eccfe31cfcfa",
+ "@id": "bids::cluster_mask_zstat1",
"Label": "cluster_mask_zstat1",
"AtLocation": "cluster_mask_zstat1",
- "GeneratedBy": "urn:11a104fa-e66b-41e8-b818-75667e809a71",
+ "GeneratedBy": "urn:cluster-6EgN0K4y",
"digest": {
"sha256": "b28c170e33d2917cac55183786616a9e976e5e7f30dc7c8666341f12ed6d0277"
}
},
{
- "@id": "urn:6cc2dc97-7d0f-4575-aae6-5ea89fc778b7",
+ "@id": "bids::thresh_zstat1",
+ "Label": "thresh_zstat1",
+ "AtLocation": "thresh_zstat1",
+ "GeneratedBy": "urn:cluster-6EgN0K4y",
+ "digest": {
+ "sha256": "662e7ba670e124d15bb3cc18b818868f76604578034b524c8882f35fc5db413f"
+ }
+ },
+ {
+ "@id": "bids::lmax_zstat1.txt",
+ "Label": "lmax_zstat1.txt",
+ "AtLocation": "lmax_zstat1.txt",
+ "GeneratedBy": "urn:cluster-6EgN0K4y",
+ "digest": {
+ "sha256": "d44ee21719775397a1a95ede6778d25404b50e8bd259dbdf02d2fde635fc81a5"
+ }
+ },
+ {
+ "@id": "bids::stats/cope1",
"Label": "cope1",
"AtLocation": "stats/cope1",
- "GeneratedBy": "urn:11a104fa-e66b-41e8-b818-75667e809a71",
+ "GeneratedBy": "urn:cluster-6EgN0K4y"
+ },
+ {
+ "@id": "bids::cluster_zstat1.txt",
+ "Label": "cluster_zstat1.txt",
+ "AtLocation": "cluster_zstat1.txt",
+ "GeneratedBy": "urn:cluster-6EgN0K4y",
"digest": {
- "sha256": "bf3b603569da6dbe3d6f0e8667d346f3ac943c9d01d2fc9743ce17abeb1547fb"
+ "sha256": "b06695ff4f0a8158fa439b1ddf224b58d344606d400885c177390d09506e8e4c"
}
},
{
- "@id": "urn:48d9754b-4a40-49db-a0de-65552667fd1b",
+ "@id": "bids::cluster_zstat1",
"Label": "cluster_zstat1",
"AtLocation": "cluster_zstat1",
"digest": {
@@ -2496,33 +2543,54 @@
}
},
{
- "@id": "urn:56b37ee0-3fb0-4a62-820c-76bcdcb90b46",
+ "@id": "bids::stats/cope2",
"Label": "cope2",
- "AtLocation": "stats/cope2",
- "digest": {
- "sha256": "5f073baabd78c1c473fed55b511738f0ffe30d9fc1f23352a16ec058daacd88c"
- }
+ "AtLocation": "stats/cope2"
},
{
- "@id": "urn:f52f63fb-e56e-41a0-8221-8fc3e1a91397",
+ "@id": "bids::cluster_mask_zstat2",
"Label": "cluster_mask_zstat2",
"AtLocation": "cluster_mask_zstat2",
- "GeneratedBy": "urn:454caa2e-6cdb-40f4-acf7-786cfbbda286",
+ "GeneratedBy": "urn:cluster-3VvOdnac",
"digest": {
"sha256": "b88bb3cd4d809827a5c0a45cb4f6aac570cb25b7e056d5986d81d879548da121"
}
},
{
- "@id": "urn:c3ed1537-0d79-498f-952f-7cc72bb2629c",
+ "@id": "bids::thresh_zstat2",
+ "Label": "thresh_zstat2",
+ "AtLocation": "thresh_zstat2",
+ "GeneratedBy": "urn:cluster-3VvOdnac",
+ "digest": {
+ "sha256": "fe707ed68d72f4376668be45a2030f2d00fa81534a3e95bf92b6a499fa8595bd"
+ }
+ },
+ {
+ "@id": "bids::lmax_zstat2.txt",
+ "Label": "lmax_zstat2.txt",
+ "AtLocation": "lmax_zstat2.txt",
+ "GeneratedBy": "urn:cluster-3VvOdnac",
+ "digest": {
+ "sha256": "23ca5266a11743c7252c1758989cf555126dd598ae07080cf11f0a7c9e8a988b"
+ }
+ },
+ {
+ "@id": "bids::stats/cope2",
"Label": "cope2",
"AtLocation": "stats/cope2",
- "GeneratedBy": "urn:454caa2e-6cdb-40f4-acf7-786cfbbda286",
+ "GeneratedBy": "urn:cluster-3VvOdnac"
+ },
+ {
+ "@id": "bids::cluster_zstat2.txt",
+ "Label": "cluster_zstat2.txt",
+ "AtLocation": "cluster_zstat2.txt",
+ "GeneratedBy": "urn:cluster-3VvOdnac",
"digest": {
- "sha256": "5f073baabd78c1c473fed55b511738f0ffe30d9fc1f23352a16ec058daacd88c"
+ "sha256": "05b4675c829a96e029b38d828f0160bb2299d2d76d7c1248cd45119f0c6c9c2e"
}
},
{
- "@id": "urn:3e2d0b3c-a9d8-459a-a5b6-1c442573c6a9",
+ "@id": "bids::cluster_zstat2",
"Label": "cluster_zstat2",
"AtLocation": "cluster_zstat2",
"digest": {
@@ -2530,16 +2598,43 @@
}
},
{
- "@id": "urn:b4fd17d8-e6fa-4d22-baaa-acd338aa8ec8",
+ "@id": "bids::cluster_mask_zfstat1",
"Label": "cluster_mask_zfstat1",
"AtLocation": "cluster_mask_zfstat1",
- "GeneratedBy": "urn:6a4f28e4-2599-49cd-a360-89709dc67815",
+ "GeneratedBy": "urn:cluster-se2emGpz",
"digest": {
"sha256": "3523a5abe83ae8c76dd74f74632bc34163aac475152d48a6b79f37eca7dfe022"
}
},
{
- "@id": "urn:b4b22bb5-74c5-4bc1-a775-35f180100e22",
+ "@id": "bids::thresh_zfstat1",
+ "Label": "thresh_zfstat1",
+ "AtLocation": "thresh_zfstat1",
+ "GeneratedBy": "urn:cluster-se2emGpz",
+ "digest": {
+ "sha256": "e4e927e247bdf8ff3b58b41cbb9db7643b27df1f7578c506950eb4b1ca2d0031"
+ }
+ },
+ {
+ "@id": "bids::lmax_zfstat1.txt",
+ "Label": "lmax_zfstat1.txt",
+ "AtLocation": "lmax_zfstat1.txt",
+ "GeneratedBy": "urn:cluster-se2emGpz",
+ "digest": {
+ "sha256": "f6140171309069ed9586f94b07f187a4bbea683c429dc6a5558047a484c5e8a1"
+ }
+ },
+ {
+ "@id": "bids::cluster_zfstat1.txt",
+ "Label": "cluster_zfstat1.txt",
+ "AtLocation": "cluster_zfstat1.txt",
+ "GeneratedBy": "urn:cluster-se2emGpz",
+ "digest": {
+ "sha256": "0b5d4fcb253267ddae2859bc1226696992a2f6db2dba10d35c80399bd51477d4"
+ }
+ },
+ {
+ "@id": "bids::cluster_zfstat1",
"Label": "cluster_zfstat1",
"AtLocation": "cluster_zfstat1",
"digest": {
@@ -2547,16 +2642,43 @@
}
},
{
- "@id": "urn:e98f18a4-0565-4a3c-82c0-2a43e2465c28",
+ "@id": "bids::cluster_mask_zfstat2",
"Label": "cluster_mask_zfstat2",
"AtLocation": "cluster_mask_zfstat2",
- "GeneratedBy": "urn:5538393a-0e9e-4399-a092-fabfef6b5282",
+ "GeneratedBy": "urn:cluster-0M7QqJvZ",
"digest": {
"sha256": "962ef7014f226d586c47fb23ebcde5968e55a03f06dae8514b358579d8457e7a"
}
},
{
- "@id": "urn:be62d30a-74c7-4d75-8b5e-a9279b6f18b9",
+ "@id": "bids::thresh_zfstat2",
+ "Label": "thresh_zfstat2",
+ "AtLocation": "thresh_zfstat2",
+ "GeneratedBy": "urn:cluster-0M7QqJvZ",
+ "digest": {
+ "sha256": "c298297997e4640c4c2d803314ca8cee706d302781975cdc53946aa6ca0d69c1"
+ }
+ },
+ {
+ "@id": "bids::lmax_zfstat2.txt",
+ "Label": "lmax_zfstat2.txt",
+ "AtLocation": "lmax_zfstat2.txt",
+ "GeneratedBy": "urn:cluster-0M7QqJvZ",
+ "digest": {
+ "sha256": "00212684d755543487d676533c59ad32790c5df6ec82c71143d2a3e634c48427"
+ }
+ },
+ {
+ "@id": "bids::cluster_zfstat2.txt",
+ "Label": "cluster_zfstat2.txt",
+ "AtLocation": "cluster_zfstat2.txt",
+ "GeneratedBy": "urn:cluster-0M7QqJvZ",
+ "digest": {
+ "sha256": "aebb5170ab0ff6dc4d5357af34587a0007aa2156e6c6920f18444bc4528f9b7c"
+ }
+ },
+ {
+ "@id": "bids::cluster_zfstat2",
"Label": "cluster_zfstat2",
"AtLocation": "cluster_zfstat2",
"digest": {
@@ -2564,16 +2686,43 @@
}
},
{
- "@id": "urn:ed233bfd-1b60-4d80-9dce-035f0c183896",
+ "@id": "bids::cluster_mask_zfstat3",
"Label": "cluster_mask_zfstat3",
"AtLocation": "cluster_mask_zfstat3",
- "GeneratedBy": "urn:7c1874c9-f93c-4559-9f77-77113ffc2a9f",
+ "GeneratedBy": "urn:cluster-OF94q1Q7",
"digest": {
"sha256": "997d113725899451840579d113cb9c7adc8de328aa80459f8a03d175003a0d8a"
}
},
{
- "@id": "urn:4a906933-51a2-44bc-b703-d09459da47ac",
+ "@id": "bids::thresh_zfstat3",
+ "Label": "thresh_zfstat3",
+ "AtLocation": "thresh_zfstat3",
+ "GeneratedBy": "urn:cluster-OF94q1Q7",
+ "digest": {
+ "sha256": "d146fc312c5094abf2cb41add06d96d79e5f36d27a64adea95365e8776a3707d"
+ }
+ },
+ {
+ "@id": "bids::lmax_zfstat3.txt",
+ "Label": "lmax_zfstat3.txt",
+ "AtLocation": "lmax_zfstat3.txt",
+ "GeneratedBy": "urn:cluster-OF94q1Q7",
+ "digest": {
+ "sha256": "f999724523256d7ffd1604f5dd2c8549de81ae00eebdd018cd74eb296009ad42"
+ }
+ },
+ {
+ "@id": "bids::cluster_zfstat3.txt",
+ "Label": "cluster_zfstat3.txt",
+ "AtLocation": "cluster_zfstat3.txt",
+ "GeneratedBy": "urn:cluster-OF94q1Q7",
+ "digest": {
+ "sha256": "c045a555ac9e779eca923e720133d375e6034573d1bbbe0114a7d4ca781c765d"
+ }
+ },
+ {
+ "@id": "bids::cluster_zfstat3",
"Label": "cluster_zfstat3",
"AtLocation": "cluster_zfstat3",
"digest": {
@@ -2581,88 +2730,217 @@
}
},
{
- "@id": "urn:ecda2a0b-105d-4589-9f0e-31dd38e8dcaf",
- "Label": "cope1",
- "AtLocation": "stats/cope1",
- "GeneratedBy": "urn:35384b90-2956-47b9-856a-48728b487eb5",
+ "@id": "bids::lmax_zstat1_std.txt",
+ "Label": "lmax_zstat1_std.txt",
+ "AtLocation": "lmax_zstat1_std.txt",
+ "GeneratedBy": "urn:cluster-iGFpF9oV",
"digest": {
- "sha256": "bf3b603569da6dbe3d6f0e8667d346f3ac943c9d01d2fc9743ce17abeb1547fb"
+ "sha256": "6e07bc0cb551deb196e084447dfb84b3b86e2b0823cfa369cdee0b7ac3023b5b"
}
},
{
- "@id": "urn:bfda1d08-51e2-4e86-b81e-30ab68c80201",
+ "@id": "bids::stats/cope1",
+ "Label": "cope1",
+ "AtLocation": "stats/cope1",
+ "GeneratedBy": "urn:cluster-iGFpF9oV"
+ },
+ {
+ "@id": "bids::reg/example_func2standard.mat",
"Label": "example_func2standard.mat",
"AtLocation": "reg/example_func2standard.mat",
- "GeneratedBy": "urn:35384b90-2956-47b9-856a-48728b487eb5",
+ "GeneratedBy": "urn:cluster-iGFpF9oV",
"digest": {
"sha256": "00d5d84b5614b2a9a7941dd4ebbaa056b8b3e3c3c38c6f2804780828a279867d"
}
},
{
- "@id": "urn:0f724e40-ad22-46fb-a8e9-f9be71cad678",
- "Label": "cope2",
- "AtLocation": "stats/cope2",
- "GeneratedBy": "urn:d6a4f09c-fd94-4b7e-8d73-f3144c571e1d",
+ "@id": "bids::reg/standard",
+ "Label": "standard",
+ "AtLocation": "reg/standard",
+ "GeneratedBy": "urn:cluster-iGFpF9oV",
+ "digest": {
+ "sha256": "96d2568b3c4aba7523d1a0ea1068edc027a4dd72ab33aa97a65df89540b241eb"
+ }
+ },
+ {
+ "@id": "bids::cluster_zstat1_std.txt",
+ "Label": "cluster_zstat1_std.txt",
+ "AtLocation": "cluster_zstat1_std.txt",
+ "GeneratedBy": "urn:cluster-iGFpF9oV",
"digest": {
- "sha256": "5f073baabd78c1c473fed55b511738f0ffe30d9fc1f23352a16ec058daacd88c"
+ "sha256": "0d6db51e999bc5119694ba29a3f9a020859149c4d58329ee02bb3ddf9ab8d25b"
}
},
{
- "@id": "urn:139db712-0505-4bae-9add-75f0bfeed399",
+ "@id": "bids::lmax_zstat2_std.txt",
+ "Label": "lmax_zstat2_std.txt",
+ "AtLocation": "lmax_zstat2_std.txt",
+ "GeneratedBy": "urn:cluster-CUsyPhtO",
+ "digest": {
+ "sha256": "ea22f72515a78860fc690ee02c41ab407dcb4cce736dc0651cec451774722b4b"
+ }
+ },
+ {
+ "@id": "bids::stats/cope2",
+ "Label": "cope2",
+ "AtLocation": "stats/cope2",
+ "GeneratedBy": "urn:cluster-CUsyPhtO"
+ },
+ {
+ "@id": "bids::reg/example_func2standard.mat",
"Label": "example_func2standard.mat",
"AtLocation": "reg/example_func2standard.mat",
- "GeneratedBy": "urn:d6a4f09c-fd94-4b7e-8d73-f3144c571e1d",
+ "GeneratedBy": "urn:cluster-CUsyPhtO",
"digest": {
"sha256": "00d5d84b5614b2a9a7941dd4ebbaa056b8b3e3c3c38c6f2804780828a279867d"
}
},
{
- "@id": "urn:fb8a8b0f-cb5a-42a1-9109-8209804e1f00",
+ "@id": "bids::reg/standard",
+ "Label": "standard",
+ "AtLocation": "reg/standard",
+ "GeneratedBy": "urn:cluster-CUsyPhtO",
+ "digest": {
+ "sha256": "96d2568b3c4aba7523d1a0ea1068edc027a4dd72ab33aa97a65df89540b241eb"
+ }
+ },
+ {
+ "@id": "bids::cluster_zstat2_std.txt",
+ "Label": "cluster_zstat2_std.txt",
+ "AtLocation": "cluster_zstat2_std.txt",
+ "GeneratedBy": "urn:cluster-CUsyPhtO",
+ "digest": {
+ "sha256": "6a0aa3dd75a95116aa80f6471bf6fd8f4fc1ff82023dd1f6dcda511e5ec7ee18"
+ }
+ },
+ {
+ "@id": "bids::lmax_zfstat1_std.txt",
+ "Label": "lmax_zfstat1_std.txt",
+ "AtLocation": "lmax_zfstat1_std.txt",
+ "GeneratedBy": "urn:cluster-PFSC1Nv3",
+ "digest": {
+ "sha256": "6e69d15d6ef40adda9d8f03318de68e572fe80fb7bf266fac9831c9448b8405f"
+ }
+ },
+ {
+ "@id": "bids::reg/example_func2standard.mat",
"Label": "example_func2standard.mat",
"AtLocation": "reg/example_func2standard.mat",
- "GeneratedBy": "urn:b17a6347-3a64-4991-8693-5df741284ef9",
+ "GeneratedBy": "urn:cluster-PFSC1Nv3",
"digest": {
"sha256": "00d5d84b5614b2a9a7941dd4ebbaa056b8b3e3c3c38c6f2804780828a279867d"
}
},
{
- "@id": "urn:4aa2539d-9cdf-474c-905c-29b831615e98",
+ "@id": "bids::reg/standard",
+ "Label": "standard",
+ "AtLocation": "reg/standard",
+ "GeneratedBy": "urn:cluster-PFSC1Nv3",
+ "digest": {
+ "sha256": "96d2568b3c4aba7523d1a0ea1068edc027a4dd72ab33aa97a65df89540b241eb"
+ }
+ },
+ {
+ "@id": "bids::cluster_zfstat1_std.txt",
+ "Label": "cluster_zfstat1_std.txt",
+ "AtLocation": "cluster_zfstat1_std.txt",
+ "GeneratedBy": "urn:cluster-PFSC1Nv3",
+ "digest": {
+ "sha256": "ae5fc0f669032293ff366947ccfc1fad566b16b1559f09d4fe6d171e7c61aee2"
+ }
+ },
+ {
+ "@id": "bids::lmax_zfstat2_std.txt",
+ "Label": "lmax_zfstat2_std.txt",
+ "AtLocation": "lmax_zfstat2_std.txt",
+ "GeneratedBy": "urn:cluster-Gzi0hcGl",
+ "digest": {
+ "sha256": "8055f97da0be00f230ad821c53068eeee68635a4d04a5454b62fd260b5449650"
+ }
+ },
+ {
+ "@id": "bids::reg/example_func2standard.mat",
"Label": "example_func2standard.mat",
"AtLocation": "reg/example_func2standard.mat",
- "GeneratedBy": "urn:bfb154e5-1622-4d36-8847-391e988e8f0a",
+ "GeneratedBy": "urn:cluster-Gzi0hcGl",
"digest": {
"sha256": "00d5d84b5614b2a9a7941dd4ebbaa056b8b3e3c3c38c6f2804780828a279867d"
}
},
{
- "@id": "urn:b46b78b3-627d-4b93-adbd-c3b0ed3dde09",
+ "@id": "bids::reg/standard",
+ "Label": "standard",
+ "AtLocation": "reg/standard",
+ "GeneratedBy": "urn:cluster-Gzi0hcGl",
+ "digest": {
+ "sha256": "96d2568b3c4aba7523d1a0ea1068edc027a4dd72ab33aa97a65df89540b241eb"
+ }
+ },
+ {
+ "@id": "bids::cluster_zfstat2_std.txt",
+ "Label": "cluster_zfstat2_std.txt",
+ "AtLocation": "cluster_zfstat2_std.txt",
+ "GeneratedBy": "urn:cluster-Gzi0hcGl",
+ "digest": {
+ "sha256": "c2f3ece54791d60b8f472da60d557cf96cdafeec983e28e03871efd4b23aef81"
+ }
+ },
+ {
+ "@id": "bids::lmax_zfstat3_std.txt",
+ "Label": "lmax_zfstat3_std.txt",
+ "AtLocation": "lmax_zfstat3_std.txt",
+ "GeneratedBy": "urn:cluster-AbETZMSV",
+ "digest": {
+ "sha256": "516c47f968640fc627efca289ca444c6f508c716d41be6f3ff2badc02e18ba1c"
+ }
+ },
+ {
+ "@id": "bids::reg/example_func2standard.mat",
"Label": "example_func2standard.mat",
"AtLocation": "reg/example_func2standard.mat",
- "GeneratedBy": "urn:c38e0853-4b73-4883-a114-f777cb6214ea",
+ "GeneratedBy": "urn:cluster-AbETZMSV",
"digest": {
"sha256": "00d5d84b5614b2a9a7941dd4ebbaa056b8b3e3c3c38c6f2804780828a279867d"
}
},
{
- "@id": "urn:82a4e9c0-dbe6-455d-bcd3-b26b934765fa",
+ "@id": "bids::reg/standard",
+ "Label": "standard",
+ "AtLocation": "reg/standard",
+ "GeneratedBy": "urn:cluster-AbETZMSV",
+ "digest": {
+ "sha256": "96d2568b3c4aba7523d1a0ea1068edc027a4dd72ab33aa97a65df89540b241eb"
+ }
+ },
+ {
+ "@id": "bids::cluster_zfstat3_std.txt",
+ "Label": "cluster_zfstat3_std.txt",
+ "AtLocation": "cluster_zfstat3_std.txt",
+ "GeneratedBy": "urn:cluster-AbETZMSV",
+ "digest": {
+ "sha256": "73b0d68e2b66f0c430085a882291d793d31cca19c399e1a3fc2c0fd6c56eed4d"
+ }
+ },
+ {
+ "@id": "bids::rendered_thresh_zstat1",
"Label": "rendered_thresh_zstat1",
"AtLocation": "rendered_thresh_zstat1",
- "GeneratedBy": "urn:2e4b5df1-9dc5-4228-9bfe-aa3e957bb791",
+ "GeneratedBy": "urn:overlay-AEeSiJRN",
"digest": {
"sha256": "de5b9d44d95f4252f491eb45c76a0ae2b4d2c75b58664fc0df7d9153810c0bf6"
}
},
{
- "@id": "urn:46da5ab8-2f93-4ab6-b07f-3229ed18cf2c",
+ "@id": "bids::rendered_thresh_zstat1.png",
"Label": "rendered_thresh_zstat1.png",
"AtLocation": "rendered_thresh_zstat1.png",
- "GeneratedBy": "urn:937b139f-5ca7-42f5-8f3d-ac6cfbb528d9",
+ "GeneratedBy": "urn:slicer-gUWrtCQu",
"digest": {
"sha256": "15d6a8bf7a902df8c5feeb7468a3d0caacf9eb3067c0840c2f4763f5e2301527"
}
},
{
- "@id": "urn:3778da3b-49b0-4064-a214-69d1eb951d03",
+ "@id": "bids::/usr/local/packages/fsl-5.0.8/etc/luts/ramp.gif",
"Label": "ramp.gif",
"AtLocation": "/usr/local/packages/fsl-5.0.8/etc/luts/ramp.gif",
"digest": {
@@ -2670,100 +2948,100 @@
}
},
{
- "@id": "urn:fa4621bc-c290-4d99-a4f0-507a34817870",
+ "@id": "bids::.ramp.gif",
"Label": ".ramp.gif",
"AtLocation": ".ramp.gif",
- "GeneratedBy": "urn:a1e86077-4609-41a2-8ca5-782d4d26bfc4",
+ "GeneratedBy": "urn:cp-XWedD4a4",
"digest": {
"sha256": "93f4284ccb854d5a41401d9360a13223017b67479cb289a33d83836922e028a4"
}
},
{
- "@id": "urn:7bbdf8ac-0ffb-4bc1-895d-8861ec9ecfac",
+ "@id": "bids::rendered_thresh_zstat2",
"Label": "rendered_thresh_zstat2",
"AtLocation": "rendered_thresh_zstat2",
- "GeneratedBy": "urn:42562745-8ff4-4e2d-8775-7ac339c7d569",
+ "GeneratedBy": "urn:overlay-CTlqYESD",
"digest": {
"sha256": "b988cb8ba2b862b6fa88f223fcd3279c70e2ea217477bd1ec664c023be079cad"
}
},
{
- "@id": "urn:447495e3-84ca-460f-81ae-cda583bde9f9",
+ "@id": "bids::rendered_thresh_zstat2.png",
"Label": "rendered_thresh_zstat2.png",
"AtLocation": "rendered_thresh_zstat2.png",
- "GeneratedBy": "urn:771ae86f-2170-4828-b748-e4319401099b",
+ "GeneratedBy": "urn:slicer-fmz6vzFn",
"digest": {
"sha256": "0d60298d9eb509148075cbac8a22e6a95de919f17a069624fb42f86c29e1e199"
}
},
{
- "@id": "urn:1ed9b558-b314-4c4c-b751-1482a25a84f4",
+ "@id": "bids::rendered_thresh_zfstat1",
"Label": "rendered_thresh_zfstat1",
"AtLocation": "rendered_thresh_zfstat1",
- "GeneratedBy": "urn:5cedd5b4-458c-4276-81ff-476367f5d9a4",
+ "GeneratedBy": "urn:overlay-7HYmK5zG",
"digest": {
"sha256": "91b064bdcf6f2eec9fb87c161e52152f3343ed4de0cf5e5ba6153f970250aa5f"
}
},
{
- "@id": "urn:26c85652-df8e-4d98-8ff4-7a8429f8f216",
+ "@id": "bids::rendered_thresh_zfstat1.png",
"Label": "rendered_thresh_zfstat1.png",
"AtLocation": "rendered_thresh_zfstat1.png",
- "GeneratedBy": "urn:9bb3b3c7-d9e7-4990-b618-54e62cdb8449",
+ "GeneratedBy": "urn:slicer-NyAy9pUv",
"digest": {
"sha256": "c4c15c63489169ecb9747342259541d6b999ff25baaedfa066ecd1c00b761067"
}
},
{
- "@id": "urn:191530b0-9eb9-46d7-8143-7d371359a1fc",
+ "@id": "bids::rendered_thresh_zfstat2",
"Label": "rendered_thresh_zfstat2",
"AtLocation": "rendered_thresh_zfstat2",
- "GeneratedBy": "urn:ddfcf1f2-5254-4261-bbd2-ef03ed5bb814",
+ "GeneratedBy": "urn:overlay-ilPFUrlv",
"digest": {
"sha256": "901aff2cd2244519833ac5a18fd3a43b354c4ad3ae33c7ac58e3ccf29aa93b3d"
}
},
{
- "@id": "urn:3cdcb204-61c7-49b5-aaf4-65a14fa0947c",
+ "@id": "bids::rendered_thresh_zfstat2.png",
"Label": "rendered_thresh_zfstat2.png",
"AtLocation": "rendered_thresh_zfstat2.png",
- "GeneratedBy": "urn:660e76f5-e52e-4958-ab9a-ca2aa5d72ee0",
+ "GeneratedBy": "urn:slicer-zwdZ7Um5",
"digest": {
"sha256": "78b5c01aea80873e039a507a8038391d22208ec3cd90e873616ee228731e4eca"
}
},
{
- "@id": "urn:7564c2c2-a931-4c72-a838-570247b2b213",
+ "@id": "bids::rendered_thresh_zfstat3",
"Label": "rendered_thresh_zfstat3",
"AtLocation": "rendered_thresh_zfstat3",
- "GeneratedBy": "urn:9706816c-e2a0-4428-a917-403ac5fdf50a",
+ "GeneratedBy": "urn:overlay-8fyKCoI9",
"digest": {
"sha256": "d2a9aea097d842acf99873083620be67108f0a4eb2c9fa3356ab97706e4c907a"
}
},
{
- "@id": "urn:9b32f0a2-b8d8-43c5-b93a-2021e46955f9",
+ "@id": "bids::rendered_thresh_zfstat3.png",
"Label": "rendered_thresh_zfstat3.png",
"AtLocation": "rendered_thresh_zfstat3.png",
- "GeneratedBy": "urn:0a5cfb70-7c38-4790-b0e2-bf22f32161b2",
+ "GeneratedBy": "urn:slicer-mmdzsZLM",
"digest": {
"sha256": "41a48fc5a1799c8b19b70c893c80751b1e10a91c07890dab2158dfc150f1491b"
}
},
{
- "@id": "urn:f48b9d90-4542-4e86-a17f-230fb813fba2",
+ "@id": "bids::tsplot",
"Label": "tsplot",
"AtLocation": "tsplot",
- "GeneratedBy": "urn:7bd4ef46-e596-482c-9e4d-7c5154719873",
+ "GeneratedBy": "urn:makedire-vZc4wsey",
"digest": {
"sha256": "2a74042f4edf02288edf16961307f741651efb4346e102a04b7603e781d1625e"
}
},
{
- "@id": "urn:ec0e91e7-0d5a-4651-8771-0d8218963f1c",
+ "@id": "bids::tsplot",
"Label": "tsplot",
"AtLocation": "tsplot",
- "GeneratedBy": "urn:550ce33c-c8c6-470f-ad14-5f94187fffa6",
+ "GeneratedBy": "urn:tsplot-qwfDtqRW",
"digest": {
"sha256": "2a74042f4edf02288edf16961307f741651efb4346e102a04b7603e781d1625e"
}
diff --git a/examples/from_parsers/fsl/fsl_con_f_multiple_report_log.png b/examples/from_parsers/fsl/fsl_con_f_multiple_report_log.png
index c163cc9eb..0ff7c23cc 100644
Binary files a/examples/from_parsers/fsl/fsl_con_f_multiple_report_log.png and b/examples/from_parsers/fsl/fsl_con_f_multiple_report_log.png differ
diff --git a/examples/from_parsers/fsl/fsl_con_f_report_log.html b/examples/from_parsers/fsl/fsl_con_f_report_log.html
index e7cc0973c..11a7422bc 100644
--- a/examples/from_parsers/fsl/fsl_con_f_report_log.html
+++ b/examples/from_parsers/fsl/fsl_con_f_report_log.html
@@ -35,20 +35,20 @@ Progress Report / Log
326895
Initialisation
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
Total original volumes = 104
/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1
Preprocessing:Stage 1
-/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90
+/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/example_func.nii.gz -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90
Option -F ( FEAT version parameter ) selected with argument "6.00"
Option -d ( output directory ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat"
Option -l ( logfile )input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/logs/feat2_pre"
Option -R ( html unwarping report ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/report_unwarp.html"
Option -r ( html registration report ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/report_reg.html"
Option -i ( main input ) input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/example_func.nii.gz"
-Option -h ( high-res structural image ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
+Option -h ( high-res structural image ) selected with argument "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
Option -w ( highres dof ) selected with argument "BBR"
Option -x ( highres search ) selected with argument "90"
Option -s ( standard image ) selected with argument "/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain"
@@ -59,10 +59,10 @@ Progress Report / Log
/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/reg
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head
did not find file: example_func2highres.mat. Generating transform.
@@ -128,9 +128,9 @@ Progress Report / Log
/bin/rm -rf prefiltered_func_data*
Stats
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
/usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con --fcon=design.fts
Log directory is: stats
diff --git a/examples/from_parsers/fsl/fsl_con_f_report_log.jsonld b/examples/from_parsers/fsl/fsl_con_f_report_log.jsonld
index e35dd39aa..1db9f1412 100644
--- a/examples/from_parsers/fsl/fsl_con_f_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_con_f_report_log.jsonld
@@ -4,642 +4,652 @@
"Records": {
"Software": [
{
- "@id": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:fsl-IhAeexzD",
"@type": "prov:SoftwareAgent",
"Label": "FSL",
- "Version": "xxx"
+ "Version": "xxx",
+ "AltIdentifier": "RRID:SCR_002823"
}
],
"Activities": [
{
- "@id": "urn:2112ebad-5343-4f17-b7b6-d84acc2618e4",
+ "@id": "urn:fslmaths-oc14GKDP",
"Label": "fslmaths",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
"Used": [
- "urn:9dd4e0a3-87cb-4c2a-8ce1-6921569445e2"
+ "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold"
]
},
{
- "@id": "urn:6b385db3-df78-45fb-8ca3-b2723d781363",
+ "@id": "urn:fslroi-6k5pLepL",
"Label": "fslroi",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1",
"Used": [
- "urn:7f3d1f14-a8c3-47f2-9af6-9b28a4bb791d"
+ "bids::prefiltered_func_data"
]
},
{
- "@id": "urn:42d99646-29ac-48f5-a5c0-ecc93e09dd52",
+ "@id": "urn:mainfeat-jJrIyjtr",
"Label": "mainfeatreg",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/example_func.nii.gz -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
"Used": [
- "urn:15578984-fadf-4af5-8fc4-73962d165bfd",
- "urn:2366f9b3-3f7a-4ed2-b4a5-c91f73fdfa76",
- "urn:63c5707b-1fa7-4c34-9063-481dde955061"
+ "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/example_func.nii.gz",
+ "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain",
+ "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
]
},
{
- "@id": "urn:e0154622-ff40-45c9-95b0-d152011a123e",
+ "@id": "urn:makedire-h9dkEsGr",
"Label": "Make directory",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/reg",
"Used": []
},
{
- "@id": "urn:5718e82a-6a92-4d95-94ea-33eedbc07817",
+ "@id": "urn:fslmaths-rkVMg3eS",
"Label": "fslmaths",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
"Used": [
- "urn:2366f9b3-3f7a-4ed2-b4a5-c91f73fdfa76"
+ "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
]
},
{
- "@id": "urn:1e702c29-b4e1-41fa-bc95-23dfe6921348",
+ "@id": "urn:fslmaths-y3rdENXm",
"Label": "fslmaths",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
"Used": [
- "urn:91e1e931-b451-49d1-9166-6fbc67b1335f"
+ "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w"
]
},
{
- "@id": "urn:5a04266d-2945-46c5-9e01-ac3564a3bc81",
+ "@id": "urn:epireg-SrLJqoNK",
"Label": "epi_reg",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres",
- "Used": []
+ "Used": [
+ "bids::example_func",
+ "bids::highres",
+ "bids::highres_head"
+ ]
},
{
- "@id": "urn:ea5183ba-9f9d-4703-8055-ad9ac1aaf1f0",
+ "@id": "urn:convertx-0XwNnwAf",
"Label": "convert_xfm",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat",
"Used": [
- "urn:b6be9a53-13e4-4fdc-a78f-6e0ba8ae41d2"
+ "bids::example_func2highres.mat"
]
},
{
- "@id": "urn:d35acdb2-65ca-430b-977c-ec6062fccd3f",
+ "@id": "urn:slicer-oYAWwQEK",
"Label": "slicer",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:13b5dfe8-b7ac-4e01-a102-0ed6a57ef661",
- "urn:6c448591-7c7a-4116-a49f-ffa219c38120"
+ "bids::example_func2highres",
+ "bids::highres"
]
},
{
- "@id": "urn:8a14f7e7-6a33-44dc-a13b-7e287c052b95",
+ "@id": "urn:pngappen-ea6vl3HF",
"Label": "pngappend",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres1.png",
"Used": [
- "urn:026881b3-e898-4f69-a75e-48c164c99568",
- "urn:1cbc6101-33d2-4015-8b31-5647416620dd",
- "urn:2fa4fb99-2391-410c-a805-a4f4476069d3",
- "urn:589b66e0-ab84-4130-8846-006b115bfb26",
- "urn:65519446-a0d5-4e2f-99ae-44bf766cc3df",
- "urn:757e1873-4676-46d2-a92f-5b67fb687b7c",
- "urn:7bc01b6f-d058-4302-b0df-12b5722c8f9a",
- "urn:92acfa7c-8df3-461e-8e54-89c8affe431a",
- "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
- "urn:ab218459-a4c9-43cd-944e-ac16838e74b7",
- "urn:d4e1ec48-2884-40d8-9e9d-1dbb2a02e5a6",
- "urn:d50cffba-0a06-4acb-83ec-fef24b78dfda"
+ "bids::sla.png",
+ "bids::slb.png",
+ "bids::slc.png",
+ "bids::sld.png",
+ "bids::sle.png",
+ "bids::slf.png",
+ "bids::slg.png",
+ "bids::slh.png",
+ "bids::sli.png",
+ "bids::slj.png",
+ "bids::slk.png",
+ "bids::sll.png"
]
},
{
- "@id": "urn:a12f67fa-445a-4453-bfea-0530ee29ab2d",
+ "@id": "urn:slicer-NaQlNrU9",
"Label": "slicer",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:13b5dfe8-b7ac-4e01-a102-0ed6a57ef661",
- "urn:6c448591-7c7a-4116-a49f-ffa219c38120"
+ "bids::example_func2highres",
+ "bids::highres"
]
},
{
- "@id": "urn:7b00a100-6f32-4b46-9aed-9ac5252fcdbf",
+ "@id": "urn:pngappen-KHqutS7T",
"Label": "pngappend",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres2.png",
"Used": [
- "urn:026881b3-e898-4f69-a75e-48c164c99568",
- "urn:1cbc6101-33d2-4015-8b31-5647416620dd",
- "urn:2fa4fb99-2391-410c-a805-a4f4476069d3",
- "urn:589b66e0-ab84-4130-8846-006b115bfb26",
- "urn:65519446-a0d5-4e2f-99ae-44bf766cc3df",
- "urn:757e1873-4676-46d2-a92f-5b67fb687b7c",
- "urn:7bc01b6f-d058-4302-b0df-12b5722c8f9a",
- "urn:92acfa7c-8df3-461e-8e54-89c8affe431a",
- "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
- "urn:ab218459-a4c9-43cd-944e-ac16838e74b7",
- "urn:d4e1ec48-2884-40d8-9e9d-1dbb2a02e5a6",
- "urn:d50cffba-0a06-4acb-83ec-fef24b78dfda"
+ "bids::sla.png",
+ "bids::slb.png",
+ "bids::slc.png",
+ "bids::sld.png",
+ "bids::sle.png",
+ "bids::slf.png",
+ "bids::slg.png",
+ "bids::slh.png",
+ "bids::sli.png",
+ "bids::slj.png",
+ "bids::slk.png",
+ "bids::sll.png"
]
},
{
- "@id": "urn:5f3b06ec-bc29-436d-b9b9-286e16290002",
+ "@id": "urn:pngappen-buPbtlmN",
"Label": "pngappend",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend example_func2highres1.png example_func2highres2.png example_func2highres.png",
"Used": [
- "urn:0d2d17a2-b566-4927-927c-9f4a9d8d2883",
- "urn:c2e05bfa-95fe-4158-86df-ac105d6aa838"
+ "bids::example_func2highres1.png",
+ "bids::example_func2highres2.png"
]
},
{
- "@id": "urn:7638c2af-8a37-4b27-9b47-40735fced5d7",
+ "@id": "urn:rm-G2QoZwJo",
"Label": "rm",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/bin/rm -f sl?.png example_func2highres2.png",
"Used": [
- "urn:0d2d17a2-b566-4927-927c-9f4a9d8d2883",
- "urn:61ad5e58-0713-429a-9ed7-a5bbfa9bea59"
+ "bids::example_func2highres2.png",
+ "bids::sl?.png"
]
},
{
- "@id": "urn:ca5ab9bf-eb66-4b0a-90e7-eec0cc934c5e",
+ "@id": "urn:rm-4GTCd5W3",
"Label": "rm",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/bin/rm example_func2highres1.png",
"Used": [
- "urn:c2e05bfa-95fe-4158-86df-ac105d6aa838"
+ "bids::example_func2highres1.png"
]
},
{
- "@id": "urn:f8579074-adae-4f6c-8795-99bf5647aa6e",
+ "@id": "urn:mcflirt-nb93z6pl",
"Label": "mcflirt",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs -spline_final",
"Used": [
- "urn:7f3d1f14-a8c3-47f2-9af6-9b28a4bb791d"
+ "bids::prefiltered_func_data"
]
},
{
- "@id": "urn:3d913eb5-ba20-4cc6-99d1-a6b7887c18c8",
+ "@id": "urn:makedire-BdY1mJzW",
"Label": "Make directory",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/bin/mkdir -p mc",
"Used": []
},
{
- "@id": "urn:e46c42c1-f6d7-4c6d-8965-c5f7011cae42",
+ "@id": "urn:mv-MwSL31tw",
"Label": "mv",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc",
"Used": [
- "urn:1077cd25-b4bf-47ce-b006-37f8dec7d4ac",
- "urn:42c7cfa6-3436-47fc-9b0e-0efd39381912",
- "urn:5ad4f4c3-0369-486a-a649-2860f71566eb",
- "urn:9d49b392-18a6-4089-a524-a4d2ea45b105",
- "urn:a152686d-7cc6-42b9-9157-dc6099e600ce",
- "urn:c8093403-2eb5-4edc-965e-1cb81bb8aec7"
+ "bids::prefiltered_func_data_mcf.mat",
+ "bids::prefiltered_func_data_mcf.par",
+ "bids::prefiltered_func_data_mcf_abs.rms",
+ "bids::prefiltered_func_data_mcf_abs_mean.rms",
+ "bids::prefiltered_func_data_mcf_rel.rms",
+ "bids::prefiltered_func_data_mcf_rel_mean.rms"
]
},
{
- "@id": "urn:849de179-0714-449c-972c-9bd0385b606a",
+ "@id": "urn:fsltsplo-CmX0rhkg",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png",
"Used": [
- "urn:42c7cfa6-3436-47fc-9b0e-0efd39381912"
+ "bids::prefiltered_func_data_mcf.par"
]
},
{
- "@id": "urn:41da3ae7-d09c-401e-8d9f-c440dcdfc993",
+ "@id": "urn:fsltsplo-xZvlJGJR",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png",
"Used": [
- "urn:42c7cfa6-3436-47fc-9b0e-0efd39381912"
+ "bids::prefiltered_func_data_mcf.par"
]
},
{
- "@id": "urn:059c5470-f710-433e-b7f0-16be8f4d6632",
+ "@id": "urn:fsltsplo-y1QUR534",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png",
"Used": [
- "urn:926a47a6-ea55-4ad2-9e72-15447c30aeae"
+ "bids::prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms"
]
},
{
- "@id": "urn:b44ee1b6-ca32-4efe-b5b2-2295397c29f9",
+ "@id": "urn:fslmaths-b0cbKTer",
"Label": "fslmaths",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func",
"Used": [
- "urn:f2e2545b-dc53-4ac0-8a68-40994b1b2d60"
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:57bd302c-cbfd-4a43-a6e6-1604de3d3428",
+ "@id": "urn:bet2-xVedVR2i",
"Label": "bet2",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/bet2 mean_func mask -f 0.3 -n -m",
"Used": [
- "urn:ded1c7ec-5883-4f97-8990-ab8bbaf2c4ff"
+ "bids::mean_func"
]
},
{
- "@id": "urn:dd8157e4-5f84-4055-8577-d34fe317c4c9",
+ "@id": "urn:immv-XyQRaHT9",
"Label": "immv",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/immv mask_mask mask",
"Used": [
- "urn:6c0a31ef-4f45-4001-a08d-138d9a603d2d"
+ "bids::mask_mask"
]
},
{
- "@id": "urn:1d60fb80-4134-40ee-a4a7-9fec8e81944a",
+ "@id": "urn:fslmaths-6R9f17aP",
"Label": "fslmaths",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet",
"Used": [
- "urn:31e0a47f-bd71-463f-8e81-315d673c0f72",
- "urn:f2e2545b-dc53-4ac0-8a68-40994b1b2d60"
+ "bids::mask",
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:150bb5a4-2723-4470-8249-b8a11cf37033",
+ "@id": "urn:fslstats-ETmNlzhi",
"Label": "fslstats",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_bet -p 2 -p 98",
"Used": [
- "urn:ed19e957-8570-4268-b348-1c8a82e4f2e1"
+ "bids::prefiltered_func_data_bet"
]
},
{
- "@id": "urn:cccc4f59-e637-443d-afc8-653b7d3c359d",
+ "@id": "urn:fslmaths-zvMwGcMe",
"Label": "fslmaths",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_bet -thr 74.4585571 -Tmin -bin mask -odt char",
"Used": [
- "urn:ed19e957-8570-4268-b348-1c8a82e4f2e1"
+ "bids::prefiltered_func_data_bet"
]
},
{
- "@id": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "@id": "urn:fslstats-9pVn8GVH",
"Label": "fslstats",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_mcf -k mask -p 50",
"Used": [
- "urn:f2e2545b-dc53-4ac0-8a68-40994b1b2d60"
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:4b562a15-6bf7-4e4d-aa40-ce2850c3ad1e",
+ "@id": "urn:fslmaths-JXsIsq2q",
"Label": "fslmaths",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -dilF mask",
"Used": [
- "urn:31e0a47f-bd71-463f-8e81-315d673c0f72"
+ "bids::mask"
]
},
{
- "@id": "urn:5e833f79-5816-4ba7-aba6-6aa5c0860121",
+ "@id": "urn:fslmaths-i1BTSETh",
"Label": "fslmaths",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh",
"Used": [
- "urn:31e0a47f-bd71-463f-8e81-315d673c0f72",
- "urn:f2e2545b-dc53-4ac0-8a68-40994b1b2d60"
+ "bids::mask",
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:19fbe20a-d53a-4526-a882-a3fe0e9e8bea",
+ "@id": "urn:fslmaths-QNoJTpOa",
"Label": "fslmaths",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func",
"Used": [
- "urn:7ee58b52-0d8d-455d-bd78-b48d8d308cb5"
+ "bids::prefiltered_func_data_thresh"
]
},
{
- "@id": "urn:f542fa6c-2d9f-427c-86d8-d9a9a2ba5436",
+ "@id": "urn:susan-j7lDL1a2",
"Label": "susan",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/susan prefiltered_func_data_thresh 445.8289035 2.54777070064 3 1 1 mean_func 445.8289035 prefiltered_func_data_smooth",
"Used": [
- "urn:7ee58b52-0d8d-455d-bd78-b48d8d308cb5"
+ "bids::prefiltered_func_data_thresh"
]
},
{
- "@id": "urn:ec1e16aa-96dd-498e-b63c-edbe048ab155",
+ "@id": "urn:fslmaths-eaHPEfI0",
"Label": "fslmaths",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth",
"Used": [
- "urn:31e0a47f-bd71-463f-8e81-315d673c0f72",
- "urn:a3c9a40b-6244-4a75-a576-433e5217bf0a"
+ "bids::mask",
+ "bids::prefiltered_func_data_smooth"
]
},
{
- "@id": "urn:6f328faa-8b2a-4820-83bc-b21ef00175a5",
+ "@id": "urn:fslmaths-TViFxxjT",
"Label": "fslmaths",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mul 16.8225970571 prefiltered_func_data_intnorm",
"Used": [
- "urn:a3c9a40b-6244-4a75-a576-433e5217bf0a"
+ "bids::prefiltered_func_data_smooth"
]
},
{
- "@id": "urn:5fec2cf3-fa6a-4cd0-9306-fa3ba9543c53",
+ "@id": "urn:fslmaths-NSt9V9sw",
"Label": "fslmaths",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean",
"Used": [
- "urn:434be8cd-9929-453f-8644-d42a0ecab635"
+ "bids::prefiltered_func_data_intnorm"
]
},
{
- "@id": "urn:b09f1df1-7eef-43ab-b856-44362156042d",
+ "@id": "urn:fslmaths-eZHX1jve",
"Label": "fslmaths",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -bptf 15.0 -1 -add tempMean prefiltered_func_data_tempfilt",
"Used": [
- "urn:434be8cd-9929-453f-8644-d42a0ecab635",
- "urn:e77ccb11-2453-4a71-8c6a-7aa8acf1a8ad"
+ "bids::prefiltered_func_data_intnorm",
+ "bids::tempMean"
]
},
{
- "@id": "urn:8111caba-eb40-4a7e-bdba-a17cdf324f75",
+ "@id": "urn:imrm-6AsWFoz1",
"Label": "imrm",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/imrm tempMean",
"Used": [
- "urn:e77ccb11-2453-4a71-8c6a-7aa8acf1a8ad"
+ "bids::tempMean"
]
},
{
- "@id": "urn:ee130f6b-a062-46b2-b51d-4a1e42d71915",
+ "@id": "urn:fslmaths-KbrkJIBY",
"Label": "fslmaths",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data",
"Used": [
- "urn:b2670328-db1e-4674-90cb-13fcc914f630"
+ "bids::prefiltered_func_data_tempfilt"
]
},
{
- "@id": "urn:4448454e-d15c-4499-8c25-12bb3e6fe805",
+ "@id": "urn:fslmaths-TFy9OeDH",
"Label": "fslmaths",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths filtered_func_data -Tmean mean_func",
"Used": [
- "urn:afb4482f-41f7-48c4-8884-81f04334d619"
+ "bids::filtered_func_data"
]
},
{
- "@id": "urn:3d32c7eb-ba23-4b67-a36c-c499e9d77732",
+ "@id": "urn:rm-S5y4JiDJ",
"Label": "rm",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/bin/rm -rf prefiltered_func_data*",
"Used": [
- "urn:cfe72aec-bd1a-4ee1-a000-f14251902181"
+ "bids::prefiltered_func_data*"
]
},
{
- "@id": "urn:bd6c8246-39c9-4521-a578-2fbd75723ccf",
+ "@id": "urn:makedire-CYU7q463",
"Label": "Make directory",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
- "@id": "urn:7bcf3122-e120-44d2-8fb2-8e67537b56b3",
+ "@id": "urn:fslfixte-dpO7fTvF",
"Label": "fslFixText",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
"Used": [
- "urn:23a692d8-75aa-4033-a468-aa0e65da9c36"
+ "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt"
]
},
{
- "@id": "urn:aece4d2b-0460-4251-8c7f-126fce456814",
+ "@id": "urn:makedire-LmNQcVed",
"Label": "Make directory",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
- "@id": "urn:ccb973ca-2141-47aa-a525-6ea2a3e49c50",
+ "@id": "urn:fslfixte-Ru3257Bq",
"Label": "fslFixText",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
"Used": [
- "urn:4b9261b5-0c66-406d-b2ae-216ddb667897"
+ "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt"
]
},
{
- "@id": "urn:5b84a168-7b3e-4a42-939c-6ddace47728b",
+ "@id": "urn:filmgls-sDjcg2z9",
"Label": "film_gls",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con --fcon=design.fts",
- "Used": []
+ "Used": [
+ "bids::design.con",
+ "bids::design.fts",
+ "bids::design.mat",
+ "bids::filtered_func_data",
+ "bids::stats"
+ ]
},
{
- "@id": "urn:7e3a9ab1-40eb-4692-b0a6-da89e21fe018",
+ "@id": "urn:smoothes-xNwolFhT",
"Label": "smoothest",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 102 -m mask -r stats/res4d > stats/smoothness",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 102 -m mask -r stats/res4d > stats/smoothness",
"Used": [
- "urn:31e0a47f-bd71-463f-8e81-315d673c0f72",
- "urn:8c6633c0-1445-454f-9af8-3f73d297d9d1"
+ "bids::mask",
+ "bids::stats/res4d"
]
},
{
- "@id": "urn:bab2ae80-8942-4f06-84a4-3a82ba65b210",
+ "@id": "urn:fslmaths-C7DZCLIJ",
"Label": "fslmaths",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1",
"Used": [
- "urn:31e0a47f-bd71-463f-8e81-315d673c0f72",
- "urn:a0665740-7578-4953-a5d8-2febc139b4c8"
+ "bids::mask",
+ "bids::stats/zstat1"
]
},
{
- "@id": "urn:bec94431-e6e6-49b1-9844-70ed437c5011",
+ "@id": "urn:echo-1sAApjLG",
"Label": "echo",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "echo 38352 > thresh_zstat1.vol",
"Used": []
},
{
- "@id": "urn:cb9ad31a-ff52-4fc0-9e45-c50f04ad7dd1",
+ "@id": "urn:fslmaths-O3riA05d",
"Label": "fslmaths",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zfstat1 -mas mask thresh_zfstat1",
"Used": [
- "urn:02011602-f54d-43a7-b7d5-05df253f6435",
- "urn:31e0a47f-bd71-463f-8e81-315d673c0f72"
+ "bids::mask",
+ "bids::stats/zfstat1"
]
},
{
- "@id": "urn:03330031-ed4b-4c42-9765-1ce0737c19e1",
+ "@id": "urn:echo-MZ1h05oO",
"Label": "echo",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "echo 38352 > thresh_zfstat1.vol",
"Used": []
},
{
- "@id": "urn:2d8c3fda-3c56-479a-9328-deb5fc80e1e9",
+ "@id": "urn:ptoz-ia1Ulg5h",
"Label": "ptoz",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:55e6b3e5-a805-4eab-b31f-f66baccf0633",
+ "@id": "urn:cluster-q85r87w0",
"Label": "cluster",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -t 3.090232 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z --voxuncthresh -c stats/cope1 > cluster_zstat1.txt",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -t 3.090232 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z --voxuncthresh -c stats/cope1 > cluster_zstat1.txt",
"Used": [
- "urn:a9b86e5d-509c-4128-917c-3441d311007a",
- "urn:fc3626b4-6d2f-4cba-a554-f53bee1bd2f4"
+ "bids::stats/cope1",
+ "bids::thresh_zstat1"
]
},
{
- "@id": "urn:d2f4881f-3117-40fd-8b8d-cf002001b831",
+ "@id": "urn:cluster2-j4o3usk6",
"Label": "cluster2html",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat1",
"Used": [
- "urn:487a68cf-1b53-49f7-9891-e4ba3dd75314"
+ "bids::cluster_zstat1"
]
},
{
- "@id": "urn:61891cc9-48c2-4693-8cb8-8cbc53fabbf6",
+ "@id": "urn:ptoz-jqsGIdOl",
"Label": "ptoz",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:d2fd03b5-32f2-4d3f-9a7e-91a684205c9b",
+ "@id": "urn:cluster-MRZWM656",
"Label": "cluster",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zfstat1 -t 3.090232 --othresh=thresh_zfstat1 -o cluster_mask_zfstat1 --connectivity=26 --olmax=lmax_zfstat1.txt --scalarname=Z --voxuncthresh > cluster_zfstat1.txt",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zfstat1 -t 3.090232 --othresh=thresh_zfstat1 -o cluster_mask_zfstat1 --connectivity=26 --olmax=lmax_zfstat1.txt --scalarname=Z --voxuncthresh > cluster_zfstat1.txt",
"Used": [
- "urn:7d205378-c584-45cd-a840-ce5eb3edceba"
+ "bids::thresh_zfstat1"
]
},
{
- "@id": "urn:d0c0bd35-a9bc-471a-90c8-51581635290c",
+ "@id": "urn:cluster2-FSBIpyPU",
"Label": "cluster2html",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zfstat1",
"Used": [
- "urn:6b976ef1-34cd-4beb-b4df-4d827eb6e8c9"
+ "bids::cluster_zfstat1"
]
},
{
- "@id": "urn:df4f0286-cff5-4533-8b9d-da7083d40de2",
+ "@id": "urn:fslstats-dowWh0hs",
"Label": "fslstats",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat1 -l 0.0001 -R 2>/dev/null",
"Used": [
- "urn:a9b86e5d-509c-4128-917c-3441d311007a"
+ "bids::thresh_zstat1"
]
},
{
- "@id": "urn:6a7a3359-9111-448c-8d33-d9e86321c801",
+ "@id": "urn:fslstats-SgHefAry",
"Label": "fslstats",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zfstat1 -l 0.0001 -R 2>/dev/null",
"Used": [
- "urn:7d205378-c584-45cd-a840-ce5eb3edceba"
+ "bids::thresh_zfstat1"
]
},
{
- "@id": "urn:8151d2f2-5ad5-434d-863a-7e01c98263b7",
+ "@id": "urn:overlay-MzJgJACL",
"Label": "overlay",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat1 3.090250 7.488793 rendered_thresh_zstat1",
"Used": []
},
{
- "@id": "urn:c8e777cc-a609-4c27-a92d-c46856ae9e17",
+ "@id": "urn:slicer-3wFnCCy8",
"Label": "slicer",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat1 -A 750 rendered_thresh_zstat1.png",
"Used": [
- "urn:aee873fe-d817-466b-8d31-98fcb45222d3"
+ "bids::rendered_thresh_zstat1"
]
},
{
- "@id": "urn:32ca3d5b-761b-4903-b0a1-49daa50ee44d",
+ "@id": "urn:cp-SPUZKjCU",
"Label": "cp",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/bin/cp /usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif .ramp.gif",
"Used": [
- "urn:3f6ebb09-33c2-450f-a017-1aba59644f2e"
+ "bids::/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif"
]
},
{
- "@id": "urn:2e5c9e5f-35b0-41e0-832d-b95799f3925a",
+ "@id": "urn:overlay-4KIeCJr6",
"Label": "overlay",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zfstat1 3.090250 7.488793 rendered_thresh_zfstat1",
"Used": []
},
{
- "@id": "urn:48605004-13de-4ff6-9ce3-a22c66dbfeef",
+ "@id": "urn:slicer-WhXfy3dQ",
"Label": "slicer",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zfstat1 -A 750 rendered_thresh_zfstat1.png",
"Used": [
- "urn:caed8b19-3fe4-4bd7-b621-c3b31de3dcad"
+ "bids::rendered_thresh_zfstat1"
]
},
{
- "@id": "urn:3c1247bf-e04f-4b91-a57a-1960d43804e2",
+ "@id": "urn:makedire-Rbuz4y5j",
"Label": "Make directory",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "mkdir -p tsplot",
"Used": []
},
{
- "@id": "urn:be636df1-e671-4fc0-b305-d3a0366578bf",
+ "@id": "urn:tsplot-ex5pJZVe",
"Label": "tsplot",
- "AssociatedWith": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
+ "AssociatedWith": "urn:fsl-IhAeexzD",
"Command": "/usr/local/packages/fsl-5.0.10/bin/tsplot . -f filtered_func_data -o tsplot",
"Used": []
}
],
"Entities": [
{
- "@id": "urn:9dd4e0a3-87cb-4c2a-8ce1-6921569445e2",
+ "@id": "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold",
"Label": "sub-01_task-tonecounting_bold",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold",
+ "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold",
"digest": {
- "sha256": "028adf00daa36e78f06a61dcd3cb3526cd8564c1284e80516ab5520701324ac1"
+ "sha256": "33501604ae140e58832facff473a9578d5a549403bdbec53107d2b3eaab898ee"
}
},
{
- "@id": "urn:7f3d1f14-a8c3-47f2-9af6-9b28a4bb791d",
+ "@id": "bids::prefiltered_func_data",
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@@ -647,15 +657,15 @@
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@@ -663,45 +673,57 @@
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@@ -709,267 +731,259 @@
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@@ -977,25 +991,25 @@
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"sha256": "83371e264d408de4f678b8182097b39c86bd0a618ca76af6d1dfee5db0903b78"
}
},
{
- "@id": "urn:a5087b67-20a8-403c-a111-bdeb5a331f4b",
+ "@id": "bids::mc",
"Label": "mc",
"AtLocation": "mc",
- "GeneratedBy": "urn:3d913eb5-ba20-4cc6-99d1-a6b7887c18c8",
+ "GeneratedBy": "urn:makedire-BdY1mJzW",
"digest": {
"sha256": "a1a8fa7b1d2bf5bc0a263e95f926d3d9b656d2572455245d46edf48e93744ffa"
}
},
{
- "@id": "urn:9d49b392-18a6-4089-a524-a4d2ea45b105",
+ "@id": "bids::prefiltered_func_data_mcf.mat",
"Label": "prefiltered_func_data_mcf.mat",
"AtLocation": "prefiltered_func_data_mcf.mat",
"digest": {
@@ -1003,7 +1017,7 @@
}
},
{
- "@id": "urn:42c7cfa6-3436-47fc-9b0e-0efd39381912",
+ "@id": "bids::prefiltered_func_data_mcf.par",
"Label": "prefiltered_func_data_mcf.par",
"AtLocation": "prefiltered_func_data_mcf.par",
"digest": {
@@ -1011,7 +1025,7 @@
}
},
{
- "@id": "urn:a152686d-7cc6-42b9-9157-dc6099e600ce",
+ "@id": "bids::prefiltered_func_data_mcf_abs.rms",
"Label": "prefiltered_func_data_mcf_abs.rms",
"AtLocation": "prefiltered_func_data_mcf_abs.rms",
"digest": {
@@ -1019,7 +1033,7 @@
}
},
{
- "@id": "urn:c8093403-2eb5-4edc-965e-1cb81bb8aec7",
+ "@id": "bids::prefiltered_func_data_mcf_abs_mean.rms",
"Label": "prefiltered_func_data_mcf_abs_mean.rms",
"AtLocation": "prefiltered_func_data_mcf_abs_mean.rms",
"digest": {
@@ -1027,7 +1041,7 @@
}
},
{
- "@id": "urn:1077cd25-b4bf-47ce-b006-37f8dec7d4ac",
+ "@id": "bids::prefiltered_func_data_mcf_rel.rms",
"Label": "prefiltered_func_data_mcf_rel.rms",
"AtLocation": "prefiltered_func_data_mcf_rel.rms",
"digest": {
@@ -1035,7 +1049,7 @@
}
},
{
- "@id": "urn:5ad4f4c3-0369-486a-a649-2860f71566eb",
+ "@id": "bids::prefiltered_func_data_mcf_rel_mean.rms",
"Label": "prefiltered_func_data_mcf_rel_mean.rms",
"AtLocation": "prefiltered_func_data_mcf_rel_mean.rms",
"digest": {
@@ -1043,34 +1057,34 @@
}
},
{
- "@id": "urn:9b462dc8-9807-4841-b48f-e9b74eed7a81",
+ "@id": "bids::mc",
"Label": "mc",
"AtLocation": "mc",
- "GeneratedBy": "urn:e46c42c1-f6d7-4c6d-8965-c5f7011cae42",
+ "GeneratedBy": "urn:mv-MwSL31tw",
"digest": {
"sha256": "a1a8fa7b1d2bf5bc0a263e95f926d3d9b656d2572455245d46edf48e93744ffa"
}
},
{
- "@id": "urn:f06ec3d0-2cd7-457d-b277-1b3d818c1cad",
+ "@id": "bids::rot.png",
"Label": "rot.png",
"AtLocation": "rot.png",
- "GeneratedBy": "urn:849de179-0714-449c-972c-9bd0385b606a",
+ "GeneratedBy": "urn:fsltsplo-CmX0rhkg",
"digest": {
"sha256": "b8776603f8865a358b2273847d21e63491e7c2e10567fb640608dd47ba721f29"
}
},
{
- "@id": "urn:d5c50b91-bf99-44fc-8817-638474bc5ed8",
+ "@id": "bids::trans.png",
"Label": "trans.png",
"AtLocation": "trans.png",
- "GeneratedBy": "urn:41da3ae7-d09c-401e-8d9f-c440dcdfc993",
+ "GeneratedBy": "urn:fsltsplo-xZvlJGJR",
"digest": {
"sha256": "496eac1d0ac15e80928780c73766c7791a1707291b2b9a6d1781c2f6a38de3cd"
}
},
{
- "@id": "urn:926a47a6-ea55-4ad2-9e72-15447c30aeae",
+ "@id": "bids::prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"Label": "prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"AtLocation": "prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"digest": {
@@ -1078,34 +1092,34 @@
}
},
{
- "@id": "urn:2ca333a5-9e0a-45be-b763-0a5270454e92",
+ "@id": "bids::disp.png",
"Label": "disp.png",
"AtLocation": "disp.png",
- "GeneratedBy": "urn:059c5470-f710-433e-b7f0-16be8f4d6632",
+ "GeneratedBy": "urn:fsltsplo-y1QUR534",
"digest": {
"sha256": "c4615e07e04f0c390d969482634cb62e81d47c818d2866ee866ec9c64a5350fd"
}
},
{
- "@id": "urn:ded1c7ec-5883-4f97-8990-ab8bbaf2c4ff",
+ "@id": "bids::mean_func",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:b44ee1b6-ca32-4efe-b5b2-2295397c29f9",
+ "GeneratedBy": "urn:fslmaths-b0cbKTer",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:31e0a47f-bd71-463f-8e81-315d673c0f72",
+ "@id": "bids::mask",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:57bd302c-cbfd-4a43-a6e6-1604de3d3428",
+ "GeneratedBy": "urn:bet2-xVedVR2i",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:6c0a31ef-4f45-4001-a08d-138d9a603d2d",
+ "@id": "bids::mask_mask",
"Label": "mask_mask",
"AtLocation": "mask_mask",
"digest": {
@@ -1113,132 +1127,124 @@
}
},
{
- "@id": "urn:993b368d-e7e0-4da5-b496-75d6c1c7cc60",
+ "@id": "bids::mask",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:dd8157e4-5f84-4055-8577-d34fe317c4c9",
+ "GeneratedBy": "urn:immv-XyQRaHT9",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:ed19e957-8570-4268-b348-1c8a82e4f2e1",
+ "@id": "bids::prefiltered_func_data_bet",
"Label": "prefiltered_func_data_bet",
"AtLocation": "prefiltered_func_data_bet",
- "GeneratedBy": "urn:1d60fb80-4134-40ee-a4a7-9fec8e81944a",
+ "GeneratedBy": "urn:fslmaths-6R9f17aP",
"digest": {
"sha256": "c01f21947b38d9886528dec14edf23dfb55304b7da67569fe93902472b286cf4"
}
},
{
- "@id": "urn:a74b6175-36ab-47d6-ab49-76a06c0930dd",
+ "@id": "bids::mask",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:cccc4f59-e637-443d-afc8-653b7d3c359d",
+ "GeneratedBy": "urn:fslmaths-zvMwGcMe",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:71ab96a6-c63f-4d51-9ba5-44e05d4a6bff",
+ "@id": "bids::mask",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:4b562a15-6bf7-4e4d-aa40-ce2850c3ad1e",
+ "GeneratedBy": "urn:fslmaths-JXsIsq2q",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:7ee58b52-0d8d-455d-bd78-b48d8d308cb5",
+ "@id": "bids::prefiltered_func_data_thresh",
"Label": "prefiltered_func_data_thresh",
"AtLocation": "prefiltered_func_data_thresh",
- "GeneratedBy": "urn:5e833f79-5816-4ba7-aba6-6aa5c0860121",
+ "GeneratedBy": "urn:fslmaths-i1BTSETh",
"digest": {
"sha256": "c5c015a8df079b497bbce596808cbbdc09fb39411f490244de192dfa72d33640"
}
},
{
- "@id": "urn:d59db81f-1eaf-446c-be91-a7e7e07425c4",
+ "@id": "bids::mean_func",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:19fbe20a-d53a-4526-a882-a3fe0e9e8bea",
+ "GeneratedBy": "urn:fslmaths-QNoJTpOa",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:a3c9a40b-6244-4a75-a576-433e5217bf0a",
+ "@id": "bids::prefiltered_func_data_smooth",
"Label": "prefiltered_func_data_smooth",
"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:f542fa6c-2d9f-427c-86d8-d9a9a2ba5436",
+ "GeneratedBy": "urn:susan-j7lDL1a2",
"digest": {
"sha256": "2a4901d885fce0b083c9f99364da8dcff184635e74ab011f53a68cfc6827b429"
}
},
{
- "@id": "urn:e7b2e4af-beef-4f6a-8237-0d0680e02e9a",
+ "@id": "bids::prefiltered_func_data_smooth",
"Label": "prefiltered_func_data_smooth",
"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:ec1e16aa-96dd-498e-b63c-edbe048ab155",
+ "GeneratedBy": "urn:fslmaths-eaHPEfI0",
"digest": {
"sha256": "2a4901d885fce0b083c9f99364da8dcff184635e74ab011f53a68cfc6827b429"
}
},
{
- "@id": "urn:434be8cd-9929-453f-8644-d42a0ecab635",
+ "@id": "bids::prefiltered_func_data_intnorm",
"Label": "prefiltered_func_data_intnorm",
"AtLocation": "prefiltered_func_data_intnorm",
- "GeneratedBy": "urn:6f328faa-8b2a-4820-83bc-b21ef00175a5",
+ "GeneratedBy": "urn:fslmaths-TViFxxjT",
"digest": {
"sha256": "0698a276f6f0fdccfb06033926d333a176503a09aaa87b78384fbffbf1c54dee"
}
},
{
- "@id": "urn:e77ccb11-2453-4a71-8c6a-7aa8acf1a8ad",
+ "@id": "bids::tempMean",
"Label": "tempMean",
"AtLocation": "tempMean",
- "GeneratedBy": "urn:5fec2cf3-fa6a-4cd0-9306-fa3ba9543c53",
+ "GeneratedBy": "urn:fslmaths-NSt9V9sw",
"digest": {
"sha256": "1a01513c76bc17516b60df315a1922789ce79d72e66e105fbf2723df9cb1b038"
}
},
{
- "@id": "urn:bad1b199-f926-4892-9e5d-b40f8fbd3997",
- "Label": "15.0",
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- "GeneratedBy": "urn:b09f1df1-7eef-43ab-b856-44362156042d",
- "digest": {
- "sha256": "552db91328a881034f16ec50203ba34d4af448f52c616eb28db6c07aa575a286"
- }
- },
- {
- "@id": "urn:b2670328-db1e-4674-90cb-13fcc914f630",
+ "@id": "bids::prefiltered_func_data_tempfilt",
"Label": "prefiltered_func_data_tempfilt",
"AtLocation": "prefiltered_func_data_tempfilt",
+ "GeneratedBy": "urn:fslmaths-eZHX1jve",
"digest": {
"sha256": "a1836f4694e7ffdb50484626724602498c7b22b4f3cdd1e7d105efd336cbc8bd"
}
},
{
- "@id": "urn:afb4482f-41f7-48c4-8884-81f04334d619",
+ "@id": "bids::filtered_func_data",
"Label": "filtered_func_data",
"AtLocation": "filtered_func_data",
- "GeneratedBy": "urn:ee130f6b-a062-46b2-b51d-4a1e42d71915",
+ "GeneratedBy": "urn:fslmaths-KbrkJIBY",
"digest": {
"sha256": "2a1854e3b48a54f88e063191e25159015a0afbd300d18a1cfda37b4b68a1ee69"
}
},
{
- "@id": "urn:f53199d2-d78d-4610-ba41-c25c2fed43d4",
+ "@id": "bids::mean_func",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:4448454e-d15c-4499-8c25-12bb3e6fe805",
+ "GeneratedBy": "urn:fslmaths-TFy9OeDH",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:cfe72aec-bd1a-4ee1-a000-f14251902181",
+ "@id": "bids::prefiltered_func_data*",
"Label": "prefiltered_func_data*",
"AtLocation": "prefiltered_func_data*",
"digest": {
@@ -1246,130 +1252,180 @@
}
},
{
- "@id": "urn:09b2ca30-3c1a-4e49-9157-1698e71f13b0",
+ "@id": "bids::custom_timing_files",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:bd6c8246-39c9-4521-a578-2fbd75723ccf",
+ "GeneratedBy": "urn:makedire-CYU7q463",
"digest": {
"sha256": "1d7e19792328d5040f2f9fb3c15d59de90fc771785f81c67039a043bd5f2ed20"
}
},
{
- "@id": "urn:23a692d8-75aa-4033-a468-aa0e65da9c36",
+ "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
"Label": "sub-01_tone_counting.txt",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
+ "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
"digest": {
- "sha256": "c120d27b9d5d81a91be0e55f5cb880b2cb7de6c655554d9c15c9c04c6232ea8e"
+ "sha256": "165398224a205d2fc0b19354e15d9b085c6d81e333b69c4697b7894a2549be0b"
}
},
{
- "@id": "urn:d8cb9afd-8dc9-4f9a-8770-c49d73892b8b",
+ "@id": "bids::custom_timing_files/ev1.txt",
"Label": "ev1.txt",
"AtLocation": "custom_timing_files/ev1.txt",
- "GeneratedBy": "urn:7bcf3122-e120-44d2-8fb2-8e67537b56b3"
+ "GeneratedBy": "urn:fslfixte-dpO7fTvF"
},
{
- "@id": "urn:a5e6e3c8-5a2d-4230-b3ae-7d5cc1e7afb8",
+ "@id": "bids::custom_timing_files",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:aece4d2b-0460-4251-8c7f-126fce456814",
+ "GeneratedBy": "urn:makedire-LmNQcVed",
"digest": {
"sha256": "1d7e19792328d5040f2f9fb3c15d59de90fc771785f81c67039a043bd5f2ed20"
}
},
{
- "@id": "urn:4b9261b5-0c66-406d-b2ae-216ddb667897",
+ "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
"Label": "sub-01_tone_counting_probe.txt",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
+ "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
"digest": {
- "sha256": "f09eeb82fa0be8e8759a5269403f36ec2b7dbf2c5b6caba1f0f985cc6cb3f703"
+ "sha256": "8b912293767f1a5e082311f6aaf0c44fc91fe45b0f2ae7f80e368bc2f4c2918a"
}
},
{
- "@id": "urn:754ec45e-6b37-49ed-8902-ae1b5b9610bd",
+ "@id": "bids::custom_timing_files/ev2.txt",
"Label": "ev2.txt",
"AtLocation": "custom_timing_files/ev2.txt",
- "GeneratedBy": "urn:ccb973ca-2141-47aa-a525-6ea2a3e49c50"
+ "GeneratedBy": "urn:fslfixte-Ru3257Bq"
},
{
- "@id": "urn:8c6633c0-1445-454f-9af8-3f73d297d9d1",
- "Label": "res4d",
- "AtLocation": "stats/res4d",
+ "@id": "bids::stats",
+ "Label": "stats",
+ "AtLocation": "stats",
"digest": {
- "sha256": "8845286f36caedf891a02afddc4175ea46f18f830b59a8c5026962184a530699"
+ "sha256": "a9f3e135372514a16d11a8038262b3eff94ccd69a9b35c4724b2759cfc944a07"
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},
{
- "@id": "urn:a3198397-f5bd-445e-9b58-1981dd0a6dba",
- "Label": "smoothness",
- "AtLocation": "stats/smoothness",
- "GeneratedBy": "urn:7e3a9ab1-40eb-4692-b0a6-da89e21fe018",
+ "@id": "bids::design.mat",
+ "Label": "design.mat",
+ "AtLocation": "design.mat",
"digest": {
- "sha256": "67b0aaf95a257beff60d331b56265034807ca51e67e2d312d481d5835ef0b1d0"
+ "sha256": "1c1a6ef59a355e1f6f81e741e157784ccbe066ba3594a07aa9b16781e3d5bb25"
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},
{
- "@id": "urn:a0665740-7578-4953-a5d8-2febc139b4c8",
- "Label": "zstat1",
- "AtLocation": "stats/zstat1",
+ "@id": "bids::design.con",
+ "Label": "design.con",
+ "AtLocation": "design.con",
+ "digest": {
+ "sha256": "5808d1be37dd8f2a4906b710bb384fbee62faa4a46b2bc6847afc8962ed4eb54"
+ }
+ },
+ {
+ "@id": "bids::design.fts",
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+ "AtLocation": "design.fts",
+ "digest": {
+ "sha256": "02a711eee20a847faffeeb6f54318dca6c1508e74c4de8a3016cec0a070ddb77"
+ }
+ },
+ {
+ "@id": "bids::stats",
+ "Label": "stats",
+ "AtLocation": "stats",
+ "GeneratedBy": "urn:filmgls-sDjcg2z9",
"digest": {
- "sha256": "70ae47cee1ea1d3f1f6f8aa7ac51f2641cb2fcb745dfd8cc54a389346e6fa094"
+ "sha256": "a9f3e135372514a16d11a8038262b3eff94ccd69a9b35c4724b2759cfc944a07"
}
},
{
- "@id": "urn:a9b86e5d-509c-4128-917c-3441d311007a",
+ "@id": "bids::stats/res4d",
+ "Label": "res4d",
+ "AtLocation": "stats/res4d"
+ },
+ {
+ "@id": "bids::stats/smoothness",
+ "Label": "smoothness",
+ "AtLocation": "stats/smoothness",
+ "GeneratedBy": "urn:smoothes-xNwolFhT"
+ },
+ {
+ "@id": "bids::stats/zstat1",
+ "Label": "zstat1",
+ "AtLocation": "stats/zstat1"
+ },
+ {
+ "@id": "bids::thresh_zstat1",
"Label": "thresh_zstat1",
"AtLocation": "thresh_zstat1",
- "GeneratedBy": "urn:bab2ae80-8942-4f06-84a4-3a82ba65b210",
+ "GeneratedBy": "urn:fslmaths-C7DZCLIJ",
"digest": {
"sha256": "662e7ba670e124d15bb3cc18b818868f76604578034b524c8882f35fc5db413f"
}
},
{
- "@id": "urn:02011602-f54d-43a7-b7d5-05df253f6435",
+ "@id": "bids::stats/zfstat1",
"Label": "zfstat1",
- "AtLocation": "stats/zfstat1",
- "digest": {
- "sha256": "7411c38cb93415865a53b21dc0427506ed7994230aca73062e72251f77549cb9"
- }
+ "AtLocation": "stats/zfstat1"
},
{
- "@id": "urn:7d205378-c584-45cd-a840-ce5eb3edceba",
+ "@id": "bids::thresh_zfstat1",
"Label": "thresh_zfstat1",
"AtLocation": "thresh_zfstat1",
- "GeneratedBy": "urn:cb9ad31a-ff52-4fc0-9e45-c50f04ad7dd1",
+ "GeneratedBy": "urn:fslmaths-O3riA05d",
"digest": {
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}
},
{
- "@id": "urn:fc3626b4-6d2f-4cba-a554-f53bee1bd2f4",
+ "@id": "bids::stats/cope1",
"Label": "cope1",
- "AtLocation": "stats/cope1",
- "digest": {
- "sha256": "bf3b603569da6dbe3d6f0e8667d346f3ac943c9d01d2fc9743ce17abeb1547fb"
- }
+ "AtLocation": "stats/cope1"
},
{
- "@id": "urn:e6ac643a-e587-4706-8235-e0d9c5bd1350",
+ "@id": "bids::cluster_mask_zstat1",
"Label": "cluster_mask_zstat1",
"AtLocation": "cluster_mask_zstat1",
- "GeneratedBy": "urn:55e6b3e5-a805-4eab-b31f-f66baccf0633",
+ "GeneratedBy": "urn:cluster-q85r87w0",
"digest": {
"sha256": "b28c170e33d2917cac55183786616a9e976e5e7f30dc7c8666341f12ed6d0277"
}
},
{
- "@id": "urn:dec7cd8d-b963-4546-b3e6-5a63b61ef300",
+ "@id": "bids::thresh_zstat1",
+ "Label": "thresh_zstat1",
+ "AtLocation": "thresh_zstat1",
+ "GeneratedBy": "urn:cluster-q85r87w0",
+ "digest": {
+ "sha256": "662e7ba670e124d15bb3cc18b818868f76604578034b524c8882f35fc5db413f"
+ }
+ },
+ {
+ "@id": "bids::lmax_zstat1.txt",
+ "Label": "lmax_zstat1.txt",
+ "AtLocation": "lmax_zstat1.txt",
+ "GeneratedBy": "urn:cluster-q85r87w0",
+ "digest": {
+ "sha256": "d44ee21719775397a1a95ede6778d25404b50e8bd259dbdf02d2fde635fc81a5"
+ }
+ },
+ {
+ "@id": "bids::stats/cope1",
"Label": "cope1",
"AtLocation": "stats/cope1",
- "GeneratedBy": "urn:55e6b3e5-a805-4eab-b31f-f66baccf0633",
+ "GeneratedBy": "urn:cluster-q85r87w0"
+ },
+ {
+ "@id": "bids::cluster_zstat1.txt",
+ "Label": "cluster_zstat1.txt",
+ "AtLocation": "cluster_zstat1.txt",
+ "GeneratedBy": "urn:cluster-q85r87w0",
"digest": {
- "sha256": "bf3b603569da6dbe3d6f0e8667d346f3ac943c9d01d2fc9743ce17abeb1547fb"
+ "sha256": "b06695ff4f0a8158fa439b1ddf224b58d344606d400885c177390d09506e8e4c"
}
},
{
- "@id": "urn:487a68cf-1b53-49f7-9891-e4ba3dd75314",
+ "@id": "bids::cluster_zstat1",
"Label": "cluster_zstat1",
"AtLocation": "cluster_zstat1",
"digest": {
@@ -1377,16 +1433,43 @@
}
},
{
- "@id": "urn:b7a893d5-a985-4693-b6c6-2f732211170d",
+ "@id": "bids::cluster_mask_zfstat1",
"Label": "cluster_mask_zfstat1",
"AtLocation": "cluster_mask_zfstat1",
- "GeneratedBy": "urn:d2fd03b5-32f2-4d3f-9a7e-91a684205c9b",
+ "GeneratedBy": "urn:cluster-MRZWM656",
"digest": {
"sha256": "3523a5abe83ae8c76dd74f74632bc34163aac475152d48a6b79f37eca7dfe022"
}
},
{
- "@id": "urn:6b976ef1-34cd-4beb-b4df-4d827eb6e8c9",
+ "@id": "bids::thresh_zfstat1",
+ "Label": "thresh_zfstat1",
+ "AtLocation": "thresh_zfstat1",
+ "GeneratedBy": "urn:cluster-MRZWM656",
+ "digest": {
+ "sha256": "e4e927e247bdf8ff3b58b41cbb9db7643b27df1f7578c506950eb4b1ca2d0031"
+ }
+ },
+ {
+ "@id": "bids::lmax_zfstat1.txt",
+ "Label": "lmax_zfstat1.txt",
+ "AtLocation": "lmax_zfstat1.txt",
+ "GeneratedBy": "urn:cluster-MRZWM656",
+ "digest": {
+ "sha256": "f6140171309069ed9586f94b07f187a4bbea683c429dc6a5558047a484c5e8a1"
+ }
+ },
+ {
+ "@id": "bids::cluster_zfstat1.txt",
+ "Label": "cluster_zfstat1.txt",
+ "AtLocation": "cluster_zfstat1.txt",
+ "GeneratedBy": "urn:cluster-MRZWM656",
+ "digest": {
+ "sha256": "0b5d4fcb253267ddae2859bc1226696992a2f6db2dba10d35c80399bd51477d4"
+ }
+ },
+ {
+ "@id": "bids::cluster_zfstat1",
"Label": "cluster_zfstat1",
"AtLocation": "cluster_zfstat1",
"digest": {
@@ -1394,25 +1477,25 @@
}
},
{
- "@id": "urn:aee873fe-d817-466b-8d31-98fcb45222d3",
+ "@id": "bids::rendered_thresh_zstat1",
"Label": "rendered_thresh_zstat1",
"AtLocation": "rendered_thresh_zstat1",
- "GeneratedBy": "urn:8151d2f2-5ad5-434d-863a-7e01c98263b7",
+ "GeneratedBy": "urn:overlay-MzJgJACL",
"digest": {
"sha256": "de5b9d44d95f4252f491eb45c76a0ae2b4d2c75b58664fc0df7d9153810c0bf6"
}
},
{
- "@id": "urn:9dbd4acf-480e-4f44-9312-2ba368f1eefb",
+ "@id": "bids::rendered_thresh_zstat1.png",
"Label": "rendered_thresh_zstat1.png",
"AtLocation": "rendered_thresh_zstat1.png",
- "GeneratedBy": "urn:c8e777cc-a609-4c27-a92d-c46856ae9e17",
+ "GeneratedBy": "urn:slicer-3wFnCCy8",
"digest": {
"sha256": "15d6a8bf7a902df8c5feeb7468a3d0caacf9eb3067c0840c2f4763f5e2301527"
}
},
{
- "@id": "urn:3f6ebb09-33c2-450f-a017-1aba59644f2e",
+ "@id": "bids::/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif",
"Label": "ramp.gif",
"AtLocation": "/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif",
"digest": {
@@ -1420,46 +1503,46 @@
}
},
{
- "@id": "urn:f7f2f055-f692-42dd-b871-eb23b1fa7842",
+ "@id": "bids::.ramp.gif",
"Label": ".ramp.gif",
"AtLocation": ".ramp.gif",
- "GeneratedBy": "urn:32ca3d5b-761b-4903-b0a1-49daa50ee44d",
+ "GeneratedBy": "urn:cp-SPUZKjCU",
"digest": {
"sha256": "93f4284ccb854d5a41401d9360a13223017b67479cb289a33d83836922e028a4"
}
},
{
- "@id": "urn:caed8b19-3fe4-4bd7-b621-c3b31de3dcad",
+ "@id": "bids::rendered_thresh_zfstat1",
"Label": "rendered_thresh_zfstat1",
"AtLocation": "rendered_thresh_zfstat1",
- "GeneratedBy": "urn:2e5c9e5f-35b0-41e0-832d-b95799f3925a",
+ "GeneratedBy": "urn:overlay-4KIeCJr6",
"digest": {
"sha256": "91b064bdcf6f2eec9fb87c161e52152f3343ed4de0cf5e5ba6153f970250aa5f"
}
},
{
- "@id": "urn:19ca205d-a4a5-46a2-8920-bfedeae3ad91",
+ "@id": "bids::rendered_thresh_zfstat1.png",
"Label": "rendered_thresh_zfstat1.png",
"AtLocation": "rendered_thresh_zfstat1.png",
- "GeneratedBy": "urn:48605004-13de-4ff6-9ce3-a22c66dbfeef",
+ "GeneratedBy": "urn:slicer-WhXfy3dQ",
"digest": {
"sha256": "c4c15c63489169ecb9747342259541d6b999ff25baaedfa066ecd1c00b761067"
}
},
{
- "@id": "urn:b68a04ce-2150-411b-bc22-d4623ca669ae",
+ "@id": "bids::tsplot",
"Label": "tsplot",
"AtLocation": "tsplot",
- "GeneratedBy": "urn:3c1247bf-e04f-4b91-a57a-1960d43804e2",
+ "GeneratedBy": "urn:makedire-Rbuz4y5j",
"digest": {
"sha256": "2a74042f4edf02288edf16961307f741651efb4346e102a04b7603e781d1625e"
}
},
{
- "@id": "urn:153fa781-92e7-4922-ad3d-98ee7ca75991",
+ "@id": "bids::tsplot",
"Label": "tsplot",
"AtLocation": "tsplot",
- "GeneratedBy": "urn:be636df1-e671-4fc0-b305-d3a0366578bf",
+ "GeneratedBy": "urn:tsplot-ex5pJZVe",
"digest": {
"sha256": "2a74042f4edf02288edf16961307f741651efb4346e102a04b7603e781d1625e"
}
diff --git a/examples/from_parsers/fsl/fsl_con_f_report_log.png b/examples/from_parsers/fsl/fsl_con_f_report_log.png
index 516bbab0b..aa30bfd99 100644
Binary files a/examples/from_parsers/fsl/fsl_con_f_report_log.png and b/examples/from_parsers/fsl/fsl_con_f_report_log.png differ
diff --git a/examples/from_parsers/fsl/fsl_contrast_mask_report_log.html b/examples/from_parsers/fsl/fsl_contrast_mask_report_log.html
index 18017d462..0c14551ab 100644
--- a/examples/from_parsers/fsl/fsl_contrast_mask_report_log.html
+++ b/examples/from_parsers/fsl/fsl_contrast_mask_report_log.html
@@ -35,20 +35,20 @@ Progress Report / Log
326900
Initialisation
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
Total original volumes = 104
/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1
Preprocessing:Stage 1
-/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90
+/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/example_func.nii.gz -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90
Option -F ( FEAT version parameter ) selected with argument "6.00"
Option -d ( output directory ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat"
Option -l ( logfile )input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/logs/feat2_pre"
Option -R ( html unwarping report ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/report_unwarp.html"
Option -r ( html registration report ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/report_reg.html"
Option -i ( main input ) input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/example_func.nii.gz"
-Option -h ( high-res structural image ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
+Option -h ( high-res structural image ) selected with argument "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
Option -w ( highres dof ) selected with argument "BBR"
Option -x ( highres search ) selected with argument "90"
Option -s ( standard image ) selected with argument "/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain"
@@ -59,10 +59,10 @@ Progress Report / Log
/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/reg
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head
did not find file: example_func2highres.mat. Generating transform.
@@ -128,9 +128,9 @@ Progress Report / Log
/bin/rm -rf prefiltered_func_data*
Stats
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
/usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con
Log directory is: stats
diff --git a/examples/from_parsers/fsl/fsl_contrast_mask_report_log.jsonld b/examples/from_parsers/fsl/fsl_contrast_mask_report_log.jsonld
index 2d2d71407..c0c031cbe 100644
--- a/examples/from_parsers/fsl/fsl_contrast_mask_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_contrast_mask_report_log.jsonld
@@ -4,723 +4,732 @@
"Records": {
"Software": [
{
- "@id": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:fsl-JIPD22pA",
"@type": "prov:SoftwareAgent",
"Label": "FSL",
- "Version": "xxx"
+ "Version": "xxx",
+ "AltIdentifier": "RRID:SCR_002823"
}
],
"Activities": [
{
- "@id": "urn:0d259108-198a-403f-b1d3-bba09529827d",
+ "@id": "urn:fslmaths-Xuyim67B",
"Label": "fslmaths",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
"Used": [
- "urn:d1308046-3332-4a11-9764-824e4f5a8e75"
+ "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold"
]
},
{
- "@id": "urn:2f679b50-65f1-46d1-9294-aba74a8d3c0c",
+ "@id": "urn:fslroi-3d5HkXKh",
"Label": "fslroi",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1",
"Used": [
- "urn:97d913aa-b73f-4d76-9c34-a50085ef0573"
+ "bids::prefiltered_func_data"
]
},
{
- "@id": "urn:60a4f73b-8332-4571-9dcf-91085ea56e3e",
+ "@id": "urn:mainfeat-uc29xqXi",
"Label": "mainfeatreg",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/example_func.nii.gz -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
"Used": [
- "urn:6025627a-83a3-456d-8132-1ccb33c06fd5",
- "urn:7821235c-3bfa-4236-abb0-1b9543708a70",
- "urn:c0fd6a9f-7767-48f7-87b4-28b648727fbc"
+ "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/example_func.nii.gz",
+ "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain",
+ "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
]
},
{
- "@id": "urn:10441440-f68c-4a5f-b183-f563d2e794c3",
+ "@id": "urn:makedire-HB3mMbwP",
"Label": "Make directory",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/reg",
"Used": []
},
{
- "@id": "urn:7d111d8e-f5f6-42f6-97de-0a3f8ffaebac",
+ "@id": "urn:fslmaths-YiN6wsRz",
"Label": "fslmaths",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
"Used": [
- "urn:7821235c-3bfa-4236-abb0-1b9543708a70"
+ "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
]
},
{
- "@id": "urn:223a4067-5f9c-4c22-88f3-a4a2c47ed665",
+ "@id": "urn:fslmaths-YCDMAWXA",
"Label": "fslmaths",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
"Used": [
- "urn:3f4994fb-b29d-46be-80da-ba384b45215f"
+ "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w"
]
},
{
- "@id": "urn:5d191212-57cc-456b-85cd-85783c7fe6b9",
+ "@id": "urn:epireg-JxbV7pkT",
"Label": "epi_reg",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres",
- "Used": []
+ "Used": [
+ "bids::example_func",
+ "bids::highres",
+ "bids::highres_head"
+ ]
},
{
- "@id": "urn:f23d9404-3d29-4aac-88c7-b9e3faa48487",
+ "@id": "urn:convertx-BjiVbzit",
"Label": "convert_xfm",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat",
"Used": [
- "urn:056d59d8-964b-4d0f-bb91-9a8707d359dc"
+ "bids::example_func2highres.mat"
]
},
{
- "@id": "urn:959a07c6-ac7e-4701-968c-9b5af5c5ed5a",
+ "@id": "urn:slicer-bEbtJCop",
"Label": "slicer",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:045b5f7d-291b-4fa3-9c79-73625dc7cf0c",
- "urn:0c49fdd7-6558-49b0-82a6-00e2cc8ef411"
+ "bids::example_func2highres",
+ "bids::highres"
]
},
{
- "@id": "urn:f6a7d888-b32e-41fd-986d-4a7ced3524ee",
+ "@id": "urn:pngappen-m18AYAi4",
"Label": "pngappend",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres1.png",
"Used": [
- "urn:0349cc92-fbb2-4fe8-9be3-c1fe0458e549",
- "urn:03dd0219-7bd8-48db-a3c8-226e556c956e",
- "urn:3a9caa74-65f8-4212-8dfb-9f6105f65c2c",
- "urn:61b64622-dc1f-468f-8581-bdb63b72173d",
- "urn:65b903a1-5eeb-488d-b160-9bbf997f6387",
- "urn:6c62078a-2203-4119-9ef8-6f736b6b4888",
- "urn:827ed196-545b-4a41-ba1b-fbb5e32fad7d",
- "urn:89482764-88d8-4c62-a56d-1411b5ccfdee",
- "urn:9447a47e-334a-4e72-9711-9ea32ad4d8da",
- "urn:eb9db1b8-6977-4048-9ed9-2874cb7976f6",
- "urn:f1f79801-0474-444d-9932-f7e5d0d51daf",
- "urn:f6e491b8-c07b-4a3f-87c8-7454d74ed5f7"
+ "bids::sla.png",
+ "bids::slb.png",
+ "bids::slc.png",
+ "bids::sld.png",
+ "bids::sle.png",
+ "bids::slf.png",
+ "bids::slg.png",
+ "bids::slh.png",
+ "bids::sli.png",
+ "bids::slj.png",
+ "bids::slk.png",
+ "bids::sll.png"
]
},
{
- "@id": "urn:124643ff-622e-404b-84b0-7cad78f62a3b",
+ "@id": "urn:slicer-XbZXqIgv",
"Label": "slicer",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:045b5f7d-291b-4fa3-9c79-73625dc7cf0c",
- "urn:0c49fdd7-6558-49b0-82a6-00e2cc8ef411"
+ "bids::example_func2highres",
+ "bids::highres"
]
},
{
- "@id": "urn:0d1cb971-95db-4b51-b754-8ce32ce31cfd",
+ "@id": "urn:pngappen-epl9TLVc",
"Label": "pngappend",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres2.png",
"Used": [
- "urn:0349cc92-fbb2-4fe8-9be3-c1fe0458e549",
- "urn:03dd0219-7bd8-48db-a3c8-226e556c956e",
- "urn:3a9caa74-65f8-4212-8dfb-9f6105f65c2c",
- "urn:61b64622-dc1f-468f-8581-bdb63b72173d",
- "urn:65b903a1-5eeb-488d-b160-9bbf997f6387",
- "urn:6c62078a-2203-4119-9ef8-6f736b6b4888",
- "urn:827ed196-545b-4a41-ba1b-fbb5e32fad7d",
- "urn:89482764-88d8-4c62-a56d-1411b5ccfdee",
- "urn:9447a47e-334a-4e72-9711-9ea32ad4d8da",
- "urn:eb9db1b8-6977-4048-9ed9-2874cb7976f6",
- "urn:f1f79801-0474-444d-9932-f7e5d0d51daf",
- "urn:f6e491b8-c07b-4a3f-87c8-7454d74ed5f7"
+ "bids::sla.png",
+ "bids::slb.png",
+ "bids::slc.png",
+ "bids::sld.png",
+ "bids::sle.png",
+ "bids::slf.png",
+ "bids::slg.png",
+ "bids::slh.png",
+ "bids::sli.png",
+ "bids::slj.png",
+ "bids::slk.png",
+ "bids::sll.png"
]
},
{
- "@id": "urn:8b776a89-917e-4216-94da-cadb9a07b265",
+ "@id": "urn:pngappen-10ldR3vU",
"Label": "pngappend",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend example_func2highres1.png example_func2highres2.png example_func2highres.png",
"Used": [
- "urn:26e3d878-ff09-4d57-83a2-45bf6fe593cc",
- "urn:50ead67b-b66d-47dc-8aee-be571fc00c19"
+ "bids::example_func2highres1.png",
+ "bids::example_func2highres2.png"
]
},
{
- "@id": "urn:21ce6ea2-0d8f-4eaa-be21-880b62c9ab38",
+ "@id": "urn:rm-wWRksZcv",
"Label": "rm",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/bin/rm -f sl?.png example_func2highres2.png",
"Used": [
- "urn:50ead67b-b66d-47dc-8aee-be571fc00c19",
- "urn:f8b05ae4-a7fd-46b4-ac40-1481adeda215"
+ "bids::example_func2highres2.png",
+ "bids::sl?.png"
]
},
{
- "@id": "urn:c97ff4a4-ddf7-4077-9c60-e2181964bcf3",
+ "@id": "urn:rm-sJLZbIki",
"Label": "rm",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/bin/rm example_func2highres1.png",
"Used": [
- "urn:26e3d878-ff09-4d57-83a2-45bf6fe593cc"
+ "bids::example_func2highres1.png"
]
},
{
- "@id": "urn:c79e05de-7c3b-4e36-8f80-4812d920289a",
+ "@id": "urn:mcflirt-yfIrHolT",
"Label": "mcflirt",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs -spline_final",
"Used": [
- "urn:97d913aa-b73f-4d76-9c34-a50085ef0573"
+ "bids::prefiltered_func_data"
]
},
{
- "@id": "urn:639b42b5-1531-4197-b8b3-f73a720c0784",
+ "@id": "urn:makedire-8o9UTCSS",
"Label": "Make directory",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/bin/mkdir -p mc",
"Used": []
},
{
- "@id": "urn:f89527ff-6fb9-4848-b83b-87187c2e9d94",
+ "@id": "urn:mv-563E2MPP",
"Label": "mv",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc",
"Used": [
- "urn:0311f37c-f2a7-47a1-a6e1-737b040a0e6a",
- "urn:2100f2d2-fa6a-4e97-9fa9-c324da777313",
- "urn:232b639e-d198-4461-82dd-6b5b7ca29858",
- "urn:31341309-06dc-46cd-9c02-fa385ae1eec9",
- "urn:684f7ba6-b516-4db0-93e6-b786d6415f9d",
- "urn:b86e41c0-61e4-4d07-93a0-f9e89005b630"
+ "bids::prefiltered_func_data_mcf.mat",
+ "bids::prefiltered_func_data_mcf.par",
+ "bids::prefiltered_func_data_mcf_abs.rms",
+ "bids::prefiltered_func_data_mcf_abs_mean.rms",
+ "bids::prefiltered_func_data_mcf_rel.rms",
+ "bids::prefiltered_func_data_mcf_rel_mean.rms"
]
},
{
- "@id": "urn:25b87dfc-baa6-4412-be96-835e2fe3ac8c",
+ "@id": "urn:fsltsplo-fxUJXTgT",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png",
"Used": [
- "urn:232b639e-d198-4461-82dd-6b5b7ca29858"
+ "bids::prefiltered_func_data_mcf.par"
]
},
{
- "@id": "urn:a6fa4bdd-b3f6-41fd-a285-b7f9d200b503",
+ "@id": "urn:fsltsplo-UxjDo0NZ",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png",
"Used": [
- "urn:232b639e-d198-4461-82dd-6b5b7ca29858"
+ "bids::prefiltered_func_data_mcf.par"
]
},
{
- "@id": "urn:45cc2b39-a6fc-4f39-a6fe-09a7aad4c016",
+ "@id": "urn:fsltsplo-mRcnuaAd",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png",
"Used": [
- "urn:430aa6bb-c922-45b6-b4c0-41c23d4ae499"
+ "bids::prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms"
]
},
{
- "@id": "urn:ee82e800-0280-4a09-b8c4-0a2a14dcc69c",
+ "@id": "urn:fslmaths-SKesHBPT",
"Label": "fslmaths",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func",
"Used": [
- "urn:f1f9de70-1d2c-44c4-8ef9-59d0c9a7f575"
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:5582b83e-b803-4011-9d05-9221fe1af3cc",
+ "@id": "urn:bet2-z8jTqNMY",
"Label": "bet2",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/bet2 mean_func mask -f 0.3 -n -m",
"Used": [
- "urn:14707e2a-ffce-4246-a25e-d714c32d5d8e"
+ "bids::mean_func"
]
},
{
- "@id": "urn:abbbef99-660a-46ab-b917-207de09017a4",
+ "@id": "urn:immv-2Aycx2Pp",
"Label": "immv",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/immv mask_mask mask",
"Used": [
- "urn:493a1ce5-093b-4e18-9438-ddcd75cb57c4"
+ "bids::mask_mask"
]
},
{
- "@id": "urn:2cfcc313-2bea-437e-bf9d-6527d3f0031b",
+ "@id": "urn:fslmaths-WLFMXeqd",
"Label": "fslmaths",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet",
"Used": [
- "urn:5a293a71-dd01-4b34-9f1f-4c1ba7891935",
- "urn:f1f9de70-1d2c-44c4-8ef9-59d0c9a7f575"
+ "bids::mask",
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:d0a9229a-d145-4388-8b89-496b9a9266d8",
+ "@id": "urn:fslstats-Sxs64kSH",
"Label": "fslstats",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_bet -p 2 -p 98",
"Used": [
- "urn:e754d79a-e6e3-4c4f-bbfb-a62a217b6c42"
+ "bids::prefiltered_func_data_bet"
]
},
{
- "@id": "urn:7fa64d13-6d3d-43f7-aa1f-f869c24716ee",
+ "@id": "urn:fslmaths-eHWA2R63",
"Label": "fslmaths",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_bet -thr 74.4585571 -Tmin -bin mask -odt char",
"Used": [
- "urn:e754d79a-e6e3-4c4f-bbfb-a62a217b6c42"
+ "bids::prefiltered_func_data_bet"
]
},
{
- "@id": "urn:710997cd-11a2-4320-9c4a-056dac485b20",
+ "@id": "urn:fslstats-Nute5Xvq",
"Label": "fslstats",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_mcf -k mask -p 50",
"Used": [
- "urn:f1f9de70-1d2c-44c4-8ef9-59d0c9a7f575"
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:f269a3d8-4740-47ae-a43d-bbac404ea0a9",
+ "@id": "urn:fslmaths-pyfyjzeh",
"Label": "fslmaths",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -dilF mask",
"Used": [
- "urn:5a293a71-dd01-4b34-9f1f-4c1ba7891935"
+ "bids::mask"
]
},
{
- "@id": "urn:926975f6-7027-49ca-9ee7-dddc5a6ae44f",
+ "@id": "urn:fslmaths-uF6O4TLB",
"Label": "fslmaths",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh",
"Used": [
- "urn:5a293a71-dd01-4b34-9f1f-4c1ba7891935",
- "urn:f1f9de70-1d2c-44c4-8ef9-59d0c9a7f575"
+ "bids::mask",
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:d066b14b-96f0-4d46-80c0-11d5d99d23f4",
+ "@id": "urn:fslmaths-W7rvUch0",
"Label": "fslmaths",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func",
"Used": [
- "urn:58153dd9-1796-4d62-8438-89bb2ba3464b"
+ "bids::prefiltered_func_data_thresh"
]
},
{
- "@id": "urn:b60656a1-c732-49cd-8d5b-91fcbe73fe6c",
+ "@id": "urn:susan-bgDTUD0R",
"Label": "susan",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/susan prefiltered_func_data_thresh 445.8289035 2.54777070064 3 1 1 mean_func 445.8289035 prefiltered_func_data_smooth",
"Used": [
- "urn:58153dd9-1796-4d62-8438-89bb2ba3464b"
+ "bids::prefiltered_func_data_thresh"
]
},
{
- "@id": "urn:aca19fbd-0414-496a-8e00-ef764f356192",
+ "@id": "urn:fslmaths-BZVuhqW9",
"Label": "fslmaths",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth",
"Used": [
- "urn:5a293a71-dd01-4b34-9f1f-4c1ba7891935",
- "urn:7a9b565b-7038-4a86-b762-6b83937ae1b1"
+ "bids::mask",
+ "bids::prefiltered_func_data_smooth"
]
},
{
- "@id": "urn:f6c58562-64eb-4875-b481-83d9e0a584b8",
+ "@id": "urn:fslmaths-5gSV2JIW",
"Label": "fslmaths",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mul 16.8225970571 prefiltered_func_data_intnorm",
"Used": [
- "urn:7a9b565b-7038-4a86-b762-6b83937ae1b1"
+ "bids::prefiltered_func_data_smooth"
]
},
{
- "@id": "urn:48fe3b0d-bdc4-4e54-b3fd-f7776047617b",
+ "@id": "urn:fslmaths-of0s39J8",
"Label": "fslmaths",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean",
"Used": [
- "urn:ab849afd-a79f-4ad0-87a2-d2655ba48ea4"
+ "bids::prefiltered_func_data_intnorm"
]
},
{
- "@id": "urn:0e73fabf-9e09-4b08-a8b7-b3db9968479e",
+ "@id": "urn:fslmaths-0Yxn67qj",
"Label": "fslmaths",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -bptf 15.0 -1 -add tempMean prefiltered_func_data_tempfilt",
"Used": [
- "urn:0b85a8dd-c5fa-4f84-bd05-454b4d43f12c",
- "urn:ab849afd-a79f-4ad0-87a2-d2655ba48ea4"
+ "bids::prefiltered_func_data_intnorm",
+ "bids::tempMean"
]
},
{
- "@id": "urn:f1d5be76-d997-4d40-bb01-f7503c81c6f1",
+ "@id": "urn:imrm-ZIinjJYn",
"Label": "imrm",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/imrm tempMean",
"Used": [
- "urn:0b85a8dd-c5fa-4f84-bd05-454b4d43f12c"
+ "bids::tempMean"
]
},
{
- "@id": "urn:d7052af7-241a-44ce-99ce-8a5b42550975",
+ "@id": "urn:fslmaths-zQn78yon",
"Label": "fslmaths",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data",
"Used": [
- "urn:770417db-0b49-4407-baa9-5a149a92cbeb"
+ "bids::prefiltered_func_data_tempfilt"
]
},
{
- "@id": "urn:151c4564-2b06-42e4-805f-a53e7471f4a6",
+ "@id": "urn:fslmaths-AoENJ4vu",
"Label": "fslmaths",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths filtered_func_data -Tmean mean_func",
"Used": [
- "urn:efba00c8-2a39-48f4-940b-565cc201efb5"
+ "bids::filtered_func_data"
]
},
{
- "@id": "urn:641a67fa-1634-4f9c-b6ee-d1f21bebe649",
+ "@id": "urn:rm-F8kdvqWr",
"Label": "rm",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/bin/rm -rf prefiltered_func_data*",
"Used": [
- "urn:5ad7a5b7-40a3-4380-acf7-c1ab546a53bd"
+ "bids::prefiltered_func_data*"
]
},
{
- "@id": "urn:0b206421-73e5-4bf5-8789-644ea60eaf35",
+ "@id": "urn:makedire-BNU0v0w6",
"Label": "Make directory",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
- "@id": "urn:444e272d-4747-44c5-9303-f886994a0c7d",
+ "@id": "urn:fslfixte-gPWYR3x8",
"Label": "fslFixText",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
"Used": [
- "urn:d03f734d-f6ba-498d-8149-97a8b8a95585"
+ "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt"
]
},
{
- "@id": "urn:78fb79a4-45b9-4060-869a-dc0b08c9f54c",
+ "@id": "urn:makedire-fqvNCFv9",
"Label": "Make directory",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
- "@id": "urn:e84f94ca-11f1-4b1b-8371-0ab06012a4e7",
+ "@id": "urn:fslfixte-6BH43olN",
"Label": "fslFixText",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
"Used": [
- "urn:fee67aaa-0c67-496a-8d33-670b4d2ae6b8"
+ "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt"
]
},
{
- "@id": "urn:5a9b6daa-84ee-4db2-b58a-ad7d4f4d568c",
+ "@id": "urn:filmgls-hnXGCyIa",
"Label": "film_gls",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con",
- "Used": []
+ "Used": [
+ "bids::design.con",
+ "bids::design.mat",
+ "bids::filtered_func_data",
+ "bids::stats"
+ ]
},
{
- "@id": "urn:798246d9-8c8f-4fcc-8e7b-ae1753dd7cbd",
+ "@id": "urn:smoothes-HqoKWOFV",
"Label": "smoothest",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 102 -m mask -r stats/res4d > stats/smoothness",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 102 -m mask -r stats/res4d > stats/smoothness",
"Used": [
- "urn:5a293a71-dd01-4b34-9f1f-4c1ba7891935",
- "urn:e4db7414-e073-47db-9e40-61194372f726"
+ "bids::mask",
+ "bids::stats/res4d"
]
},
{
- "@id": "urn:4c04841c-f3d0-445c-a066-028babe31e33",
+ "@id": "urn:fslmaths-BRCsyWxk",
"Label": "fslmaths",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1",
"Used": [
- "urn:2dbe13bd-50d1-4dd5-862a-81490d6be7b1",
- "urn:5a293a71-dd01-4b34-9f1f-4c1ba7891935"
+ "bids::mask",
+ "bids::stats/zstat1"
]
},
{
- "@id": "urn:da7df978-8511-4e8c-82bb-0453bfa8cf21",
+ "@id": "urn:echo-yV2rC6mn",
"Label": "echo",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "echo 38352 > thresh_zstat1.vol",
"Used": []
},
{
- "@id": "urn:3138a4a5-eed0-4499-9bf3-458190b4bca6",
+ "@id": "urn:fslmaths-5zja6ybF",
"Label": "fslmaths",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat2 -mas mask thresh_zstat2",
"Used": [
- "urn:02e35e36-1794-41be-83d8-3fdc4b2d3731",
- "urn:5a293a71-dd01-4b34-9f1f-4c1ba7891935"
+ "bids::mask",
+ "bids::stats/zstat2"
]
},
{
- "@id": "urn:a3042f5e-5d72-4015-97c0-e5b43d94a6b9",
+ "@id": "urn:echo-I9XfYCFO",
"Label": "echo",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "echo 38352 > thresh_zstat2.vol",
"Used": []
},
{
- "@id": "urn:3475f16e-a857-4c43-9775-51dc7649402d",
+ "@id": "urn:ptoz-gSLlUd7H",
"Label": "ptoz",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:e960ebac-d05a-4cf4-9343-37287329f1f5",
+ "@id": "urn:cluster-KIgiCoyq",
"Label": "cluster",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -t 3.090232 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z --voxuncthresh -c stats/cope1 > cluster_zstat1.txt",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -t 3.090232 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z --voxuncthresh -c stats/cope1 > cluster_zstat1.txt",
"Used": [
- "urn:0a49a6e7-bc51-4b1b-94aa-c7a709053518",
- "urn:c89142a2-cb00-4e74-a5fe-c88971d7120e"
+ "bids::stats/cope1",
+ "bids::thresh_zstat1"
]
},
{
- "@id": "urn:eff460af-b89a-4118-964b-439f86162e8e",
+ "@id": "urn:cluster2-mHF7PeTK",
"Label": "cluster2html",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat1",
"Used": [
- "urn:316e32ea-3f08-47e1-9e28-5e94e420c1d1"
+ "bids::cluster_zstat1"
]
},
{
- "@id": "urn:64912b9e-1cf0-436d-8547-23ba6dc6224c",
+ "@id": "urn:ptoz-EzAWsACC",
"Label": "ptoz",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:38bbfab4-7b95-45e4-9ba4-525c395261f2",
+ "@id": "urn:cluster-MRFJ9REm",
"Label": "cluster",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat2 -t 3.090232 --othresh=thresh_zstat2 -o cluster_mask_zstat2 --connectivity=26 --olmax=lmax_zstat2.txt --scalarname=Z --voxuncthresh -c stats/cope2 > cluster_zstat2.txt",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat2 -t 3.090232 --othresh=thresh_zstat2 -o cluster_mask_zstat2 --connectivity=26 --olmax=lmax_zstat2.txt --scalarname=Z --voxuncthresh -c stats/cope2 > cluster_zstat2.txt",
"Used": [
- "urn:a4d007e1-5feb-48dd-9610-1eed703cff19",
- "urn:ad8c2146-4bbe-408a-a107-9d9ba36aa1ec"
+ "bids::stats/cope2",
+ "bids::thresh_zstat2"
]
},
{
- "@id": "urn:575fd253-32e1-43da-9c0a-0055fe577fd1",
+ "@id": "urn:cluster2-fL0yiugD",
"Label": "cluster2html",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat2",
"Used": [
- "urn:4c25fcf4-4122-4b47-9726-3209f7f4367e"
+ "bids::cluster_zstat2"
]
},
{
- "@id": "urn:7bb7e554-8502-404a-8243-e149af1372ef",
+ "@id": "urn:makedire-7qR7aS7n",
"Label": "Make directory",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "mkdir -p conmask",
"Used": []
},
{
- "@id": "urn:12b6efb2-c7ca-4ebf-8624-3a3975555f75",
+ "@id": "urn:fslmaths-l6gT6VDx",
"Label": "fslmaths",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths thresh_zstat1 -mas thresh_zstat2 conmask/thresh_zstat1",
"Used": [
- "urn:0a49a6e7-bc51-4b1b-94aa-c7a709053518",
- "urn:ad8c2146-4bbe-408a-a107-9d9ba36aa1ec"
+ "bids::thresh_zstat1",
+ "bids::thresh_zstat2"
]
},
{
- "@id": "urn:10fcf5d7-a537-4730-bc72-bf8ef9f51d4c",
+ "@id": "urn:mv-cM6i4hre",
"Label": "mv",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/bin/mv -f conmask/* .",
"Used": [
- "urn:11270f30-6cd9-40e4-ae09-0ce252d2c167"
+ "bids::conmask/*"
]
},
{
- "@id": "urn:14750bd8-418c-4693-a721-60f2611ced60",
+ "@id": "urn:rmdir-MvjZDLjS",
"Label": "rmdir",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "rmdir conmask",
"Used": [
- "urn:4ae6b32f-e8fd-4b05-aec2-42ede6e29f8d"
+ "bids::conmask"
]
},
{
- "@id": "urn:36b54ead-04d7-4cb4-9ea0-a5de7228bf94",
+ "@id": "urn:ptoz-jEOVCEWD",
"Label": "ptoz",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:ef7f41f7-4571-4fa9-87af-5ba336c823d3",
+ "@id": "urn:cluster-KSF2yOj5",
"Label": "cluster",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -c stats/cope1 -t 3.090232 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z > cluster_zstat1.txt",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -c stats/cope1 -t 3.090232 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z > cluster_zstat1.txt",
"Used": [
- "urn:0a49a6e7-bc51-4b1b-94aa-c7a709053518",
- "urn:c89142a2-cb00-4e74-a5fe-c88971d7120e"
+ "bids::stats/cope1",
+ "bids::thresh_zstat1"
]
},
{
- "@id": "urn:421c49d8-7ce1-4fa8-89f0-1505da961f79",
+ "@id": "urn:cluster2-6ftEMoV3",
"Label": "cluster2html",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat1",
"Used": [
- "urn:316e32ea-3f08-47e1-9e28-5e94e420c1d1"
+ "bids::cluster_zstat1"
]
},
{
- "@id": "urn:b0786995-aa20-4cc1-ba11-56821df58c7e",
+ "@id": "urn:cluster-9sTEgQIH",
"Label": "cluster",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat2 -c stats/cope2 -t 3.090232 --othresh=thresh_zstat2 -o cluster_mask_zstat2 --connectivity=26 --olmax=lmax_zstat2.txt --scalarname=Z > cluster_zstat2.txt",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat2 -c stats/cope2 -t 3.090232 --othresh=thresh_zstat2 -o cluster_mask_zstat2 --connectivity=26 --olmax=lmax_zstat2.txt --scalarname=Z > cluster_zstat2.txt",
"Used": [
- "urn:a4d007e1-5feb-48dd-9610-1eed703cff19",
- "urn:ad8c2146-4bbe-408a-a107-9d9ba36aa1ec"
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+ "bids::thresh_zstat2"
]
},
{
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"Label": "cluster2html",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
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"Used": [
- "urn:4c25fcf4-4122-4b47-9726-3209f7f4367e"
+ "bids::cluster_zstat2"
]
},
{
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"Label": "fslstats",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
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+ "bids::thresh_zstat1"
]
},
{
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"Label": "fslstats",
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+ "AssociatedWith": "urn:fsl-JIPD22pA",
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"Used": [
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+ "bids::thresh_zstat2"
]
},
{
- "@id": "urn:73df9179-e121-4c94-96c2-38bfe982ce72",
+ "@id": "urn:overlay-N8rFrcHs",
"Label": "overlay",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
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"Used": []
},
{
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+ "@id": "urn:slicer-yKHiTJ8J",
"Label": "slicer",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat1 -A 750 rendered_thresh_zstat1.png",
"Used": [
- "urn:b173fa0a-f3c8-498e-a012-a3414336895e"
+ "bids::rendered_thresh_zstat1"
]
},
{
- "@id": "urn:6552ba36-0e4e-49ce-9503-1172a5ba4ac6",
+ "@id": "urn:cp-NwMvSfas",
"Label": "cp",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/bin/cp /usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif .ramp.gif",
"Used": [
- "urn:95b72fdb-64f4-42c3-ab59-c9671b5d34d3"
+ "bids::/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif"
]
},
{
- "@id": "urn:fe37daf8-4ff1-48bc-bd5b-b30ae0ff8ba2",
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"Label": "overlay",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
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"Used": []
},
{
- "@id": "urn:189b1f16-0e39-43a0-a97d-ed70d61f5d4e",
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"Label": "slicer",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
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"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat2 -A 750 rendered_thresh_zstat2.png",
"Used": [
- "urn:6f522c1e-c787-422d-9842-4ad8f23ec517"
+ "bids::rendered_thresh_zstat2"
]
},
{
- "@id": "urn:251e120d-e2c9-4d1e-8bc2-2e76c724c515",
+ "@id": "urn:makedire-1Dvf4Uew",
"Label": "Make directory",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "mkdir -p tsplot",
"Used": []
},
{
- "@id": "urn:f0e1ca2a-5db1-405d-88fd-954cf41a91bf",
+ "@id": "urn:tsplot-7pwv5ldO",
"Label": "tsplot",
- "AssociatedWith": "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "AssociatedWith": "urn:fsl-JIPD22pA",
"Command": "/usr/local/packages/fsl-5.0.10/bin/tsplot . -f filtered_func_data -o tsplot",
"Used": []
}
],
"Entities": [
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- "@id": "urn:d1308046-3332-4a11-9764-824e4f5a8e75",
+ "@id": "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold",
"Label": "sub-01_task-tonecounting_bold",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold",
+ "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold",
"digest": {
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}
},
{
- "@id": "urn:97d913aa-b73f-4d76-9c34-a50085ef0573",
+ "@id": "bids::prefiltered_func_data",
"Label": "prefiltered_func_data",
"AtLocation": "prefiltered_func_data",
- "GeneratedBy": "urn:0d259108-198a-403f-b1d3-bba09529827d",
+ "GeneratedBy": "urn:fslmaths-Xuyim67B",
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}
},
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- "@id": "urn:3cb3b1c6-e903-4569-a9fb-c6c5b3e5c4c5",
+ "@id": "bids::example_func",
"Label": "example_func",
"AtLocation": "example_func",
- "GeneratedBy": "urn:2f679b50-65f1-46d1-9294-aba74a8d3c0c",
+ "GeneratedBy": "urn:fslroi-3d5HkXKh",
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+ "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_contrast_mask.feat/example_func.nii.gz",
"Label": "example_func.nii.gz",
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"digest": {
@@ -728,15 +737,15 @@
}
},
{
- "@id": "urn:7821235c-3bfa-4236-abb0-1b9543708a70",
+ "@id": "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
"Label": "sub-01_T1w_brain",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
+ "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
"digest": {
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{
- "@id": "urn:6025627a-83a3-456d-8132-1ccb33c06fd5",
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"AtLocation": "/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain",
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@@ -744,45 +753,57 @@
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- "GeneratedBy": "urn:60a4f73b-8332-4571-9dcf-91085ea56e3e"
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- "GeneratedBy": "urn:10441440-f68c-4a5f-b183-f563d2e794c3",
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{
- "@id": "urn:0c49fdd7-6558-49b0-82a6-00e2cc8ef411",
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"Label": "highres",
"AtLocation": "highres",
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- "GeneratedBy": "urn:223a4067-5f9c-4c22-88f3-a4a2c47ed665"
+ "@id": "bids::highres_head",
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+ "GeneratedBy": "urn:fslmaths-YCDMAWXA",
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@@ -790,267 +811,259 @@
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- "GeneratedBy": "urn:124643ff-622e-404b-84b0-7cad78f62a3b",
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{
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- "GeneratedBy": "urn:124643ff-622e-404b-84b0-7cad78f62a3b",
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{
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"AtLocation": "sle.png",
- "GeneratedBy": "urn:124643ff-622e-404b-84b0-7cad78f62a3b",
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{
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"Label": "slf.png",
"AtLocation": "slf.png",
- "GeneratedBy": "urn:124643ff-622e-404b-84b0-7cad78f62a3b",
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{
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- "GeneratedBy": "urn:124643ff-622e-404b-84b0-7cad78f62a3b",
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{
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- "GeneratedBy": "urn:124643ff-622e-404b-84b0-7cad78f62a3b",
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{
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- "GeneratedBy": "urn:124643ff-622e-404b-84b0-7cad78f62a3b",
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{
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- "GeneratedBy": "urn:124643ff-622e-404b-84b0-7cad78f62a3b",
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{
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- "GeneratedBy": "urn:124643ff-622e-404b-84b0-7cad78f62a3b",
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},
{
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- "GeneratedBy": "urn:124643ff-622e-404b-84b0-7cad78f62a3b",
+ "GeneratedBy": "urn:slicer-XbZXqIgv",
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},
{
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"AtLocation": "example_func2highres2.png",
- "GeneratedBy": "urn:0d1cb971-95db-4b51-b754-8ce32ce31cfd",
+ "GeneratedBy": "urn:pngappen-epl9TLVc",
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{
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"AtLocation": "example_func2highres.png",
- "GeneratedBy": "urn:8b776a89-917e-4216-94da-cadb9a07b265",
+ "GeneratedBy": "urn:pngappen-10ldR3vU",
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{
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+ "@id": "bids::sl?.png",
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@@ -1058,25 +1071,25 @@
}
},
{
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+ "@id": "bids::prefiltered_func_data_mcf",
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"AtLocation": "prefiltered_func_data_mcf",
- "GeneratedBy": "urn:c79e05de-7c3b-4e36-8f80-4812d920289a",
+ "GeneratedBy": "urn:mcflirt-yfIrHolT",
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{
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- "GeneratedBy": "urn:639b42b5-1531-4197-b8b3-f73a720c0784",
+ "GeneratedBy": "urn:makedire-8o9UTCSS",
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{
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+ "@id": "bids::prefiltered_func_data_mcf.mat",
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"digest": {
@@ -1084,7 +1097,7 @@
}
},
{
- "@id": "urn:232b639e-d198-4461-82dd-6b5b7ca29858",
+ "@id": "bids::prefiltered_func_data_mcf.par",
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"digest": {
@@ -1092,7 +1105,7 @@
}
},
{
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+ "@id": "bids::prefiltered_func_data_mcf_abs.rms",
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"AtLocation": "prefiltered_func_data_mcf_abs.rms",
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@@ -1100,7 +1113,7 @@
}
},
{
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+ "@id": "bids::prefiltered_func_data_mcf_abs_mean.rms",
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"AtLocation": "prefiltered_func_data_mcf_abs_mean.rms",
"digest": {
@@ -1108,7 +1121,7 @@
}
},
{
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"AtLocation": "prefiltered_func_data_mcf_rel.rms",
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@@ -1116,7 +1129,7 @@
}
},
{
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+ "@id": "bids::prefiltered_func_data_mcf_rel_mean.rms",
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"AtLocation": "prefiltered_func_data_mcf_rel_mean.rms",
"digest": {
@@ -1124,34 +1137,34 @@
}
},
{
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- "GeneratedBy": "urn:f89527ff-6fb9-4848-b83b-87187c2e9d94",
+ "GeneratedBy": "urn:mv-563E2MPP",
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}
},
{
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- "GeneratedBy": "urn:25b87dfc-baa6-4412-be96-835e2fe3ac8c",
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{
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- "GeneratedBy": "urn:a6fa4bdd-b3f6-41fd-a285-b7f9d200b503",
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{
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@@ -1159,34 +1172,34 @@
}
},
{
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- "GeneratedBy": "urn:45cc2b39-a6fc-4f39-a6fe-09a7aad4c016",
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{
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"AtLocation": "mean_func",
- "GeneratedBy": "urn:ee82e800-0280-4a09-b8c4-0a2a14dcc69c",
+ "GeneratedBy": "urn:fslmaths-SKesHBPT",
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{
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- "GeneratedBy": "urn:5582b83e-b803-4011-9d05-9221fe1af3cc",
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{
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+ "@id": "bids::mask_mask",
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"digest": {
@@ -1194,132 +1207,124 @@
}
},
{
- "@id": "urn:5ea3f15a-8e99-46ef-840d-fb49ab3c2002",
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{
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"AtLocation": "prefiltered_func_data_bet",
- "GeneratedBy": "urn:2cfcc313-2bea-437e-bf9d-6527d3f0031b",
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{
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- "GeneratedBy": "urn:7fa64d13-6d3d-43f7-aa1f-f869c24716ee",
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{
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{
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"AtLocation": "prefiltered_func_data_thresh",
- "GeneratedBy": "urn:926975f6-7027-49ca-9ee7-dddc5a6ae44f",
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{
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"AtLocation": "mean_func",
- "GeneratedBy": "urn:d066b14b-96f0-4d46-80c0-11d5d99d23f4",
+ "GeneratedBy": "urn:fslmaths-W7rvUch0",
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{
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"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:b60656a1-c732-49cd-8d5b-91fcbe73fe6c",
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{
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"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:aca19fbd-0414-496a-8e00-ef764f356192",
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},
{
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"AtLocation": "prefiltered_func_data_intnorm",
- "GeneratedBy": "urn:f6c58562-64eb-4875-b481-83d9e0a584b8",
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{
- "@id": "urn:0b85a8dd-c5fa-4f84-bd05-454b4d43f12c",
+ "@id": "bids::tempMean",
"Label": "tempMean",
"AtLocation": "tempMean",
- "GeneratedBy": "urn:48fe3b0d-bdc4-4e54-b3fd-f7776047617b",
+ "GeneratedBy": "urn:fslmaths-of0s39J8",
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{
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- {
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+ "@id": "bids::prefiltered_func_data_tempfilt",
"Label": "prefiltered_func_data_tempfilt",
"AtLocation": "prefiltered_func_data_tempfilt",
+ "GeneratedBy": "urn:fslmaths-0Yxn67qj",
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}
},
{
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+ "@id": "bids::filtered_func_data",
"Label": "filtered_func_data",
"AtLocation": "filtered_func_data",
- "GeneratedBy": "urn:d7052af7-241a-44ce-99ce-8a5b42550975",
+ "GeneratedBy": "urn:fslmaths-zQn78yon",
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}
},
{
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+ "@id": "bids::mean_func",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:151c4564-2b06-42e4-805f-a53e7471f4a6",
+ "GeneratedBy": "urn:fslmaths-AoENJ4vu",
"digest": {
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},
{
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+ "@id": "bids::prefiltered_func_data*",
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"AtLocation": "prefiltered_func_data*",
"digest": {
@@ -1327,130 +1332,172 @@
}
},
{
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"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:0b206421-73e5-4bf5-8789-644ea60eaf35",
+ "GeneratedBy": "urn:makedire-BNU0v0w6",
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{
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- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
+ "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
"digest": {
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},
{
- "@id": "urn:13b1ec0e-170e-4925-98f7-d951ed4266fa",
+ "@id": "bids::custom_timing_files/ev1.txt",
"Label": "ev1.txt",
"AtLocation": "custom_timing_files/ev1.txt",
- "GeneratedBy": "urn:444e272d-4747-44c5-9303-f886994a0c7d"
+ "GeneratedBy": "urn:fslfixte-gPWYR3x8"
},
{
- "@id": "urn:fb65f5b1-ad32-4991-8df8-f81b4389f41f",
+ "@id": "bids::custom_timing_files",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:78fb79a4-45b9-4060-869a-dc0b08c9f54c",
+ "GeneratedBy": "urn:makedire-fqvNCFv9",
"digest": {
"sha256": "1d7e19792328d5040f2f9fb3c15d59de90fc771785f81c67039a043bd5f2ed20"
}
},
{
- "@id": "urn:fee67aaa-0c67-496a-8d33-670b4d2ae6b8",
+ "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
"Label": "sub-01_tone_counting_probe.txt",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
+ "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
"digest": {
- "sha256": "f09eeb82fa0be8e8759a5269403f36ec2b7dbf2c5b6caba1f0f985cc6cb3f703"
+ "sha256": "8b912293767f1a5e082311f6aaf0c44fc91fe45b0f2ae7f80e368bc2f4c2918a"
}
},
{
- "@id": "urn:b2ccbeed-b081-4ae1-867f-7e2c32c60ea1",
+ "@id": "bids::custom_timing_files/ev2.txt",
"Label": "ev2.txt",
"AtLocation": "custom_timing_files/ev2.txt",
- "GeneratedBy": "urn:e84f94ca-11f1-4b1b-8371-0ab06012a4e7"
+ "GeneratedBy": "urn:fslfixte-6BH43olN"
},
{
- "@id": "urn:e4db7414-e073-47db-9e40-61194372f726",
- "Label": "res4d",
- "AtLocation": "stats/res4d",
+ "@id": "bids::stats",
+ "Label": "stats",
+ "AtLocation": "stats",
"digest": {
- "sha256": "8845286f36caedf891a02afddc4175ea46f18f830b59a8c5026962184a530699"
+ "sha256": "a9f3e135372514a16d11a8038262b3eff94ccd69a9b35c4724b2759cfc944a07"
}
},
{
- "@id": "urn:f423a330-8b0f-4cfd-bdb3-b609ec991da6",
- "Label": "smoothness",
- "AtLocation": "stats/smoothness",
- "GeneratedBy": "urn:798246d9-8c8f-4fcc-8e7b-ae1753dd7cbd",
+ "@id": "bids::design.mat",
+ "Label": "design.mat",
+ "AtLocation": "design.mat",
"digest": {
- "sha256": "67b0aaf95a257beff60d331b56265034807ca51e67e2d312d481d5835ef0b1d0"
+ "sha256": "1c1a6ef59a355e1f6f81e741e157784ccbe066ba3594a07aa9b16781e3d5bb25"
}
},
{
- "@id": "urn:2dbe13bd-50d1-4dd5-862a-81490d6be7b1",
- "Label": "zstat1",
- "AtLocation": "stats/zstat1",
+ "@id": "bids::design.con",
+ "Label": "design.con",
+ "AtLocation": "design.con",
"digest": {
- "sha256": "70ae47cee1ea1d3f1f6f8aa7ac51f2641cb2fcb745dfd8cc54a389346e6fa094"
+ "sha256": "5808d1be37dd8f2a4906b710bb384fbee62faa4a46b2bc6847afc8962ed4eb54"
}
},
{
- "@id": "urn:0a49a6e7-bc51-4b1b-94aa-c7a709053518",
+ "@id": "bids::stats",
+ "Label": "stats",
+ "AtLocation": "stats",
+ "GeneratedBy": "urn:filmgls-hnXGCyIa",
+ "digest": {
+ "sha256": "a9f3e135372514a16d11a8038262b3eff94ccd69a9b35c4724b2759cfc944a07"
+ }
+ },
+ {
+ "@id": "bids::stats/res4d",
+ "Label": "res4d",
+ "AtLocation": "stats/res4d"
+ },
+ {
+ "@id": "bids::stats/smoothness",
+ "Label": "smoothness",
+ "AtLocation": "stats/smoothness",
+ "GeneratedBy": "urn:smoothes-HqoKWOFV"
+ },
+ {
+ "@id": "bids::stats/zstat1",
+ "Label": "zstat1",
+ "AtLocation": "stats/zstat1"
+ },
+ {
+ "@id": "bids::thresh_zstat1",
"Label": "thresh_zstat1",
"AtLocation": "thresh_zstat1",
- "GeneratedBy": "urn:4c04841c-f3d0-445c-a066-028babe31e33",
+ "GeneratedBy": "urn:fslmaths-BRCsyWxk",
"digest": {
"sha256": "662e7ba670e124d15bb3cc18b818868f76604578034b524c8882f35fc5db413f"
}
},
{
- "@id": "urn:02e35e36-1794-41be-83d8-3fdc4b2d3731",
+ "@id": "bids::stats/zstat2",
"Label": "zstat2",
- "AtLocation": "stats/zstat2",
- "digest": {
- "sha256": "b6b265908257e91648f7007e172c3ba159d9231b0acfce7fbf48d754f8cfe52c"
- }
+ "AtLocation": "stats/zstat2"
},
{
- "@id": "urn:ad8c2146-4bbe-408a-a107-9d9ba36aa1ec",
+ "@id": "bids::thresh_zstat2",
"Label": "thresh_zstat2",
"AtLocation": "thresh_zstat2",
- "GeneratedBy": "urn:3138a4a5-eed0-4499-9bf3-458190b4bca6",
+ "GeneratedBy": "urn:fslmaths-5zja6ybF",
"digest": {
"sha256": "fe707ed68d72f4376668be45a2030f2d00fa81534a3e95bf92b6a499fa8595bd"
}
},
{
- "@id": "urn:c89142a2-cb00-4e74-a5fe-c88971d7120e",
+ "@id": "bids::stats/cope1",
"Label": "cope1",
- "AtLocation": "stats/cope1",
- "digest": {
- "sha256": "bf3b603569da6dbe3d6f0e8667d346f3ac943c9d01d2fc9743ce17abeb1547fb"
- }
+ "AtLocation": "stats/cope1"
},
{
- "@id": "urn:74707900-30d5-4930-b467-4a69f7a019c1",
+ "@id": "bids::cluster_mask_zstat1",
"Label": "cluster_mask_zstat1",
"AtLocation": "cluster_mask_zstat1",
- "GeneratedBy": "urn:e960ebac-d05a-4cf4-9343-37287329f1f5",
+ "GeneratedBy": "urn:cluster-KIgiCoyq",
"digest": {
"sha256": "b28c170e33d2917cac55183786616a9e976e5e7f30dc7c8666341f12ed6d0277"
}
},
{
- "@id": "urn:43900715-a661-4411-9a8b-c5ffe9330f19",
+ "@id": "bids::thresh_zstat1",
+ "Label": "thresh_zstat1",
+ "AtLocation": "thresh_zstat1",
+ "GeneratedBy": "urn:cluster-KIgiCoyq",
+ "digest": {
+ "sha256": "662e7ba670e124d15bb3cc18b818868f76604578034b524c8882f35fc5db413f"
+ }
+ },
+ {
+ "@id": "bids::lmax_zstat1.txt",
+ "Label": "lmax_zstat1.txt",
+ "AtLocation": "lmax_zstat1.txt",
+ "GeneratedBy": "urn:cluster-KIgiCoyq",
+ "digest": {
+ "sha256": "d44ee21719775397a1a95ede6778d25404b50e8bd259dbdf02d2fde635fc81a5"
+ }
+ },
+ {
+ "@id": "bids::stats/cope1",
"Label": "cope1",
"AtLocation": "stats/cope1",
- "GeneratedBy": "urn:e960ebac-d05a-4cf4-9343-37287329f1f5",
+ "GeneratedBy": "urn:cluster-KIgiCoyq"
+ },
+ {
+ "@id": "bids::cluster_zstat1.txt",
+ "Label": "cluster_zstat1.txt",
+ "AtLocation": "cluster_zstat1.txt",
+ "GeneratedBy": "urn:cluster-KIgiCoyq",
"digest": {
- "sha256": "bf3b603569da6dbe3d6f0e8667d346f3ac943c9d01d2fc9743ce17abeb1547fb"
+ "sha256": "b06695ff4f0a8158fa439b1ddf224b58d344606d400885c177390d09506e8e4c"
}
},
{
- "@id": "urn:316e32ea-3f08-47e1-9e28-5e94e420c1d1",
+ "@id": "bids::cluster_zstat1",
"Label": "cluster_zstat1",
"AtLocation": "cluster_zstat1",
"digest": {
@@ -1458,33 +1505,54 @@
}
},
{
- "@id": "urn:a4d007e1-5feb-48dd-9610-1eed703cff19",
+ "@id": "bids::stats/cope2",
"Label": "cope2",
- "AtLocation": "stats/cope2",
- "digest": {
- "sha256": "5f073baabd78c1c473fed55b511738f0ffe30d9fc1f23352a16ec058daacd88c"
- }
+ "AtLocation": "stats/cope2"
},
{
- "@id": "urn:c4e51ee7-9fbf-400b-bc74-7153286c3cf4",
+ "@id": "bids::cluster_mask_zstat2",
"Label": "cluster_mask_zstat2",
"AtLocation": "cluster_mask_zstat2",
- "GeneratedBy": "urn:38bbfab4-7b95-45e4-9ba4-525c395261f2",
+ "GeneratedBy": "urn:cluster-MRFJ9REm",
"digest": {
"sha256": "b88bb3cd4d809827a5c0a45cb4f6aac570cb25b7e056d5986d81d879548da121"
}
},
{
- "@id": "urn:02815627-f827-4fe8-9b0e-ca4d9125d0fc",
+ "@id": "bids::thresh_zstat2",
+ "Label": "thresh_zstat2",
+ "AtLocation": "thresh_zstat2",
+ "GeneratedBy": "urn:cluster-MRFJ9REm",
+ "digest": {
+ "sha256": "fe707ed68d72f4376668be45a2030f2d00fa81534a3e95bf92b6a499fa8595bd"
+ }
+ },
+ {
+ "@id": "bids::lmax_zstat2.txt",
+ "Label": "lmax_zstat2.txt",
+ "AtLocation": "lmax_zstat2.txt",
+ "GeneratedBy": "urn:cluster-MRFJ9REm",
+ "digest": {
+ "sha256": "23ca5266a11743c7252c1758989cf555126dd598ae07080cf11f0a7c9e8a988b"
+ }
+ },
+ {
+ "@id": "bids::stats/cope2",
"Label": "cope2",
"AtLocation": "stats/cope2",
- "GeneratedBy": "urn:38bbfab4-7b95-45e4-9ba4-525c395261f2",
+ "GeneratedBy": "urn:cluster-MRFJ9REm"
+ },
+ {
+ "@id": "bids::cluster_zstat2.txt",
+ "Label": "cluster_zstat2.txt",
+ "AtLocation": "cluster_zstat2.txt",
+ "GeneratedBy": "urn:cluster-MRFJ9REm",
"digest": {
- "sha256": "5f073baabd78c1c473fed55b511738f0ffe30d9fc1f23352a16ec058daacd88c"
+ "sha256": "05b4675c829a96e029b38d828f0160bb2299d2d76d7c1248cd45119f0c6c9c2e"
}
},
{
- "@id": "urn:4c25fcf4-4122-4b47-9726-3209f7f4367e",
+ "@id": "bids::cluster_zstat2",
"Label": "cluster_zstat2",
"AtLocation": "cluster_zstat2",
"digest": {
@@ -1492,87 +1560,135 @@
}
},
{
- "@id": "urn:4ae6b32f-e8fd-4b05-aec2-42ede6e29f8d",
+ "@id": "bids::conmask",
"Label": "conmask",
"AtLocation": "conmask",
- "GeneratedBy": "urn:7bb7e554-8502-404a-8243-e149af1372ef",
+ "GeneratedBy": "urn:makedire-7qR7aS7n",
"digest": {
"sha256": "f555349cd698b294f93ff993006671506ca822960218ca0076bb984de8105368"
}
},
{
- "@id": "urn:32084514-f878-4737-93ab-677a29eebbcb",
+ "@id": "bids::conmask/thresh_zstat1",
"Label": "thresh_zstat1",
"AtLocation": "conmask/thresh_zstat1",
- "GeneratedBy": "urn:12b6efb2-c7ca-4ebf-8624-3a3975555f75"
+ "GeneratedBy": "urn:fslmaths-l6gT6VDx"
},
{
- "@id": "urn:11270f30-6cd9-40e4-ae09-0ce252d2c167",
+ "@id": "bids::conmask/*",
"Label": "*",
"AtLocation": "conmask/*"
},
{
- "@id": "urn:d8b43881-6d32-44ce-ba30-b38cd97af127",
+ "@id": "urn:uuid:ba7d0551-bbd3-4b75-9717-70b3d9d90fb6",
"Label": ".",
"AtLocation": ".",
- "GeneratedBy": "urn:10fcf5d7-a537-4730-bc72-bf8ef9f51d4c"
+ "GeneratedBy": "urn:mv-cM6i4hre"
},
{
- "@id": "urn:20a6b127-11b9-43ab-a94c-ba9606110b3d",
+ "@id": "bids::cluster_mask_zstat1",
"Label": "cluster_mask_zstat1",
"AtLocation": "cluster_mask_zstat1",
- "GeneratedBy": "urn:ef7f41f7-4571-4fa9-87af-5ba336c823d3",
+ "GeneratedBy": "urn:cluster-KSF2yOj5",
"digest": {
"sha256": "b28c170e33d2917cac55183786616a9e976e5e7f30dc7c8666341f12ed6d0277"
}
},
{
- "@id": "urn:4fceab9a-bf44-40b9-87c0-a24eaa4d9c83",
+ "@id": "bids::thresh_zstat1",
+ "Label": "thresh_zstat1",
+ "AtLocation": "thresh_zstat1",
+ "GeneratedBy": "urn:cluster-KSF2yOj5",
+ "digest": {
+ "sha256": "662e7ba670e124d15bb3cc18b818868f76604578034b524c8882f35fc5db413f"
+ }
+ },
+ {
+ "@id": "bids::lmax_zstat1.txt",
+ "Label": "lmax_zstat1.txt",
+ "AtLocation": "lmax_zstat1.txt",
+ "GeneratedBy": "urn:cluster-KSF2yOj5",
+ "digest": {
+ "sha256": "d44ee21719775397a1a95ede6778d25404b50e8bd259dbdf02d2fde635fc81a5"
+ }
+ },
+ {
+ "@id": "bids::stats/cope1",
"Label": "cope1",
"AtLocation": "stats/cope1",
- "GeneratedBy": "urn:ef7f41f7-4571-4fa9-87af-5ba336c823d3",
+ "GeneratedBy": "urn:cluster-KSF2yOj5"
+ },
+ {
+ "@id": "bids::cluster_zstat1.txt",
+ "Label": "cluster_zstat1.txt",
+ "AtLocation": "cluster_zstat1.txt",
+ "GeneratedBy": "urn:cluster-KSF2yOj5",
"digest": {
- "sha256": "bf3b603569da6dbe3d6f0e8667d346f3ac943c9d01d2fc9743ce17abeb1547fb"
+ "sha256": "b06695ff4f0a8158fa439b1ddf224b58d344606d400885c177390d09506e8e4c"
}
},
{
- "@id": "urn:ef629af8-b933-4616-a6b8-dde38842024d",
+ "@id": "bids::cluster_mask_zstat2",
"Label": "cluster_mask_zstat2",
"AtLocation": "cluster_mask_zstat2",
- "GeneratedBy": "urn:b0786995-aa20-4cc1-ba11-56821df58c7e",
+ "GeneratedBy": "urn:cluster-9sTEgQIH",
"digest": {
"sha256": "b88bb3cd4d809827a5c0a45cb4f6aac570cb25b7e056d5986d81d879548da121"
}
},
{
- "@id": "urn:4385eb5c-9057-44f4-9f34-5bec6fdc03b8",
+ "@id": "bids::thresh_zstat2",
+ "Label": "thresh_zstat2",
+ "AtLocation": "thresh_zstat2",
+ "GeneratedBy": "urn:cluster-9sTEgQIH",
+ "digest": {
+ "sha256": "fe707ed68d72f4376668be45a2030f2d00fa81534a3e95bf92b6a499fa8595bd"
+ }
+ },
+ {
+ "@id": "bids::lmax_zstat2.txt",
+ "Label": "lmax_zstat2.txt",
+ "AtLocation": "lmax_zstat2.txt",
+ "GeneratedBy": "urn:cluster-9sTEgQIH",
+ "digest": {
+ "sha256": "23ca5266a11743c7252c1758989cf555126dd598ae07080cf11f0a7c9e8a988b"
+ }
+ },
+ {
+ "@id": "bids::stats/cope2",
"Label": "cope2",
"AtLocation": "stats/cope2",
- "GeneratedBy": "urn:b0786995-aa20-4cc1-ba11-56821df58c7e",
+ "GeneratedBy": "urn:cluster-9sTEgQIH"
+ },
+ {
+ "@id": "bids::cluster_zstat2.txt",
+ "Label": "cluster_zstat2.txt",
+ "AtLocation": "cluster_zstat2.txt",
+ "GeneratedBy": "urn:cluster-9sTEgQIH",
"digest": {
- "sha256": "5f073baabd78c1c473fed55b511738f0ffe30d9fc1f23352a16ec058daacd88c"
+ "sha256": "05b4675c829a96e029b38d828f0160bb2299d2d76d7c1248cd45119f0c6c9c2e"
}
},
{
- "@id": "urn:b173fa0a-f3c8-498e-a012-a3414336895e",
+ "@id": "bids::rendered_thresh_zstat1",
"Label": "rendered_thresh_zstat1",
"AtLocation": "rendered_thresh_zstat1",
- "GeneratedBy": "urn:73df9179-e121-4c94-96c2-38bfe982ce72",
+ "GeneratedBy": "urn:overlay-N8rFrcHs",
"digest": {
"sha256": "de5b9d44d95f4252f491eb45c76a0ae2b4d2c75b58664fc0df7d9153810c0bf6"
}
},
{
- "@id": "urn:a6dd74d2-ceb5-4d2c-88c5-0072cc353649",
+ "@id": "bids::rendered_thresh_zstat1.png",
"Label": "rendered_thresh_zstat1.png",
"AtLocation": "rendered_thresh_zstat1.png",
- "GeneratedBy": "urn:9edd7dc8-198e-47f2-97a0-a0c502f60628",
+ "GeneratedBy": "urn:slicer-yKHiTJ8J",
"digest": {
"sha256": "15d6a8bf7a902df8c5feeb7468a3d0caacf9eb3067c0840c2f4763f5e2301527"
}
},
{
- "@id": "urn:95b72fdb-64f4-42c3-ab59-c9671b5d34d3",
+ "@id": "bids::/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif",
"Label": "ramp.gif",
"AtLocation": "/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif",
"digest": {
@@ -1580,46 +1696,46 @@
}
},
{
- "@id": "urn:9d4ba426-e4ef-4863-8c94-1a122c95de90",
+ "@id": "bids::.ramp.gif",
"Label": ".ramp.gif",
"AtLocation": ".ramp.gif",
- "GeneratedBy": "urn:6552ba36-0e4e-49ce-9503-1172a5ba4ac6",
+ "GeneratedBy": "urn:cp-NwMvSfas",
"digest": {
"sha256": "93f4284ccb854d5a41401d9360a13223017b67479cb289a33d83836922e028a4"
}
},
{
- "@id": "urn:6f522c1e-c787-422d-9842-4ad8f23ec517",
+ "@id": "bids::rendered_thresh_zstat2",
"Label": "rendered_thresh_zstat2",
"AtLocation": "rendered_thresh_zstat2",
- "GeneratedBy": "urn:fe37daf8-4ff1-48bc-bd5b-b30ae0ff8ba2",
+ "GeneratedBy": "urn:overlay-7Z2044QX",
"digest": {
"sha256": "b988cb8ba2b862b6fa88f223fcd3279c70e2ea217477bd1ec664c023be079cad"
}
},
{
- "@id": "urn:783b074d-fd7b-4e3f-bc14-df2af149aa0b",
+ "@id": "bids::rendered_thresh_zstat2.png",
"Label": "rendered_thresh_zstat2.png",
"AtLocation": "rendered_thresh_zstat2.png",
- "GeneratedBy": "urn:189b1f16-0e39-43a0-a97d-ed70d61f5d4e",
+ "GeneratedBy": "urn:slicer-uH9J1HCB",
"digest": {
"sha256": "0d60298d9eb509148075cbac8a22e6a95de919f17a069624fb42f86c29e1e199"
}
},
{
- "@id": "urn:060115b8-449f-4a4a-8cb5-b5ed45d61f56",
+ "@id": "bids::tsplot",
"Label": "tsplot",
"AtLocation": "tsplot",
- "GeneratedBy": "urn:251e120d-e2c9-4d1e-8bc2-2e76c724c515",
+ "GeneratedBy": "urn:makedire-1Dvf4Uew",
"digest": {
"sha256": "2a74042f4edf02288edf16961307f741651efb4346e102a04b7603e781d1625e"
}
},
{
- "@id": "urn:1baa48ee-1e56-49ad-96f5-71720a81df53",
+ "@id": "bids::tsplot",
"Label": "tsplot",
"AtLocation": "tsplot",
- "GeneratedBy": "urn:f0e1ca2a-5db1-405d-88fd-954cf41a91bf",
+ "GeneratedBy": "urn:tsplot-7pwv5ldO",
"digest": {
"sha256": "2a74042f4edf02288edf16961307f741651efb4346e102a04b7603e781d1625e"
}
diff --git a/examples/from_parsers/fsl/fsl_contrast_mask_report_log.png b/examples/from_parsers/fsl/fsl_contrast_mask_report_log.png
index 308b0a63a..f36b91cc9 100644
Binary files a/examples/from_parsers/fsl/fsl_contrast_mask_report_log.png and b/examples/from_parsers/fsl/fsl_contrast_mask_report_log.png differ
diff --git a/examples/from_parsers/fsl/fsl_default_report_log.html b/examples/from_parsers/fsl/fsl_default_report_log.html
index 9fa11fc8d..72b140ae8 100644
--- a/examples/from_parsers/fsl/fsl_default_report_log.html
+++ b/examples/from_parsers/fsl/fsl_default_report_log.html
@@ -35,20 +35,20 @@ Progress Report / Log
326905
Initialisation
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
Total original volumes = 104
/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1
Preprocessing:Stage 1
-/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90
+/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/example_func.nii.gz -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90
Option -F ( FEAT version parameter ) selected with argument "6.00"
Option -d ( output directory ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat"
Option -l ( logfile )input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/logs/feat2_pre"
Option -R ( html unwarping report ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/report_unwarp.html"
Option -r ( html registration report ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/report_reg.html"
Option -i ( main input ) input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/example_func.nii.gz"
-Option -h ( high-res structural image ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
+Option -h ( high-res structural image ) selected with argument "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
Option -w ( highres dof ) selected with argument "BBR"
Option -x ( highres search ) selected with argument "90"
Option -s ( standard image ) selected with argument "/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain"
@@ -59,10 +59,10 @@ Progress Report / Log
/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/reg
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head
did not find file: example_func2highres.mat. Generating transform.
@@ -128,9 +128,9 @@ Progress Report / Log
/bin/rm -rf prefiltered_func_data*
Stats
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
/usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con
Log directory is: stats
diff --git a/examples/from_parsers/fsl/fsl_default_report_log.jsonld b/examples/from_parsers/fsl/fsl_default_report_log.jsonld
index 8b772cbfc..08e5cbd55 100644
--- a/examples/from_parsers/fsl/fsl_default_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_default_report_log.jsonld
@@ -4,575 +4,584 @@
"Records": {
"Software": [
{
- "@id": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:fsl-E4ALjxdM",
"@type": "prov:SoftwareAgent",
"Label": "FSL",
- "Version": "xxx"
+ "Version": "xxx",
+ "AltIdentifier": "RRID:SCR_002823"
}
],
"Activities": [
{
- "@id": "urn:b00d4ecd-cbf3-4779-a8bf-ad46c28ae579",
+ "@id": "urn:fslmaths-fcSIwVMX",
"Label": "fslmaths",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
"Used": [
- "urn:3452a9ca-42b6-4997-bcca-cfb7b55db048"
+ "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold"
]
},
{
- "@id": "urn:a97cc948-6aa2-425a-b953-f1d83ceed350",
+ "@id": "urn:fslroi-OG3P6KqD",
"Label": "fslroi",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1",
"Used": [
- "urn:8e066908-75d0-41b0-a0cf-9685bf3a5785"
+ "bids::prefiltered_func_data"
]
},
{
- "@id": "urn:7567208c-e138-45bd-92fd-e04cbbbe5798",
+ "@id": "urn:mainfeat-DMP0PTOA",
"Label": "mainfeatreg",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/example_func.nii.gz -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
"Used": [
- "urn:5f833946-20fb-421f-bad6-7314076eefc9",
- "urn:664b43fb-669a-401f-ae8b-84fe61d94430",
- "urn:f0341414-568b-486a-a4d1-510de6bfe1df"
+ "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/example_func.nii.gz",
+ "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain",
+ "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
]
},
{
- "@id": "urn:2f4ce27c-6f45-4c41-b2f6-5c56cd245544",
+ "@id": "urn:makedire-BYrQI1M0",
"Label": "Make directory",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/reg",
"Used": []
},
{
- "@id": "urn:06bc5b94-8010-4257-9815-dade77c76107",
+ "@id": "urn:fslmaths-wMZbWTyd",
"Label": "fslmaths",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
"Used": [
- "urn:f0341414-568b-486a-a4d1-510de6bfe1df"
+ "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
]
},
{
- "@id": "urn:0aef9850-8080-416b-b56e-b15d2f9b7ad3",
+ "@id": "urn:fslmaths-Ddt8tGbY",
"Label": "fslmaths",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
"Used": [
- "urn:d53e0107-1254-40e5-86e7-d8d9c3e13410"
+ "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w"
]
},
{
- "@id": "urn:5a684948-c866-433e-85cb-f5badd6af3ee",
+ "@id": "urn:epireg-H7ZIk7pS",
"Label": "epi_reg",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/usr/local/packages/fsl-5.0.10/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres",
- "Used": []
+ "Used": [
+ "bids::example_func",
+ "bids::highres",
+ "bids::highres_head"
+ ]
},
{
- "@id": "urn:06b5a9d8-853c-4b4e-977e-d596dc959c46",
+ "@id": "urn:convertx-yjHkcYPz",
"Label": "convert_xfm",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/usr/local/packages/fsl-5.0.10/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat",
"Used": [
- "urn:a06f1142-ca51-461c-a20f-80e2f40ffb15"
+ "bids::example_func2highres.mat"
]
},
{
- "@id": "urn:e3ee0fd1-763c-4aa9-a09a-de1c91eadfac",
+ "@id": "urn:slicer-FHEZSaNt",
"Label": "slicer",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:9fa885f9-9119-4a5a-a21f-c08970524468",
- "urn:9fb33f03-76f5-46d7-970f-e644098dbcac"
+ "bids::example_func2highres",
+ "bids::highres"
]
},
{
- "@id": "urn:fabf4f69-def8-49d7-9611-c11f35a72be7",
+ "@id": "urn:pngappen-SFkxyMJz",
"Label": "pngappend",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres1.png",
"Used": [
- "urn:0f8fdd76-c020-44cd-8b51-47396be17e01",
- "urn:3e320bc6-bbc2-4e05-ba6b-c6954f914af3",
- "urn:468f97b6-fcd4-424e-8298-910a84f5dee9",
- "urn:4e751535-4490-4cab-a8d0-fd2b0f897f07",
- "urn:4eb9bfc6-31fe-4f23-b060-da82621ef6b7",
- "urn:5597e536-cc2e-4140-a887-f9cf062a7cc8",
- "urn:8577bb07-1c01-44d3-bb9d-7aaa8458e8cc",
- "urn:888face6-0e08-4aa6-8bda-c8a0262c4cb1",
- "urn:b68a203c-17bc-4181-9131-451583349b15",
- "urn:b91a4495-095e-4698-850a-7413ec6cbcab",
- "urn:ba31de6b-e88d-443c-8864-b0d51d5f35ff",
- "urn:ef0c3f4e-4e67-4cfb-b6a4-e9c40b2dc7e9"
+ "bids::sla.png",
+ "bids::slb.png",
+ "bids::slc.png",
+ "bids::sld.png",
+ "bids::sle.png",
+ "bids::slf.png",
+ "bids::slg.png",
+ "bids::slh.png",
+ "bids::sli.png",
+ "bids::slj.png",
+ "bids::slk.png",
+ "bids::sll.png"
]
},
{
- "@id": "urn:ff437011-9364-42c4-a64d-7a8b7a8562eb",
+ "@id": "urn:slicer-sJLXpGr2",
"Label": "slicer",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:9fa885f9-9119-4a5a-a21f-c08970524468",
- "urn:9fb33f03-76f5-46d7-970f-e644098dbcac"
+ "bids::example_func2highres",
+ "bids::highres"
]
},
{
- "@id": "urn:ed65319b-bef9-45d6-9ef4-1d7df77a0226",
+ "@id": "urn:pngappen-RUvG0ImG",
"Label": "pngappend",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres2.png",
"Used": [
- "urn:0f8fdd76-c020-44cd-8b51-47396be17e01",
- "urn:3e320bc6-bbc2-4e05-ba6b-c6954f914af3",
- "urn:468f97b6-fcd4-424e-8298-910a84f5dee9",
- "urn:4e751535-4490-4cab-a8d0-fd2b0f897f07",
- "urn:4eb9bfc6-31fe-4f23-b060-da82621ef6b7",
- "urn:5597e536-cc2e-4140-a887-f9cf062a7cc8",
- "urn:8577bb07-1c01-44d3-bb9d-7aaa8458e8cc",
- "urn:888face6-0e08-4aa6-8bda-c8a0262c4cb1",
- "urn:b68a203c-17bc-4181-9131-451583349b15",
- "urn:b91a4495-095e-4698-850a-7413ec6cbcab",
- "urn:ba31de6b-e88d-443c-8864-b0d51d5f35ff",
- "urn:ef0c3f4e-4e67-4cfb-b6a4-e9c40b2dc7e9"
+ "bids::sla.png",
+ "bids::slb.png",
+ "bids::slc.png",
+ "bids::sld.png",
+ "bids::sle.png",
+ "bids::slf.png",
+ "bids::slg.png",
+ "bids::slh.png",
+ "bids::sli.png",
+ "bids::slj.png",
+ "bids::slk.png",
+ "bids::sll.png"
]
},
{
- "@id": "urn:0617f869-1d93-49de-8802-eebcca654cec",
+ "@id": "urn:pngappen-FtOA4j1l",
"Label": "pngappend",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend example_func2highres1.png example_func2highres2.png example_func2highres.png",
"Used": [
- "urn:1aafcb00-576a-4e22-9480-b02789555f8d",
- "urn:5b6ece1d-f451-442f-a3c6-c9f484150172"
+ "bids::example_func2highres1.png",
+ "bids::example_func2highres2.png"
]
},
{
- "@id": "urn:18d4af4a-989e-47c8-9149-ab508e95264e",
+ "@id": "urn:rm-wjUAGwJx",
"Label": "rm",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/bin/rm -f sl?.png example_func2highres2.png",
"Used": [
- "urn:5b6ece1d-f451-442f-a3c6-c9f484150172",
- "urn:c7abed1c-541a-416f-a69b-7d91ad6de028"
+ "bids::example_func2highres2.png",
+ "bids::sl?.png"
]
},
{
- "@id": "urn:2988ce82-4171-40d3-83f1-a52e190aeeb3",
+ "@id": "urn:rm-WsyCazgR",
"Label": "rm",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/bin/rm example_func2highres1.png",
"Used": [
- "urn:1aafcb00-576a-4e22-9480-b02789555f8d"
+ "bids::example_func2highres1.png"
]
},
{
- "@id": "urn:e2444068-c742-4dd1-84c7-0641984fb6d9",
+ "@id": "urn:mcflirt-psopAuVm",
"Label": "mcflirt",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/usr/local/packages/fsl-5.0.10/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs -spline_final",
"Used": [
- "urn:8e066908-75d0-41b0-a0cf-9685bf3a5785"
+ "bids::prefiltered_func_data"
]
},
{
- "@id": "urn:43063405-3837-4669-9cc4-0ae7fb24aa6c",
+ "@id": "urn:makedire-4wMbJbeY",
"Label": "Make directory",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/bin/mkdir -p mc",
"Used": []
},
{
- "@id": "urn:6011531f-aa09-47ce-a04f-e5201123c5a8",
+ "@id": "urn:mv-5vMsPN6O",
"Label": "mv",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc",
"Used": [
- "urn:1b69e3f5-5564-4aa3-a5c9-de11f6e13e18",
- "urn:1b7afc2f-569a-4de1-b8e4-aa3e690095ca",
- "urn:571d1fdc-8ad5-4ae2-8dbe-bfb8d5bee9e0",
- "urn:8b99de74-04a3-4a04-ab08-a2af09fa3473",
- "urn:d6c4bcf4-12c5-438c-9367-b4d2d5946dfe",
- "urn:e1f4504e-a931-4560-b135-c4b165528bc3"
+ "bids::prefiltered_func_data_mcf.mat",
+ "bids::prefiltered_func_data_mcf.par",
+ "bids::prefiltered_func_data_mcf_abs.rms",
+ "bids::prefiltered_func_data_mcf_abs_mean.rms",
+ "bids::prefiltered_func_data_mcf_rel.rms",
+ "bids::prefiltered_func_data_mcf_rel_mean.rms"
]
},
{
- "@id": "urn:0f4a4e05-e37b-4628-96fe-b0474b7d5184",
+ "@id": "urn:fsltsplo-VAnxKfBU",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png",
"Used": [
- "urn:d6c4bcf4-12c5-438c-9367-b4d2d5946dfe"
+ "bids::prefiltered_func_data_mcf.par"
]
},
{
- "@id": "urn:9096b2e5-fbcf-4047-a54e-8a5c2aeb68a4",
+ "@id": "urn:fsltsplo-mhaEcLEl",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png",
"Used": [
- "urn:d6c4bcf4-12c5-438c-9367-b4d2d5946dfe"
+ "bids::prefiltered_func_data_mcf.par"
]
},
{
- "@id": "urn:a51452a7-71ed-46f1-b3f9-63b70b3cfd70",
+ "@id": "urn:fsltsplo-kJvjcgIP",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png",
"Used": [
- "urn:063be7f7-a32c-4d48-b5a4-fbe6cecd07c3"
+ "bids::prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms"
]
},
{
- "@id": "urn:2d5ccef6-0f80-48b9-925a-36720b12df94",
+ "@id": "urn:fslmaths-xN4svDa6",
"Label": "fslmaths",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func",
"Used": [
- "urn:04cf21b4-d8f2-416b-91dc-098aaede3b3b"
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:5c9bd078-6db8-4b60-b5e2-aff1b54efc40",
+ "@id": "urn:bet2-dCRCwC4Q",
"Label": "bet2",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/usr/local/packages/fsl-5.0.10/bin/bet2 mean_func mask -f 0.3 -n -m",
"Used": [
- "urn:434ccaa0-1c21-4718-9ca3-4659154e28cd"
+ "bids::mean_func"
]
},
{
- "@id": "urn:260b6abf-d0ed-41b7-9357-f4dd9ad1d5c7",
+ "@id": "urn:immv-rj6XOp5N",
"Label": "immv",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/usr/local/packages/fsl-5.0.10/bin/immv mask_mask mask",
"Used": [
- "urn:7432af95-c46f-44b9-95d5-3ae073e9ad67"
+ "bids::mask_mask"
]
},
{
- "@id": "urn:89c4e160-0920-4f79-8e68-1b551e450cfd",
+ "@id": "urn:fslmaths-uHMcxkxd",
"Label": "fslmaths",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet",
"Used": [
- "urn:04cf21b4-d8f2-416b-91dc-098aaede3b3b",
- "urn:2140f53b-4cd5-4241-a26a-b5784ee52d7c"
+ "bids::mask",
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:5fef3b34-c5f1-40d0-9aea-2f73c630a76d",
+ "@id": "urn:fslstats-v3Akthn6",
"Label": "fslstats",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_bet -p 2 -p 98",
"Used": [
- "urn:324e8c1b-67a7-4216-8461-2cc4d2493a0d"
+ "bids::prefiltered_func_data_bet"
]
},
{
- "@id": "urn:4e8d8c44-d8ce-416c-affc-54c861d69d74",
+ "@id": "urn:fslmaths-9NPek5gf",
"Label": "fslmaths",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_bet -thr 74.4585571 -Tmin -bin mask -odt char",
"Used": [
- "urn:324e8c1b-67a7-4216-8461-2cc4d2493a0d"
+ "bids::prefiltered_func_data_bet"
]
},
{
- "@id": "urn:c5769ca5-ef3b-4107-a8bf-68949d5efc1d",
+ "@id": "urn:fslstats-xvXfXEBP",
"Label": "fslstats",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_mcf -k mask -p 50",
"Used": [
- "urn:04cf21b4-d8f2-416b-91dc-098aaede3b3b"
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:819c043e-ead2-4552-8e12-041ff73e323f",
+ "@id": "urn:fslmaths-OgFigMP9",
"Label": "fslmaths",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -dilF mask",
"Used": [
- "urn:2140f53b-4cd5-4241-a26a-b5784ee52d7c"
+ "bids::mask"
]
},
{
- "@id": "urn:b03f2346-70cd-49f6-a995-232920cbf408",
+ "@id": "urn:fslmaths-JDkXh2Ek",
"Label": "fslmaths",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh",
"Used": [
- "urn:04cf21b4-d8f2-416b-91dc-098aaede3b3b",
- "urn:2140f53b-4cd5-4241-a26a-b5784ee52d7c"
+ "bids::mask",
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:96f5bf66-b838-41b0-9eb6-9bf8e0a1fd0a",
+ "@id": "urn:fslmaths-6tB3QPvV",
"Label": "fslmaths",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func",
"Used": [
- "urn:476c572f-a2bc-434d-9299-303b612766fb"
+ "bids::prefiltered_func_data_thresh"
]
},
{
- "@id": "urn:a8876dcf-5b2e-4d0f-9559-26f088731cff",
+ "@id": "urn:susan-yEISM3Bq",
"Label": "susan",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/usr/local/packages/fsl-5.0.10/bin/susan prefiltered_func_data_thresh 445.8289035 2.54777070064 3 1 1 mean_func 445.8289035 prefiltered_func_data_smooth",
"Used": [
- "urn:476c572f-a2bc-434d-9299-303b612766fb"
+ "bids::prefiltered_func_data_thresh"
]
},
{
- "@id": "urn:5153bb2a-e317-45d6-b735-34a7e7e4ed70",
+ "@id": "urn:fslmaths-i8mmZH4R",
"Label": "fslmaths",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth",
"Used": [
- "urn:2140f53b-4cd5-4241-a26a-b5784ee52d7c",
- "urn:6855557e-cac2-4c2c-8f4c-99dc46c313da"
+ "bids::mask",
+ "bids::prefiltered_func_data_smooth"
]
},
{
- "@id": "urn:18b46de4-cda4-45c6-8b8c-a772424da1c8",
+ "@id": "urn:fslmaths-8mVq8ArW",
"Label": "fslmaths",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mul 16.8225970571 prefiltered_func_data_intnorm",
"Used": [
- "urn:6855557e-cac2-4c2c-8f4c-99dc46c313da"
+ "bids::prefiltered_func_data_smooth"
]
},
{
- "@id": "urn:fb4e2311-201d-4500-bfed-86410f92c0fe",
+ "@id": "urn:fslmaths-PxrisfAb",
"Label": "fslmaths",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean",
"Used": [
- "urn:9b8d1d9b-abd7-4aa3-969f-7bfe9ca49bf9"
+ "bids::prefiltered_func_data_intnorm"
]
},
{
- "@id": "urn:38783393-8687-499e-af74-4c389b7a07f8",
+ "@id": "urn:fslmaths-dEwDEqMs",
"Label": "fslmaths",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -bptf 15.0 -1 -add tempMean prefiltered_func_data_tempfilt",
"Used": [
- "urn:9b8d1d9b-abd7-4aa3-969f-7bfe9ca49bf9",
- "urn:aa937459-3615-478b-9878-ca3f30fbd2db"
+ "bids::prefiltered_func_data_intnorm",
+ "bids::tempMean"
]
},
{
- "@id": "urn:94ada5b6-7c58-4d21-ace8-a7427a655b89",
+ "@id": "urn:imrm-9EqLmaK5",
"Label": "imrm",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/usr/local/packages/fsl-5.0.10/bin/imrm tempMean",
"Used": [
- "urn:aa937459-3615-478b-9878-ca3f30fbd2db"
+ "bids::tempMean"
]
},
{
- "@id": "urn:02bac1d5-5bff-45e9-af9e-bd8cb8544e48",
+ "@id": "urn:fslmaths-ZNc1S4EG",
"Label": "fslmaths",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data",
"Used": [
- "urn:a5aa38fd-d304-44a9-92b2-14f06c963626"
+ "bids::prefiltered_func_data_tempfilt"
]
},
{
- "@id": "urn:03155384-991a-4f87-b1f4-b56ea90b5ccb",
+ "@id": "urn:fslmaths-b1QMiBd0",
"Label": "fslmaths",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths filtered_func_data -Tmean mean_func",
"Used": [
- "urn:6158b642-a0ac-4038-948f-738eaa9fd738"
+ "bids::filtered_func_data"
]
},
{
- "@id": "urn:7687e560-68ce-415d-abaa-18a1c6b032df",
+ "@id": "urn:rm-HbfJKC7Y",
"Label": "rm",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/bin/rm -rf prefiltered_func_data*",
"Used": [
- "urn:dc81bcc2-7d97-408d-91ba-5edf765cf2c7"
+ "bids::prefiltered_func_data*"
]
},
{
- "@id": "urn:aef87910-bf4c-4baf-b74b-862b0f9916e6",
+ "@id": "urn:makedire-nIMQRQkl",
"Label": "Make directory",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
- "@id": "urn:e491e8a4-7a73-446f-a215-8fd224c0788f",
+ "@id": "urn:fslfixte-bHzmy5Rc",
"Label": "fslFixText",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
"Used": [
- "urn:9d0204dd-562e-4760-ae27-0eabbfb6c2e7"
+ "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt"
]
},
{
- "@id": "urn:66e9a593-4c31-41b9-95f3-d37201741051",
+ "@id": "urn:makedire-uK8ar6PC",
"Label": "Make directory",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
- "@id": "urn:60181192-775f-4634-98d3-66d692c27341",
+ "@id": "urn:fslfixte-UK3whvWC",
"Label": "fslFixText",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
"Used": [
- "urn:f3920868-80ba-4883-a1b3-ab0fb63e9d35"
+ "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt"
]
},
{
- "@id": "urn:89e608d8-2eb1-437b-a979-248aa6bb8bfb",
+ "@id": "urn:filmgls-4inTDGsm",
"Label": "film_gls",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con",
- "Used": []
+ "Used": [
+ "bids::design.con",
+ "bids::design.mat",
+ "bids::filtered_func_data",
+ "bids::stats"
+ ]
},
{
- "@id": "urn:cb25ef56-6a4a-4fd5-8796-a09c2ecc1733",
+ "@id": "urn:smoothes-y9B7AsN0",
"Label": "smoothest",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 102 -m mask -r stats/res4d > stats/smoothness",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 102 -m mask -r stats/res4d > stats/smoothness",
"Used": [
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- "urn:66a6c02a-7aed-4920-a165-fbbbefe73c7f"
+ "bids::mask",
+ "bids::stats/res4d"
]
},
{
- "@id": "urn:55c66188-f142-4cf4-a2ff-f4c281fa69b6",
+ "@id": "urn:fslmaths-AOfrEHao",
"Label": "fslmaths",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1",
"Used": [
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- "urn:a9b05b37-91c1-4fc8-8744-6d437d5ca73b"
+ "bids::mask",
+ "bids::stats/zstat1"
]
},
{
- "@id": "urn:bf6e9b43-33c5-4777-addd-1b726f712d5e",
+ "@id": "urn:echo-mE5BoYda",
"Label": "echo",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "echo 38352 > thresh_zstat1.vol",
"Used": []
},
{
- "@id": "urn:f30b3e68-c42c-4cf2-b4a2-3662c40763a4",
+ "@id": "urn:ptoz-PLLGjThF",
"Label": "ptoz",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:45320a4c-88f2-4d46-aab7-8f2ed1459d9a",
+ "@id": "urn:cluster-UwBXCmUj",
"Label": "cluster",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -t 3.090232 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z --voxuncthresh -c stats/cope1 > cluster_zstat1.txt",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -t 3.090232 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z --voxuncthresh -c stats/cope1 > cluster_zstat1.txt",
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- "urn:041ab7bf-20d1-46ca-aafa-ff46b15bf8d2",
- "urn:79638e82-9f85-4be7-b17a-4a2cce96034c"
+ "bids::stats/cope1",
+ "bids::thresh_zstat1"
]
},
{
- "@id": "urn:b0be6445-9afb-4e3f-a7c1-33449fd2a793",
+ "@id": "urn:cluster2-0MFqmsA1",
"Label": "cluster2html",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat1",
"Used": [
- "urn:b236da14-0060-43c1-8ae8-a2ca27c4743a"
+ "bids::cluster_zstat1"
]
},
{
- "@id": "urn:84a84eaa-0c31-43ce-9cf0-399b5f70f147",
+ "@id": "urn:fslstats-96CGPa1j",
"Label": "fslstats",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat1 -l 0.0001 -R 2>/dev/null",
"Used": [
- "urn:041ab7bf-20d1-46ca-aafa-ff46b15bf8d2"
+ "bids::thresh_zstat1"
]
},
{
- "@id": "urn:8d7109c7-7ffa-45f0-be88-19d8cf59f902",
+ "@id": "urn:overlay-0XOXZytD",
"Label": "overlay",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat1 3.090524 7.488793 rendered_thresh_zstat1",
"Used": []
},
{
- "@id": "urn:35c1f502-94fe-4cbc-aef7-63f633acd45e",
+ "@id": "urn:slicer-naOf7SVy",
"Label": "slicer",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat1 -A 750 rendered_thresh_zstat1.png",
"Used": [
- "urn:4cc74bde-de10-4407-9512-a9c834be1ceb"
+ "bids::rendered_thresh_zstat1"
]
},
{
- "@id": "urn:9d3714d6-1102-4f17-acbb-5753b73a730a",
+ "@id": "urn:cp-oC4qeHWI",
"Label": "cp",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/bin/cp /usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif .ramp.gif",
"Used": [
- "urn:4a529a6f-ea0b-4554-b924-20f9e84a6d17"
+ "bids::/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif"
]
},
{
- "@id": "urn:0823c534-eb6d-474b-bb65-02c92e9c5d39",
+ "@id": "urn:makedire-0SY3kjho",
"Label": "Make directory",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "mkdir -p tsplot",
"Used": []
},
{
- "@id": "urn:d9243bae-0e1c-48ea-b2b8-d670ffa89dcd",
+ "@id": "urn:tsplot-BPGsLPU3",
"Label": "tsplot",
- "AssociatedWith": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
+ "AssociatedWith": "urn:fsl-E4ALjxdM",
"Command": "/usr/local/packages/fsl-5.0.10/bin/tsplot . -f filtered_func_data -o tsplot",
"Used": []
}
],
"Entities": [
{
- "@id": "urn:3452a9ca-42b6-4997-bcca-cfb7b55db048",
+ "@id": "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold",
"Label": "sub-01_task-tonecounting_bold",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold",
+ "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold",
"digest": {
- "sha256": "028adf00daa36e78f06a61dcd3cb3526cd8564c1284e80516ab5520701324ac1"
+ "sha256": "33501604ae140e58832facff473a9578d5a549403bdbec53107d2b3eaab898ee"
}
},
{
- "@id": "urn:8e066908-75d0-41b0-a0cf-9685bf3a5785",
+ "@id": "bids::prefiltered_func_data",
"Label": "prefiltered_func_data",
"AtLocation": "prefiltered_func_data",
- "GeneratedBy": "urn:b00d4ecd-cbf3-4779-a8bf-ad46c28ae579",
+ "GeneratedBy": "urn:fslmaths-fcSIwVMX",
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}
},
{
- "@id": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "@id": "bids::example_func",
"Label": "example_func",
"AtLocation": "example_func",
- "GeneratedBy": "urn:a97cc948-6aa2-425a-b953-f1d83ceed350",
+ "GeneratedBy": "urn:fslroi-OG3P6KqD",
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},
{
- "@id": "urn:5f833946-20fb-421f-bad6-7314076eefc9",
+ "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/example_func.nii.gz",
"Label": "example_func.nii.gz",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/example_func.nii.gz",
"digest": {
@@ -580,15 +589,15 @@
}
},
{
- "@id": "urn:f0341414-568b-486a-a4d1-510de6bfe1df",
+ "@id": "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
"Label": "sub-01_T1w_brain",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
+ "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
"digest": {
- "sha256": "ccb9a4d1def67002e358c45bd912034053ffc221ab52c2a19aa55f72c3236279"
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}
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{
- "@id": "urn:664b43fb-669a-401f-ae8b-84fe61d94430",
+ "@id": "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain",
"Label": "MNI152_T1_2mm_brain",
"AtLocation": "/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain",
"digest": {
@@ -596,45 +605,57 @@
}
},
{
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+ "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat",
"Label": "fsl_voxelwise_p0001.feat",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat",
- "GeneratedBy": "urn:7567208c-e138-45bd-92fd-e04cbbbe5798"
+ "GeneratedBy": "urn:mainfeat-DMP0PTOA"
},
{
- "@id": "urn:b21e6503-bf58-4c64-af2c-a7dd75598c0b",
+ "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/reg",
"Label": "reg",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/reg",
- "GeneratedBy": "urn:2f4ce27c-6f45-4c41-b2f6-5c56cd245544",
+ "GeneratedBy": "urn:makedire-BYrQI1M0",
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}
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{
- "@id": "urn:9fa885f9-9119-4a5a-a21f-c08970524468",
+ "@id": "bids::highres",
"Label": "highres",
"AtLocation": "highres",
- "GeneratedBy": "urn:06bc5b94-8010-4257-9815-dade77c76107",
+ "GeneratedBy": "urn:fslmaths-wMZbWTyd",
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- "@id": "urn:d53e0107-1254-40e5-86e7-d8d9c3e13410",
+ "@id": "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
"Label": "sub-01_T1w",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
+ "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
"digest": {
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- "Label": "",
- "AtLocation": "",
- "GeneratedBy": "urn:0aef9850-8080-416b-b56e-b15d2f9b7ad3"
+ "@id": "bids::highres_head",
+ "Label": "highres_head",
+ "AtLocation": "highres_head",
+ "GeneratedBy": "urn:fslmaths-Ddt8tGbY",
+ "digest": {
+ "sha256": "590f180bade23162ef1567a5a61d86ee93155e4c7dc59c04c8ac5d6b7a20ea51"
+ }
+ },
+ {
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+ "Label": "example_func2highres",
+ "AtLocation": "example_func2highres",
+ "GeneratedBy": "urn:epireg-H7ZIk7pS",
+ "digest": {
+ "sha256": "00c021d82b83d2dc562c77f76528ece0f7425d4982f292f22021467afce1ba59"
+ }
},
{
- "@id": "urn:a06f1142-ca51-461c-a20f-80e2f40ffb15",
+ "@id": "bids::example_func2highres.mat",
"Label": "example_func2highres.mat",
"AtLocation": "example_func2highres.mat",
"digest": {
@@ -642,267 +663,259 @@
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},
{
- "@id": "urn:f15dc3f1-5707-4d5e-af3f-7650223df45c",
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"AtLocation": "highres2example_func.mat",
- "GeneratedBy": "urn:06b5a9d8-853c-4b4e-977e-d596dc959c46",
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"Label": "sla.png",
"AtLocation": "sla.png",
- "GeneratedBy": "urn:e3ee0fd1-763c-4aa9-a09a-de1c91eadfac",
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{
- "@id": "urn:0f8fdd76-c020-44cd-8b51-47396be17e01",
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"Label": "slc.png",
"AtLocation": "slc.png",
- "GeneratedBy": "urn:e3ee0fd1-763c-4aa9-a09a-de1c91eadfac",
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{
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"AtLocation": "sld.png",
- "GeneratedBy": "urn:e3ee0fd1-763c-4aa9-a09a-de1c91eadfac",
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"Label": "sle.png",
"AtLocation": "sle.png",
- "GeneratedBy": "urn:e3ee0fd1-763c-4aa9-a09a-de1c91eadfac",
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- "GeneratedBy": "urn:e3ee0fd1-763c-4aa9-a09a-de1c91eadfac",
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"AtLocation": "example_func2highres1.png",
- "GeneratedBy": "urn:fabf4f69-def8-49d7-9611-c11f35a72be7",
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{
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"Label": "sla.png",
"AtLocation": "sla.png",
- "GeneratedBy": "urn:ff437011-9364-42c4-a64d-7a8b7a8562eb",
+ "GeneratedBy": "urn:slicer-sJLXpGr2",
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{
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"Label": "slb.png",
"AtLocation": "slb.png",
- "GeneratedBy": "urn:ff437011-9364-42c4-a64d-7a8b7a8562eb",
+ "GeneratedBy": "urn:slicer-sJLXpGr2",
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}
},
{
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"Label": "slc.png",
"AtLocation": "slc.png",
- "GeneratedBy": "urn:ff437011-9364-42c4-a64d-7a8b7a8562eb",
+ "GeneratedBy": "urn:slicer-sJLXpGr2",
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}
},
{
- "@id": "urn:88bd7bdd-d84f-40ba-8642-3b33286e3b08",
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"Label": "sld.png",
"AtLocation": "sld.png",
- "GeneratedBy": "urn:ff437011-9364-42c4-a64d-7a8b7a8562eb",
+ "GeneratedBy": "urn:slicer-sJLXpGr2",
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}
},
{
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"Label": "sle.png",
"AtLocation": "sle.png",
- "GeneratedBy": "urn:ff437011-9364-42c4-a64d-7a8b7a8562eb",
+ "GeneratedBy": "urn:slicer-sJLXpGr2",
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}
},
{
- "@id": "urn:0ac4c5e7-ef2f-4c18-93bc-177e5bfdbbe5",
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"Label": "slf.png",
"AtLocation": "slf.png",
- "GeneratedBy": "urn:ff437011-9364-42c4-a64d-7a8b7a8562eb",
+ "GeneratedBy": "urn:slicer-sJLXpGr2",
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}
},
{
- "@id": "urn:40d6c7e1-b118-42af-a335-aa54bb525b5c",
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- "GeneratedBy": "urn:ff437011-9364-42c4-a64d-7a8b7a8562eb",
+ "GeneratedBy": "urn:slicer-sJLXpGr2",
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}
},
{
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- "GeneratedBy": "urn:ff437011-9364-42c4-a64d-7a8b7a8562eb",
+ "GeneratedBy": "urn:slicer-sJLXpGr2",
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}
},
{
- "@id": "urn:f586b952-902c-42fb-8138-8f3c80d36894",
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- "GeneratedBy": "urn:ff437011-9364-42c4-a64d-7a8b7a8562eb",
+ "GeneratedBy": "urn:slicer-sJLXpGr2",
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}
},
{
- "@id": "urn:4f09e262-ab47-40a8-9125-735ddc3b6a09",
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"AtLocation": "slj.png",
- "GeneratedBy": "urn:ff437011-9364-42c4-a64d-7a8b7a8562eb",
+ "GeneratedBy": "urn:slicer-sJLXpGr2",
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}
},
{
- "@id": "urn:618abbfe-0696-4bc2-9baf-0a6b4493c230",
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"AtLocation": "slk.png",
- "GeneratedBy": "urn:ff437011-9364-42c4-a64d-7a8b7a8562eb",
+ "GeneratedBy": "urn:slicer-sJLXpGr2",
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}
},
{
- "@id": "urn:96b1d1ae-8e5f-45b6-89c4-bf5532a8ae74",
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"Label": "sll.png",
"AtLocation": "sll.png",
- "GeneratedBy": "urn:ff437011-9364-42c4-a64d-7a8b7a8562eb",
+ "GeneratedBy": "urn:slicer-sJLXpGr2",
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}
},
{
- "@id": "urn:5b6ece1d-f451-442f-a3c6-c9f484150172",
+ "@id": "bids::example_func2highres2.png",
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"AtLocation": "example_func2highres2.png",
- "GeneratedBy": "urn:ed65319b-bef9-45d6-9ef4-1d7df77a0226",
+ "GeneratedBy": "urn:pngappen-RUvG0ImG",
"digest": {
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}
},
{
- "@id": "urn:75e04324-713b-4e74-9e24-6ff65cdf32c7",
+ "@id": "bids::example_func2highres.png",
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"AtLocation": "example_func2highres.png",
- "GeneratedBy": "urn:0617f869-1d93-49de-8802-eebcca654cec",
+ "GeneratedBy": "urn:pngappen-FtOA4j1l",
"digest": {
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}
},
{
- "@id": "urn:c7abed1c-541a-416f-a69b-7d91ad6de028",
+ "@id": "bids::sl?.png",
"Label": "sl?.png",
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"digest": {
@@ -910,25 +923,25 @@
}
},
{
- "@id": "urn:04cf21b4-d8f2-416b-91dc-098aaede3b3b",
+ "@id": "bids::prefiltered_func_data_mcf",
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"AtLocation": "prefiltered_func_data_mcf",
- "GeneratedBy": "urn:e2444068-c742-4dd1-84c7-0641984fb6d9",
+ "GeneratedBy": "urn:mcflirt-psopAuVm",
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},
{
- "@id": "urn:ae0d63b9-8eea-4635-a229-46d0e077f4f6",
+ "@id": "bids::mc",
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"AtLocation": "mc",
- "GeneratedBy": "urn:43063405-3837-4669-9cc4-0ae7fb24aa6c",
+ "GeneratedBy": "urn:makedire-4wMbJbeY",
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}
},
{
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+ "@id": "bids::prefiltered_func_data_mcf.mat",
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"AtLocation": "prefiltered_func_data_mcf.mat",
"digest": {
@@ -936,7 +949,7 @@
}
},
{
- "@id": "urn:d6c4bcf4-12c5-438c-9367-b4d2d5946dfe",
+ "@id": "bids::prefiltered_func_data_mcf.par",
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"AtLocation": "prefiltered_func_data_mcf.par",
"digest": {
@@ -944,7 +957,7 @@
}
},
{
- "@id": "urn:8b99de74-04a3-4a04-ab08-a2af09fa3473",
+ "@id": "bids::prefiltered_func_data_mcf_abs.rms",
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"AtLocation": "prefiltered_func_data_mcf_abs.rms",
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@@ -952,7 +965,7 @@
}
},
{
- "@id": "urn:1b69e3f5-5564-4aa3-a5c9-de11f6e13e18",
+ "@id": "bids::prefiltered_func_data_mcf_abs_mean.rms",
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"AtLocation": "prefiltered_func_data_mcf_abs_mean.rms",
"digest": {
@@ -960,7 +973,7 @@
}
},
{
- "@id": "urn:1b7afc2f-569a-4de1-b8e4-aa3e690095ca",
+ "@id": "bids::prefiltered_func_data_mcf_rel.rms",
"Label": "prefiltered_func_data_mcf_rel.rms",
"AtLocation": "prefiltered_func_data_mcf_rel.rms",
"digest": {
@@ -968,7 +981,7 @@
}
},
{
- "@id": "urn:571d1fdc-8ad5-4ae2-8dbe-bfb8d5bee9e0",
+ "@id": "bids::prefiltered_func_data_mcf_rel_mean.rms",
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"AtLocation": "prefiltered_func_data_mcf_rel_mean.rms",
"digest": {
@@ -976,34 +989,34 @@
}
},
{
- "@id": "urn:8583371c-165f-4916-a2d0-062b019d96bd",
+ "@id": "bids::mc",
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- "GeneratedBy": "urn:6011531f-aa09-47ce-a04f-e5201123c5a8",
+ "GeneratedBy": "urn:mv-5vMsPN6O",
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}
},
{
- "@id": "urn:09188984-37c7-42dd-882b-24f9abaaaaea",
+ "@id": "bids::rot.png",
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- "GeneratedBy": "urn:0f4a4e05-e37b-4628-96fe-b0474b7d5184",
+ "GeneratedBy": "urn:fsltsplo-VAnxKfBU",
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}
},
{
- "@id": "urn:55491742-f275-45e3-b023-a7f53aaae248",
+ "@id": "bids::trans.png",
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"AtLocation": "trans.png",
- "GeneratedBy": "urn:9096b2e5-fbcf-4047-a54e-8a5c2aeb68a4",
+ "GeneratedBy": "urn:fsltsplo-mhaEcLEl",
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}
},
{
- "@id": "urn:063be7f7-a32c-4d48-b5a4-fbe6cecd07c3",
+ "@id": "bids::prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
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"digest": {
@@ -1011,34 +1024,34 @@
}
},
{
- "@id": "urn:863b4ba4-307a-4bf6-9f3a-6e5cb31669ea",
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- "GeneratedBy": "urn:a51452a7-71ed-46f1-b3f9-63b70b3cfd70",
+ "GeneratedBy": "urn:fsltsplo-kJvjcgIP",
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}
},
{
- "@id": "urn:434ccaa0-1c21-4718-9ca3-4659154e28cd",
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"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:2d5ccef6-0f80-48b9-925a-36720b12df94",
+ "GeneratedBy": "urn:fslmaths-xN4svDa6",
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}
},
{
- "@id": "urn:2140f53b-4cd5-4241-a26a-b5784ee52d7c",
+ "@id": "bids::mask",
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"AtLocation": "mask",
- "GeneratedBy": "urn:5c9bd078-6db8-4b60-b5e2-aff1b54efc40",
+ "GeneratedBy": "urn:bet2-dCRCwC4Q",
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}
},
{
- "@id": "urn:7432af95-c46f-44b9-95d5-3ae073e9ad67",
+ "@id": "bids::mask_mask",
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"AtLocation": "mask_mask",
"digest": {
@@ -1046,132 +1059,124 @@
}
},
{
- "@id": "urn:998c136b-89ab-434d-a383-742a8fe2cce7",
+ "@id": "bids::mask",
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"AtLocation": "mask",
- "GeneratedBy": "urn:260b6abf-d0ed-41b7-9357-f4dd9ad1d5c7",
+ "GeneratedBy": "urn:immv-rj6XOp5N",
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}
},
{
- "@id": "urn:324e8c1b-67a7-4216-8461-2cc4d2493a0d",
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"AtLocation": "prefiltered_func_data_bet",
- "GeneratedBy": "urn:89c4e160-0920-4f79-8e68-1b551e450cfd",
+ "GeneratedBy": "urn:fslmaths-uHMcxkxd",
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}
},
{
- "@id": "urn:f19244b7-cdec-4f32-b146-f4960ae71b37",
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- "GeneratedBy": "urn:4e8d8c44-d8ce-416c-affc-54c861d69d74",
+ "GeneratedBy": "urn:fslmaths-9NPek5gf",
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}
},
{
- "@id": "urn:65818fda-55ce-49f1-8050-9d98c12d9a1f",
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- "GeneratedBy": "urn:819c043e-ead2-4552-8e12-041ff73e323f",
+ "GeneratedBy": "urn:fslmaths-OgFigMP9",
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}
},
{
- "@id": "urn:476c572f-a2bc-434d-9299-303b612766fb",
+ "@id": "bids::prefiltered_func_data_thresh",
"Label": "prefiltered_func_data_thresh",
"AtLocation": "prefiltered_func_data_thresh",
- "GeneratedBy": "urn:b03f2346-70cd-49f6-a995-232920cbf408",
+ "GeneratedBy": "urn:fslmaths-JDkXh2Ek",
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}
},
{
- "@id": "urn:c586e728-fcc7-4e86-b211-dfc2ab5d386c",
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"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:96f5bf66-b838-41b0-9eb6-9bf8e0a1fd0a",
+ "GeneratedBy": "urn:fslmaths-6tB3QPvV",
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}
},
{
- "@id": "urn:6855557e-cac2-4c2c-8f4c-99dc46c313da",
+ "@id": "bids::prefiltered_func_data_smooth",
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"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:a8876dcf-5b2e-4d0f-9559-26f088731cff",
+ "GeneratedBy": "urn:susan-yEISM3Bq",
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}
},
{
- "@id": "urn:3488314f-c550-4532-8db8-90bcec24624f",
+ "@id": "bids::prefiltered_func_data_smooth",
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"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:5153bb2a-e317-45d6-b735-34a7e7e4ed70",
+ "GeneratedBy": "urn:fslmaths-i8mmZH4R",
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}
},
{
- "@id": "urn:9b8d1d9b-abd7-4aa3-969f-7bfe9ca49bf9",
+ "@id": "bids::prefiltered_func_data_intnorm",
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"AtLocation": "prefiltered_func_data_intnorm",
- "GeneratedBy": "urn:18b46de4-cda4-45c6-8b8c-a772424da1c8",
+ "GeneratedBy": "urn:fslmaths-8mVq8ArW",
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}
},
{
- "@id": "urn:aa937459-3615-478b-9878-ca3f30fbd2db",
+ "@id": "bids::tempMean",
"Label": "tempMean",
"AtLocation": "tempMean",
- "GeneratedBy": "urn:fb4e2311-201d-4500-bfed-86410f92c0fe",
+ "GeneratedBy": "urn:fslmaths-PxrisfAb",
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{
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- {
- "@id": "urn:a5aa38fd-d304-44a9-92b2-14f06c963626",
+ "@id": "bids::prefiltered_func_data_tempfilt",
"Label": "prefiltered_func_data_tempfilt",
"AtLocation": "prefiltered_func_data_tempfilt",
+ "GeneratedBy": "urn:fslmaths-dEwDEqMs",
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}
},
{
- "@id": "urn:6158b642-a0ac-4038-948f-738eaa9fd738",
+ "@id": "bids::filtered_func_data",
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"AtLocation": "filtered_func_data",
- "GeneratedBy": "urn:02bac1d5-5bff-45e9-af9e-bd8cb8544e48",
+ "GeneratedBy": "urn:fslmaths-ZNc1S4EG",
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}
},
{
- "@id": "urn:4ac9e1cd-fcae-4c2e-87eb-e57eb4263733",
+ "@id": "bids::mean_func",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:03155384-991a-4f87-b1f4-b56ea90b5ccb",
+ "GeneratedBy": "urn:fslmaths-b1QMiBd0",
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}
},
{
- "@id": "urn:dc81bcc2-7d97-408d-91ba-5edf765cf2c7",
+ "@id": "bids::prefiltered_func_data*",
"Label": "prefiltered_func_data*",
"AtLocation": "prefiltered_func_data*",
"digest": {
@@ -1179,113 +1184,158 @@
}
},
{
- "@id": "urn:23f0145c-5038-48f3-923d-9dc25d3fba95",
+ "@id": "bids::custom_timing_files",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:aef87910-bf4c-4baf-b74b-862b0f9916e6",
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}
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{
- "@id": "urn:9d0204dd-562e-4760-ae27-0eabbfb6c2e7",
+ "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
"Label": "sub-01_tone_counting.txt",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
+ "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
"digest": {
- "sha256": "c120d27b9d5d81a91be0e55f5cb880b2cb7de6c655554d9c15c9c04c6232ea8e"
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}
},
{
- "@id": "urn:b96555f7-c09a-4102-82ac-6680fdd6e15f",
+ "@id": "bids::custom_timing_files/ev1.txt",
"Label": "ev1.txt",
"AtLocation": "custom_timing_files/ev1.txt",
- "GeneratedBy": "urn:e491e8a4-7a73-446f-a215-8fd224c0788f"
+ "GeneratedBy": "urn:fslfixte-bHzmy5Rc"
},
{
- "@id": "urn:7bd9021a-8ece-4eae-8527-15966a3238e0",
+ "@id": "bids::custom_timing_files",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:66e9a593-4c31-41b9-95f3-d37201741051",
+ "GeneratedBy": "urn:makedire-uK8ar6PC",
"digest": {
"sha256": "1d7e19792328d5040f2f9fb3c15d59de90fc771785f81c67039a043bd5f2ed20"
}
},
{
- "@id": "urn:f3920868-80ba-4883-a1b3-ab0fb63e9d35",
+ "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
"Label": "sub-01_tone_counting_probe.txt",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
+ "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
"digest": {
- "sha256": "f09eeb82fa0be8e8759a5269403f36ec2b7dbf2c5b6caba1f0f985cc6cb3f703"
+ "sha256": "8b912293767f1a5e082311f6aaf0c44fc91fe45b0f2ae7f80e368bc2f4c2918a"
}
},
{
- "@id": "urn:cea95345-35be-4d64-8df3-d28bc89704ac",
+ "@id": "bids::custom_timing_files/ev2.txt",
"Label": "ev2.txt",
"AtLocation": "custom_timing_files/ev2.txt",
- "GeneratedBy": "urn:60181192-775f-4634-98d3-66d692c27341"
+ "GeneratedBy": "urn:fslfixte-UK3whvWC"
},
{
- "@id": "urn:66a6c02a-7aed-4920-a165-fbbbefe73c7f",
- "Label": "res4d",
- "AtLocation": "stats/res4d",
+ "@id": "bids::stats",
+ "Label": "stats",
+ "AtLocation": "stats",
"digest": {
- "sha256": "8845286f36caedf891a02afddc4175ea46f18f830b59a8c5026962184a530699"
+ "sha256": "a9f3e135372514a16d11a8038262b3eff94ccd69a9b35c4724b2759cfc944a07"
}
},
{
- "@id": "urn:ff8dc197-561e-4ac9-8789-fe98fdd482fe",
- "Label": "smoothness",
- "AtLocation": "stats/smoothness",
- "GeneratedBy": "urn:cb25ef56-6a4a-4fd5-8796-a09c2ecc1733",
+ "@id": "bids::design.mat",
+ "Label": "design.mat",
+ "AtLocation": "design.mat",
"digest": {
- "sha256": "67b0aaf95a257beff60d331b56265034807ca51e67e2d312d481d5835ef0b1d0"
+ "sha256": "1c1a6ef59a355e1f6f81e741e157784ccbe066ba3594a07aa9b16781e3d5bb25"
}
},
{
- "@id": "urn:a9b05b37-91c1-4fc8-8744-6d437d5ca73b",
- "Label": "zstat1",
- "AtLocation": "stats/zstat1",
+ "@id": "bids::design.con",
+ "Label": "design.con",
+ "AtLocation": "design.con",
"digest": {
- "sha256": "70ae47cee1ea1d3f1f6f8aa7ac51f2641cb2fcb745dfd8cc54a389346e6fa094"
+ "sha256": "5808d1be37dd8f2a4906b710bb384fbee62faa4a46b2bc6847afc8962ed4eb54"
}
},
{
- "@id": "urn:041ab7bf-20d1-46ca-aafa-ff46b15bf8d2",
+ "@id": "bids::stats",
+ "Label": "stats",
+ "AtLocation": "stats",
+ "GeneratedBy": "urn:filmgls-4inTDGsm",
+ "digest": {
+ "sha256": "a9f3e135372514a16d11a8038262b3eff94ccd69a9b35c4724b2759cfc944a07"
+ }
+ },
+ {
+ "@id": "bids::stats/res4d",
+ "Label": "res4d",
+ "AtLocation": "stats/res4d"
+ },
+ {
+ "@id": "bids::stats/smoothness",
+ "Label": "smoothness",
+ "AtLocation": "stats/smoothness",
+ "GeneratedBy": "urn:smoothes-y9B7AsN0"
+ },
+ {
+ "@id": "bids::stats/zstat1",
+ "Label": "zstat1",
+ "AtLocation": "stats/zstat1"
+ },
+ {
+ "@id": "bids::thresh_zstat1",
"Label": "thresh_zstat1",
"AtLocation": "thresh_zstat1",
- "GeneratedBy": "urn:55c66188-f142-4cf4-a2ff-f4c281fa69b6",
+ "GeneratedBy": "urn:fslmaths-AOfrEHao",
"digest": {
"sha256": "662e7ba670e124d15bb3cc18b818868f76604578034b524c8882f35fc5db413f"
}
},
{
- "@id": "urn:79638e82-9f85-4be7-b17a-4a2cce96034c",
+ "@id": "bids::stats/cope1",
"Label": "cope1",
- "AtLocation": "stats/cope1",
- "digest": {
- "sha256": "bf3b603569da6dbe3d6f0e8667d346f3ac943c9d01d2fc9743ce17abeb1547fb"
- }
+ "AtLocation": "stats/cope1"
},
{
- "@id": "urn:e8d672f1-86f4-413e-839c-28b56632cd75",
+ "@id": "bids::cluster_mask_zstat1",
"Label": "cluster_mask_zstat1",
"AtLocation": "cluster_mask_zstat1",
- "GeneratedBy": "urn:45320a4c-88f2-4d46-aab7-8f2ed1459d9a",
+ "GeneratedBy": "urn:cluster-UwBXCmUj",
"digest": {
"sha256": "b28c170e33d2917cac55183786616a9e976e5e7f30dc7c8666341f12ed6d0277"
}
},
{
- "@id": "urn:b572d524-8479-4dc8-8805-c1cae356fc84",
+ "@id": "bids::thresh_zstat1",
+ "Label": "thresh_zstat1",
+ "AtLocation": "thresh_zstat1",
+ "GeneratedBy": "urn:cluster-UwBXCmUj",
+ "digest": {
+ "sha256": "662e7ba670e124d15bb3cc18b818868f76604578034b524c8882f35fc5db413f"
+ }
+ },
+ {
+ "@id": "bids::lmax_zstat1.txt",
+ "Label": "lmax_zstat1.txt",
+ "AtLocation": "lmax_zstat1.txt",
+ "GeneratedBy": "urn:cluster-UwBXCmUj",
+ "digest": {
+ "sha256": "d44ee21719775397a1a95ede6778d25404b50e8bd259dbdf02d2fde635fc81a5"
+ }
+ },
+ {
+ "@id": "bids::stats/cope1",
"Label": "cope1",
"AtLocation": "stats/cope1",
- "GeneratedBy": "urn:45320a4c-88f2-4d46-aab7-8f2ed1459d9a",
+ "GeneratedBy": "urn:cluster-UwBXCmUj"
+ },
+ {
+ "@id": "bids::cluster_zstat1.txt",
+ "Label": "cluster_zstat1.txt",
+ "AtLocation": "cluster_zstat1.txt",
+ "GeneratedBy": "urn:cluster-UwBXCmUj",
"digest": {
- "sha256": "bf3b603569da6dbe3d6f0e8667d346f3ac943c9d01d2fc9743ce17abeb1547fb"
+ "sha256": "b06695ff4f0a8158fa439b1ddf224b58d344606d400885c177390d09506e8e4c"
}
},
{
- "@id": "urn:b236da14-0060-43c1-8ae8-a2ca27c4743a",
+ "@id": "bids::cluster_zstat1",
"Label": "cluster_zstat1",
"AtLocation": "cluster_zstat1",
"digest": {
@@ -1293,25 +1343,25 @@
}
},
{
- "@id": "urn:4cc74bde-de10-4407-9512-a9c834be1ceb",
+ "@id": "bids::rendered_thresh_zstat1",
"Label": "rendered_thresh_zstat1",
"AtLocation": "rendered_thresh_zstat1",
- "GeneratedBy": "urn:8d7109c7-7ffa-45f0-be88-19d8cf59f902",
+ "GeneratedBy": "urn:overlay-0XOXZytD",
"digest": {
"sha256": "de5b9d44d95f4252f491eb45c76a0ae2b4d2c75b58664fc0df7d9153810c0bf6"
}
},
{
- "@id": "urn:826ddd27-db20-4698-866f-fc9f90a60588",
+ "@id": "bids::rendered_thresh_zstat1.png",
"Label": "rendered_thresh_zstat1.png",
"AtLocation": "rendered_thresh_zstat1.png",
- "GeneratedBy": "urn:35c1f502-94fe-4cbc-aef7-63f633acd45e",
+ "GeneratedBy": "urn:slicer-naOf7SVy",
"digest": {
"sha256": "15d6a8bf7a902df8c5feeb7468a3d0caacf9eb3067c0840c2f4763f5e2301527"
}
},
{
- "@id": "urn:4a529a6f-ea0b-4554-b924-20f9e84a6d17",
+ "@id": "bids::/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif",
"Label": "ramp.gif",
"AtLocation": "/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif",
"digest": {
@@ -1319,28 +1369,28 @@
}
},
{
- "@id": "urn:012b9ea7-02e5-4a39-b991-96afb57aff29",
+ "@id": "bids::.ramp.gif",
"Label": ".ramp.gif",
"AtLocation": ".ramp.gif",
- "GeneratedBy": "urn:9d3714d6-1102-4f17-acbb-5753b73a730a",
+ "GeneratedBy": "urn:cp-oC4qeHWI",
"digest": {
"sha256": "93f4284ccb854d5a41401d9360a13223017b67479cb289a33d83836922e028a4"
}
},
{
- "@id": "urn:2fe607fe-5996-4abd-b270-e284373a4352",
+ "@id": "bids::tsplot",
"Label": "tsplot",
"AtLocation": "tsplot",
- "GeneratedBy": "urn:0823c534-eb6d-474b-bb65-02c92e9c5d39",
+ "GeneratedBy": "urn:makedire-0SY3kjho",
"digest": {
"sha256": "2a74042f4edf02288edf16961307f741651efb4346e102a04b7603e781d1625e"
}
},
{
- "@id": "urn:aba7b203-7855-4289-bd83-d494632ab053",
+ "@id": "bids::tsplot",
"Label": "tsplot",
"AtLocation": "tsplot",
- "GeneratedBy": "urn:d9243bae-0e1c-48ea-b2b8-d670ffa89dcd",
+ "GeneratedBy": "urn:tsplot-BPGsLPU3",
"digest": {
"sha256": "2a74042f4edf02288edf16961307f741651efb4346e102a04b7603e781d1625e"
}
diff --git a/examples/from_parsers/fsl/fsl_default_report_log.png b/examples/from_parsers/fsl/fsl_default_report_log.png
index 120538861..1178741f0 100644
Binary files a/examples/from_parsers/fsl/fsl_default_report_log.png and b/examples/from_parsers/fsl/fsl_default_report_log.png differ
diff --git a/examples/from_parsers/fsl/fsl_full_examples001_report_log.jsonld b/examples/from_parsers/fsl/fsl_full_examples001_report_log.jsonld
index 553aa9939..f1821fc18 100644
--- a/examples/from_parsers/fsl/fsl_full_examples001_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_full_examples001_report_log.jsonld
@@ -4,758 +4,758 @@
"Records": {
"Software": [
{
- "@id": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:fsl-KLLV16PQ",
"@type": "prov:SoftwareAgent",
"Label": "FSL",
- "Version": "xxx"
+ "Version": "xxx",
+ "AltIdentifier": "RRID:SCR_002823"
}
],
"Activities": [
{
- "@id": "urn:8c85596f-7fa2-43b1-8a9d-e343dd1250dc",
+ "@id": "urn:fslmaths-b1MGvYNo",
"Label": "fslmaths",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/fslmaths /Users/cmaumet/Data/fsl_practicals/fsl_course_data/fmri/fmri_fluency/fmri prefiltered_func_data -odt float",
"Used": [
- "urn:4b6c76de-2ef4-4b43-8d3c-e6c0e5003853"
+ "bids::/Users/cmaumet/Data/fsl_practicals/fsl_course_data/fmri/fmri_fluency/fmri"
]
},
{
- "@id": "urn:6afdcda2-2b02-4320-acef-8b40a7b03680",
+ "@id": "urn:fslroi-pEfBZwC1",
"Label": "fslroi",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/fslroi prefiltered_func_data example_func 53 1",
"Used": [
- "urn:8992ddf0-b6d9-4da5-86ae-aae8b06bf498"
+ "bids::prefiltered_func_data"
]
},
{
- "@id": "urn:05ca7568-0ad0-495e-8456-fbc9ff878699",
+ "@id": "urn:mcflirt-KeW71fTO",
"Label": "mcflirt",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs",
"Used": [
- "urn:8992ddf0-b6d9-4da5-86ae-aae8b06bf498"
+ "bids::prefiltered_func_data"
]
},
{
- "@id": "urn:edc04ecc-b0d2-4ef2-9882-a31284993675",
+ "@id": "urn:makedire-QsOZPp7d",
"Label": "Make directory",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/bin/mkdir -p mc",
"Used": []
},
{
- "@id": "urn:e0181246-8e96-4072-b1d0-fa45343c01a2",
+ "@id": "urn:mv-iaHeHtFC",
"Label": "mv",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc",
"Used": [
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- "urn:579301fe-cc07-4b7e-9f44-f990d3d76bf5",
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- "urn:925c8d49-ab58-4373-8b9b-57ee08f09074",
- "urn:a50b87fb-4dad-4045-af1b-5fb7218f58f6",
- "urn:fa30e6eb-06b6-4084-8b84-2246196531dc"
+ "bids::prefiltered_func_data_mcf.mat",
+ "bids::prefiltered_func_data_mcf.par",
+ "bids::prefiltered_func_data_mcf_abs.rms",
+ "bids::prefiltered_func_data_mcf_abs_mean.rms",
+ "bids::prefiltered_func_data_mcf_rel.rms",
+ "bids::prefiltered_func_data_mcf_rel_mean.rms"
]
},
{
- "@id": "urn:859744a1-aec1-40a3-ad00-8006fdd1b111",
+ "@id": "urn:fsltsplo-B4QqMADr",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png",
"Used": [
- "urn:579301fe-cc07-4b7e-9f44-f990d3d76bf5"
+ "bids::prefiltered_func_data_mcf.par"
]
},
{
- "@id": "urn:bc2c5ca3-552a-4da0-9bd1-0c16a94c5ac2",
+ "@id": "urn:fsltsplo-PBP7q6Mm",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png",
"Used": [
- "urn:579301fe-cc07-4b7e-9f44-f990d3d76bf5"
+ "bids::prefiltered_func_data_mcf.par"
]
},
{
- "@id": "urn:a8c06dac-29ad-4202-b47d-c3852118ca61",
+ "@id": "urn:fsltsplo-FRGlfszX",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png",
"Used": [
- "urn:7b9b59ac-2c07-45fc-9bd2-6f3602b9c7d6"
+ "bids::prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms"
]
},
{
- "@id": "urn:bcd8bccb-c962-4602-bf5f-650419dcf0f2",
+ "@id": "urn:fslmaths-TFXrmtg1",
"Label": "fslmaths",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func",
"Used": [
- "urn:fbf7e4fe-124b-4f1f-8c16-6f23a9008267"
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:c4d758c0-3816-4dbd-b832-1268d95dba11",
+ "@id": "urn:bet2-906V4kHT",
"Label": "bet2",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/bet2 mean_func mask -f 0.3 -n -m",
"Used": [
- "urn:2c359c35-45bf-4507-9103-a3cb62eb98ab"
+ "bids::mean_func"
]
},
{
- "@id": "urn:be53f424-1517-47d3-9eb0-815c5bd21f4f",
+ "@id": "urn:immv-vs9RHb6O",
"Label": "immv",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/immv mask_mask mask",
"Used": [
- "urn:7badca47-0d69-4d41-ab15-65dd48fbfb3c"
+ "bids::mask_mask"
]
},
{
- "@id": "urn:49db383a-f7ce-4b02-b18a-301f09f8ca2e",
+ "@id": "urn:fslmaths-4fMxR2bm",
"Label": "fslmaths",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet",
"Used": [
- "urn:40f0ba7c-6c5e-41e3-be4d-cb51edc55892",
- "urn:fbf7e4fe-124b-4f1f-8c16-6f23a9008267"
+ "bids::mask",
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:c214ec58-1bf8-40cc-ad27-f64e3fab4f5f",
+ "@id": "urn:fslstats-4kMoZNWn",
"Label": "fslstats",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/fslstats prefiltered_func_data_bet -p 2 -p 98",
"Used": [
- "urn:f2efbcb4-3695-485f-8ac7-d1ef7a54cd5f"
+ "bids::prefiltered_func_data_bet"
]
},
{
- "@id": "urn:0f83ee71-21d4-4454-8c8e-38e6170a965d",
+ "@id": "urn:fslmaths-ZT26rDzN",
"Label": "fslmaths",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/fslmaths prefiltered_func_data_bet -thr 978.24375 -Tmin -bin mask -odt char",
"Used": [
- "urn:f2efbcb4-3695-485f-8ac7-d1ef7a54cd5f"
+ "bids::prefiltered_func_data_bet"
]
},
{
- "@id": "urn:fe869478-f885-406d-955b-bad539f054b8",
+ "@id": "urn:fslstats-C4Vkq7YG",
"Label": "fslstats",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/fslstats prefiltered_func_data_mcf -k mask -p 50",
"Used": [
- "urn:fbf7e4fe-124b-4f1f-8c16-6f23a9008267"
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:a44737d5-bbe8-45aa-bbda-e4e39c4fc2e4",
+ "@id": "urn:fslmaths-x3vBn14T",
"Label": "fslmaths",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/fslmaths mask -dilF mask",
"Used": [
- "urn:40f0ba7c-6c5e-41e3-be4d-cb51edc55892"
+ "bids::mask"
]
},
{
- "@id": "urn:f60325ef-133c-42ed-991d-cafc1d400a1c",
+ "@id": "urn:fslmaths-Ug4rV82p",
"Label": "fslmaths",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh",
"Used": [
- "urn:40f0ba7c-6c5e-41e3-be4d-cb51edc55892",
- "urn:fbf7e4fe-124b-4f1f-8c16-6f23a9008267"
+ "bids::mask",
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:1f93c51d-0af7-428b-87d0-7e9cb9f08dc1",
+ "@id": "urn:fslmaths-FtnR53jV",
"Label": "fslmaths",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func",
"Used": [
- "urn:f6ff0b38-f70a-4a10-b2da-eddaa63ba9d7"
+ "bids::prefiltered_func_data_thresh"
]
},
{
- "@id": "urn:0d20d783-5c33-47b9-acc0-d7c6c576fd63",
+ "@id": "urn:susan-FiFaiCkb",
"Label": "susan",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/susan prefiltered_func_data_thresh 5646.963501 2.97239915074 3 1 1 mean_func 5646.963501 prefiltered_func_data_smooth",
"Used": [
- "urn:f6ff0b38-f70a-4a10-b2da-eddaa63ba9d7"
+ "bids::prefiltered_func_data_thresh"
]
},
{
- "@id": "urn:bbc5cfa9-fc2a-4a19-b7cd-6eff9a5300b2",
+ "@id": "urn:fslmaths-USD6zrsf",
"Label": "fslmaths",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth",
"Used": [
- "urn:40f0ba7c-6c5e-41e3-be4d-cb51edc55892",
- "urn:514b6380-1b32-4118-8264-87546493d9db"
+ "bids::mask",
+ "bids::prefiltered_func_data_smooth"
]
},
{
- "@id": "urn:a88fe79f-9c31-48c7-a3fd-d9aa03416151",
+ "@id": "urn:fslmaths-DFXryZ4N",
"Label": "fslmaths",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/fslmaths prefiltered_func_data_smooth -mul 1.32814741917 prefiltered_func_data_intnorm",
"Used": [
- "urn:514b6380-1b32-4118-8264-87546493d9db"
+ "bids::prefiltered_func_data_smooth"
]
},
{
- "@id": "urn:62757c28-bbaf-44ef-b41d-fba68148f8c4",
+ "@id": "urn:fslmaths-YuhXjVaO",
"Label": "fslmaths",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/fslmaths prefiltered_func_data_intnorm -bptf 227.142867456 -1 prefiltered_func_data_tempfilt",
"Used": [
- "urn:9977a87f-a67e-46c5-9208-6d52284bb1ee"
+ "bids::prefiltered_func_data_intnorm"
]
},
{
- "@id": "urn:13e01b1e-8691-4c67-8b2f-3f8a6a3dc9ec",
+ "@id": "urn:fslmaths-xst3I97I",
"Label": "fslmaths",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data",
"Used": [
- "urn:2906ce55-4d86-46f2-b57b-d2e79a77c30c"
+ "bids::prefiltered_func_data_tempfilt"
]
},
{
- "@id": "urn:876868d9-b90c-4dbe-b1c0-e8081a6b5783",
+ "@id": "urn:fslmaths-YKjFeGPL",
"Label": "fslmaths",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/fslmaths filtered_func_data -Tmean mean_func",
"Used": [
- "urn:b4ab62df-3021-4a35-890e-c262a04ac86d"
+ "bids::filtered_func_data"
]
},
{
- "@id": "urn:2fa48d2a-f515-483c-a7fe-9da4123ea66a",
+ "@id": "urn:rm-KPKJQj8H",
"Label": "rm",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/bin/rm -rf prefiltered_func_data*",
"Used": [
- "urn:b1dfae7b-a755-4880-bb1b-2943bb5dabe6"
+ "bids::prefiltered_func_data*"
]
},
{
- "@id": "urn:cf35254c-cfa1-47a4-b6fa-0bbfd48f1f2e",
+ "@id": "urn:makedire-hAAbGVmy",
"Label": "Make directory",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
- "@id": "urn:5f654627-6b77-4c10-801f-0e3ed2cfe857",
+ "@id": "urn:cp-YrEeSz3m",
"Label": "cp",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/bin/cp /Users/cmaumet/Data/fsl_practicals/fsl_course_data/fmri/fmri_fluency/word_generation.txt custom_timing_files/ev1.txt",
"Used": [
- "urn:80914d4d-105b-4df0-80a9-5532aa1c7b13"
+ "bids::/Users/cmaumet/Data/fsl_practicals/fsl_course_data/fmri/fmri_fluency/word_generation.txt"
]
},
{
- "@id": "urn:3681abf1-32d8-4428-a583-4af13b61f24e",
+ "@id": "urn:makedire-zbwFEzNw",
"Label": "Make directory",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
- "@id": "urn:c9dc2bf8-a857-4706-8d48-9f7f2939138e",
+ "@id": "urn:cp-EEjL6yrM",
"Label": "cp",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/bin/cp /Users/cmaumet/Data/fsl_practicals/fsl_course_data/fmri/fmri_fluency/word_shadowing.txt custom_timing_files/ev2.txt",
"Used": [
- "urn:1b6bc660-3002-4209-b970-2bf3816c16f7"
+ "bids::/Users/cmaumet/Data/fsl_practicals/fsl_course_data/fmri/fmri_fluency/word_shadowing.txt"
]
},
{
- "@id": "urn:e3b4c9b6-c534-42ec-b134-a78421c8db3e",
+ "@id": "urn:filmgls-tfojDd6j",
"Label": "film_gls",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
- "Command": "/usr/local/fsl/bin/film_gls -rn stats -sa -ms 5 filtered_func_data design.mat 1000.0",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
+ "Command": "/usr/local/fsl/bin/film_gls -rn stats -sa -ms 5 filtered_func_data design.mat 1000.0",
"Used": []
},
{
- "@id": "urn:4912dc91-d374-4b1e-b893-ce6cf0a9dc35",
+ "@id": "urn:smoothes-RtoGXcPI",
"Label": "smoothest",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
- "Command": "/usr/local/fsl/bin/smoothest -d 102 -m mask -r stats/res4d > stats/smoothness",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
+ "Command": "/usr/local/fsl/bin/smoothest -d 102 -m mask -r stats/res4d > stats/smoothness",
"Used": [
- "urn:40f0ba7c-6c5e-41e3-be4d-cb51edc55892",
- "urn:9244d50f-27f2-4a26-9f27-b728870aaefa"
+ "bids::mask",
+ "bids::stats/res4d"
]
},
{
- "@id": "urn:aa053e5f-cbc9-42d8-abb9-b90d70044136",
+ "@id": "urn:contrast-C2PVyL9l",
"Label": "contrast_mgr",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
- "Command": "/usr/local/fsl/bin/contrast_mgr stats design.con",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
+ "Command": "/usr/local/fsl/bin/contrast_mgr stats design.con",
"Used": []
},
{
- "@id": "urn:5e66964f-ad8f-467e-b290-2956f00ef1a2",
+ "@id": "urn:fslmaths-76xeGCWn",
"Label": "fslmaths",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1",
"Used": [
- "urn:40f0ba7c-6c5e-41e3-be4d-cb51edc55892",
- "urn:bc4d9994-b998-4c15-8449-cc186f703a55"
+ "bids::mask",
+ "bids::stats/zstat1"
]
},
{
- "@id": "urn:5c10fcbd-bf1a-4dec-8e9e-4731987020fa",
+ "@id": "urn:echo-zam482ZY",
"Label": "echo",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "echo 45203 > thresh_zstat1.vol",
"Used": []
},
{
- "@id": "urn:bed41a63-8c25-475e-8018-c427a0c00a64",
+ "@id": "urn:cluster-tD3guFw2",
"Label": "cluster",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
- "Command": "/usr/local/fsl/bin/cluster -i thresh_zstat1 -c stats/cope1 -t 2.3 -p 0.05 -d 0.384676 --volume=45203 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z > cluster_zstat1.txt",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
+ "Command": "/usr/local/fsl/bin/cluster -i thresh_zstat1 -c stats/cope1 -t 2.3 -p 0.05 -d 0.384676 --volume=45203 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z > cluster_zstat1.txt",
"Used": [
- "urn:4aa4cd22-277d-4275-a53e-46b3d6ae63b5",
- "urn:9d494e57-2f2f-4ae9-9cee-f3fbb0da1e60"
+ "bids::stats/cope1",
+ "bids::thresh_zstat1"
]
},
{
- "@id": "urn:4ed3ae31-2469-4eea-8d7d-094dbe725b35",
+ "@id": "urn:cluster2-EiOgSBEx",
"Label": "cluster2html",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/cluster2html . cluster_zstat1",
"Used": [
- "urn:fb75466c-ea45-4159-9173-2a92b7963d0a"
+ "bids::cluster_zstat1"
]
},
{
- "@id": "urn:007db657-ae51-471b-bb1e-28dc9722171b",
+ "@id": "urn:fslstats-eJ5UST56",
"Label": "fslstats",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/fslstats thresh_zstat1 -l 0.0001 -R 2>/dev/null",
"Used": [
- "urn:4aa4cd22-277d-4275-a53e-46b3d6ae63b5"
+ "bids::thresh_zstat1"
]
},
{
- "@id": "urn:b25b0cf7-454a-4187-8229-3fa17241cbe3",
+ "@id": "urn:overlay-mw6P2Yl8",
"Label": "overlay",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/overlay 1 0 example_func -a thresh_zstat1 2.300331 5.793015 rendered_thresh_zstat1",
"Used": []
},
{
- "@id": "urn:a6e8a9af-35b9-4280-a896-19c0ba402b50",
+ "@id": "urn:slicer-tqi5V4Rr",
"Label": "slicer",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/slicer rendered_thresh_zstat1 -A 750 rendered_thresh_zstat1.png",
"Used": [
- "urn:93a80c83-735c-49fe-a04f-eceeb9e9716c"
+ "bids::rendered_thresh_zstat1"
]
},
{
- "@id": "urn:d6fc59d7-169a-41aa-90eb-ac368da47367",
+ "@id": "urn:cp-85L9VfbN",
"Label": "cp",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/bin/cp /usr/local/fsl/etc/luts/ramp.gif .ramp.gif",
"Used": [
- "urn:77fed1bd-e7f7-40bf-b2fc-4db30628b65e"
+ "bids::/usr/local/fsl/etc/luts/ramp.gif"
]
},
{
- "@id": "urn:b277d6f4-0e05-454d-83ee-8ebd8be563a8",
+ "@id": "urn:makedire-gCH0e57C",
"Label": "Make directory",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "mkdir -p tsplot",
"Used": []
},
{
- "@id": "urn:05d99bd1-1aa9-452a-9162-19459c4a4c71",
+ "@id": "urn:tsplot-sQPvUfWS",
"Label": "tsplot",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/tsplot . -f filtered_func_data -o tsplot",
"Used": []
},
{
- "@id": "urn:7da2e5ed-45c6-4bef-bbe6-aefef427df2c",
+ "@id": "urn:cluster-812ayXhq",
"Label": "cluster",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
- "Command": "/usr/local/fsl/bin/cluster -i thresh_zstat1 -c stats/cope1 -t 2.3 -p 0.05 -d 0.384676 --volume=45203 -x reg/example_func2standard.mat --stdvol=reg/standard --mm --connectivity=26 --olmax=lmax_zstat1_std.txt --scalarname=Z > cluster_zstat1_std.txt",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
+ "Command": "/usr/local/fsl/bin/cluster -i thresh_zstat1 -c stats/cope1 -t 2.3 -p 0.05 -d 0.384676 --volume=45203 -x reg/example_func2standard.mat --stdvol=reg/standard --mm --connectivity=26 --olmax=lmax_zstat1_std.txt --scalarname=Z > cluster_zstat1_std.txt",
"Used": [
- "urn:4aa4cd22-277d-4275-a53e-46b3d6ae63b5",
- "urn:9d494e57-2f2f-4ae9-9cee-f3fbb0da1e60"
+ "bids::stats/cope1",
+ "bids::thresh_zstat1"
]
},
{
- "@id": "urn:f416139d-e9f8-4692-b181-11e4888553af",
+ "@id": "urn:cluster2-bkJu8wYb",
"Label": "cluster2html",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/cluster2html . cluster_zstat1 -std",
"Used": [
- "urn:fb75466c-ea45-4159-9173-2a92b7963d0a"
+ "bids::cluster_zstat1"
]
},
{
- "@id": "urn:62724743-d128-48d9-b0a9-b8bb0f6800ac",
+ "@id": "urn:makedire-pxx5hor8",
"Label": "Make directory",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/bin/mkdir -p /Users/cmaumet/Data/fsl_practicals/fsl_course_data/fmri/fmri_fluency/fmri+.feat/reg",
"Used": []
},
{
- "@id": "urn:d64fafc8-6fa8-4d3b-bc70-9db4ea5d3d36",
+ "@id": "urn:fslmaths-CcrXUhxy",
"Label": "fslmaths",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/fslmaths /Users/cmaumet/Data/fsl_practicals/fsl_course_data/fmri/fmri_fluency/structural_brain highres",
"Used": [
- "urn:0ed6b3ac-dce1-4927-93ac-a8a05131d6c8"
+ "bids::/Users/cmaumet/Data/fsl_practicals/fsl_course_data/fmri/fmri_fluency/structural_brain"
]
},
{
- "@id": "urn:1bd62035-1ac7-4b81-927d-358b4ce0cb7d",
+ "@id": "urn:fslmaths-R10gGsdr",
"Label": "fslmaths",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/fslmaths /usr/local/fsl/data/standard/MNI152_T1_2mm_brain standard",
"Used": [
- "urn:473dc7c2-1028-4a00-9592-5b20a96d2401"
+ "bids::/usr/local/fsl/data/standard/MNI152_T1_2mm_brain"
]
},
{
- "@id": "urn:be1edb32-3e58-45fa-a6af-df2d560cc972",
+ "@id": "urn:flirt-fvVRPRT5",
"Label": "flirt",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/flirt -in example_func -ref highres -out example_func2highres -omat example_func2highres.mat -cost corratio -dof 7 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear",
"Used": [
- "urn:7e5f43ce-add3-40a5-9912-007b2ad1623a",
- "urn:972ae7c7-2673-4696-9362-ed2210c16011"
+ "bids::example_func",
+ "bids::highres"
]
},
{
- "@id": "urn:bbb6d66a-dbf7-476c-960f-a8b504905c26",
+ "@id": "urn:convertx-PQf5CMyQ",
"Label": "convert_xfm",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat",
"Used": [
- "urn:34ae61a6-bf83-4b75-94ac-80cd6ee10bb3"
+ "bids::example_func2highres.mat"
]
},
{
- "@id": "urn:372e1c72-64f3-4c31-b37a-a3d62f6a7933",
+ "@id": "urn:slicer-7RnnONJA",
"Label": "slicer",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:7e5f43ce-add3-40a5-9912-007b2ad1623a",
- "urn:b51a7314-e006-4e60-ba3c-388d5f9b5a35"
+ "bids::example_func2highres",
+ "bids::highres"
]
},
{
- "@id": "urn:6a86f7e6-4e1a-444d-8f14-4617146d3d26",
+ "@id": "urn:pngappen-VAGzUgxU",
"Label": "pngappend",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres1.png",
"Used": [
- "urn:27ca8d91-5360-4293-91fb-8ab8fb65ebf9",
- "urn:3a8bd22e-4fb4-4baf-b4e0-e6d37917798f",
- "urn:4e8380f4-779e-4fb0-8055-3853d04e3c3e",
- "urn:57a6d013-8c5a-4f73-903c-31102e6983f5",
- "urn:5fb0915d-c741-4a5b-802d-8b14cff8a199",
- "urn:6a224b53-f44c-4f61-b812-ea70fd0752b1",
- "urn:6ee4d50e-a3d9-4baa-8eca-fcc3e59e5f99",
- "urn:ae363fa1-5463-438c-952a-f4e2a0dfef11",
- "urn:b59e9cce-8a28-4ecc-b68a-079d48cca2b7",
- "urn:eb34f522-1fa9-4daa-acde-8c9c860d2868",
- "urn:fac605a0-fbab-47c9-bf38-7e7f3d8bacdb",
- "urn:fcf49bf1-869c-4a95-82c6-beca8a4ad40b"
+ "bids::sla.png",
+ "bids::slb.png",
+ "bids::slc.png",
+ "bids::sld.png",
+ "bids::sle.png",
+ "bids::slf.png",
+ "bids::slg.png",
+ "bids::slh.png",
+ "bids::sli.png",
+ "bids::slj.png",
+ "bids::slk.png",
+ "bids::sll.png"
]
},
{
- "@id": "urn:43812cb6-b4d0-4133-9c67-ee4cc4b43261",
+ "@id": "urn:slicer-5UQf4loB",
"Label": "slicer",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:7e5f43ce-add3-40a5-9912-007b2ad1623a",
- "urn:b51a7314-e006-4e60-ba3c-388d5f9b5a35"
+ "bids::example_func2highres",
+ "bids::highres"
]
},
{
- "@id": "urn:d1d46083-8e1b-4799-9e60-000ed0d76566",
+ "@id": "urn:pngappen-EAzSEN9O",
"Label": "pngappend",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres2.png",
"Used": [
- "urn:27ca8d91-5360-4293-91fb-8ab8fb65ebf9",
- "urn:3a8bd22e-4fb4-4baf-b4e0-e6d37917798f",
- "urn:4e8380f4-779e-4fb0-8055-3853d04e3c3e",
- "urn:57a6d013-8c5a-4f73-903c-31102e6983f5",
- "urn:5fb0915d-c741-4a5b-802d-8b14cff8a199",
- "urn:6a224b53-f44c-4f61-b812-ea70fd0752b1",
- "urn:6ee4d50e-a3d9-4baa-8eca-fcc3e59e5f99",
- "urn:ae363fa1-5463-438c-952a-f4e2a0dfef11",
- "urn:b59e9cce-8a28-4ecc-b68a-079d48cca2b7",
- "urn:eb34f522-1fa9-4daa-acde-8c9c860d2868",
- "urn:fac605a0-fbab-47c9-bf38-7e7f3d8bacdb",
- "urn:fcf49bf1-869c-4a95-82c6-beca8a4ad40b"
+ "bids::sla.png",
+ "bids::slb.png",
+ "bids::slc.png",
+ "bids::sld.png",
+ "bids::sle.png",
+ "bids::slf.png",
+ "bids::slg.png",
+ "bids::slh.png",
+ "bids::sli.png",
+ "bids::slj.png",
+ "bids::slk.png",
+ "bids::sll.png"
]
},
{
- "@id": "urn:83781569-a890-4a9e-ba7b-699412ca8c7b",
+ "@id": "urn:pngappen-MLrzExnj",
"Label": "pngappend",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/pngappend example_func2highres1.png example_func2highres2.png example_func2highres.png",
"Used": [
- "urn:121d60bf-7a45-4729-9791-31b192ac153a",
- "urn:cbe4b414-9e92-4601-a8c2-67f453efbf50"
+ "bids::example_func2highres1.png",
+ "bids::example_func2highres2.png"
]
},
{
- "@id": "urn:bd53ea95-c4bc-4c3c-874b-7a51c9d50ee6",
+ "@id": "urn:rm-6WBPdNij",
"Label": "rm",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/bin/rm -f sl?.png example_func2highres2.png",
"Used": [
- "urn:121d60bf-7a45-4729-9791-31b192ac153a",
- "urn:bfc45329-a862-495e-998f-ce799762b913"
+ "bids::example_func2highres2.png",
+ "bids::sl?.png"
]
},
{
- "@id": "urn:6e74cc21-a8a0-4cfd-8d1a-dc6800a91871",
+ "@id": "urn:rm-I9krhlSI",
"Label": "rm",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/bin/rm example_func2highres1.png",
"Used": [
- "urn:cbe4b414-9e92-4601-a8c2-67f453efbf50"
+ "bids::example_func2highres1.png"
]
},
{
- "@id": "urn:23b47ba8-6c77-47fa-8455-53b53de084b8",
+ "@id": "urn:flirt-neRhcE4N",
"Label": "flirt",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/flirt -in highres -ref standard -out highres2standard -omat highres2standard.mat -cost corratio -dof 12 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear",
"Used": [
- "urn:7e5f43ce-add3-40a5-9912-007b2ad1623a",
- "urn:e76c13e2-2635-44ea-9631-0f1dd0ed99d8"
+ "bids::highres",
+ "bids::standard"
]
},
{
- "@id": "urn:e9f64176-30cf-4e1d-9d99-1b0e3eb88593",
+ "@id": "urn:convertx-8teOYoH5",
"Label": "convert_xfm",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/convert_xfm -inverse -omat standard2highres.mat highres2standard.mat",
"Used": [
- "urn:a527cfca-63f6-4674-b6e7-c63704924e3e"
+ "bids::highres2standard.mat"
]
},
{
- "@id": "urn:bbfa134b-682f-48e7-b299-9bec9bb3e53d",
+ "@id": "urn:slicer-M7ZeWOyi",
"Label": "slicer",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/slicer highres2standard standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:6ff9de7c-6cda-4e3a-b954-3f47e4155ef0",
- "urn:e76c13e2-2635-44ea-9631-0f1dd0ed99d8"
+ "bids::highres2standard",
+ "bids::standard"
]
},
{
- "@id": "urn:083776f4-f5fb-4355-b941-9a7bfd3bab23",
+ "@id": "urn:pngappen-1m297Xyj",
"Label": "pngappend",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png highres2standard1.png",
"Used": [
- "urn:27ca8d91-5360-4293-91fb-8ab8fb65ebf9",
- "urn:3a8bd22e-4fb4-4baf-b4e0-e6d37917798f",
- "urn:4e8380f4-779e-4fb0-8055-3853d04e3c3e",
- "urn:57a6d013-8c5a-4f73-903c-31102e6983f5",
- "urn:5fb0915d-c741-4a5b-802d-8b14cff8a199",
- "urn:6a224b53-f44c-4f61-b812-ea70fd0752b1",
- "urn:6ee4d50e-a3d9-4baa-8eca-fcc3e59e5f99",
- "urn:ae363fa1-5463-438c-952a-f4e2a0dfef11",
- "urn:b59e9cce-8a28-4ecc-b68a-079d48cca2b7",
- "urn:eb34f522-1fa9-4daa-acde-8c9c860d2868",
- "urn:fac605a0-fbab-47c9-bf38-7e7f3d8bacdb",
- "urn:fcf49bf1-869c-4a95-82c6-beca8a4ad40b"
+ "bids::sla.png",
+ "bids::slb.png",
+ "bids::slc.png",
+ "bids::sld.png",
+ "bids::sle.png",
+ "bids::slf.png",
+ "bids::slg.png",
+ "bids::slh.png",
+ "bids::sli.png",
+ "bids::slj.png",
+ "bids::slk.png",
+ "bids::sll.png"
]
},
{
- "@id": "urn:4771e140-336c-4b07-a440-c46f2046a8af",
+ "@id": "urn:slicer-m8Q5vCPD",
"Label": "slicer",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/slicer standard highres2standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:6ff9de7c-6cda-4e3a-b954-3f47e4155ef0",
- "urn:e76c13e2-2635-44ea-9631-0f1dd0ed99d8"
+ "bids::highres2standard",
+ "bids::standard"
]
},
{
- "@id": "urn:e294213a-d7da-4e5a-9dd7-95e1c68790a6",
+ "@id": "urn:pngappen-4NNLd5ew",
"Label": "pngappend",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png highres2standard2.png",
"Used": [
- "urn:27ca8d91-5360-4293-91fb-8ab8fb65ebf9",
- "urn:3a8bd22e-4fb4-4baf-b4e0-e6d37917798f",
- "urn:4e8380f4-779e-4fb0-8055-3853d04e3c3e",
- "urn:57a6d013-8c5a-4f73-903c-31102e6983f5",
- "urn:5fb0915d-c741-4a5b-802d-8b14cff8a199",
- "urn:6a224b53-f44c-4f61-b812-ea70fd0752b1",
- "urn:6ee4d50e-a3d9-4baa-8eca-fcc3e59e5f99",
- "urn:ae363fa1-5463-438c-952a-f4e2a0dfef11",
- "urn:b59e9cce-8a28-4ecc-b68a-079d48cca2b7",
- "urn:eb34f522-1fa9-4daa-acde-8c9c860d2868",
- "urn:fac605a0-fbab-47c9-bf38-7e7f3d8bacdb",
- "urn:fcf49bf1-869c-4a95-82c6-beca8a4ad40b"
+ "bids::sla.png",
+ "bids::slb.png",
+ "bids::slc.png",
+ "bids::sld.png",
+ "bids::sle.png",
+ "bids::slf.png",
+ "bids::slg.png",
+ "bids::slh.png",
+ "bids::sli.png",
+ "bids::slj.png",
+ "bids::slk.png",
+ "bids::sll.png"
]
},
{
- "@id": "urn:0c66a7a9-738b-44a1-b1da-50f88520f931",
+ "@id": "urn:pngappen-7rOC9QLu",
"Label": "pngappend",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/pngappend highres2standard1.png highres2standard2.png highres2standard.png",
"Used": [
- "urn:32edece5-173f-46ee-86b5-133112f3c425",
- "urn:3c25815d-a3e0-4a17-a4c8-28d906e9e4c0"
+ "bids::highres2standard1.png",
+ "bids::highres2standard2.png"
]
},
{
- "@id": "urn:08355dcf-1747-4b0f-845e-d473074c2b77",
+ "@id": "urn:rm-p2L9F5qN",
"Label": "rm",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/bin/rm -f sl?.png highres2standard2.png",
"Used": [
- "urn:32edece5-173f-46ee-86b5-133112f3c425",
- "urn:bfc45329-a862-495e-998f-ce799762b913"
+ "bids::highres2standard2.png",
+ "bids::sl?.png"
]
},
{
- "@id": "urn:94fcbf68-6140-4336-ad2a-d3d398da3adf",
+ "@id": "urn:rm-8gdMveqq",
"Label": "rm",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/bin/rm highres2standard1.png",
"Used": [
- "urn:3c25815d-a3e0-4a17-a4c8-28d906e9e4c0"
+ "bids::highres2standard1.png"
]
},
{
- "@id": "urn:212a4f61-604b-4b36-bd51-f9624408a2e4",
+ "@id": "urn:convertx-zzaEDYj0",
"Label": "convert_xfm",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/convert_xfm -omat example_func2standard.mat -concat highres2standard.mat example_func2highres.mat",
"Used": [
- "urn:34ae61a6-bf83-4b75-94ac-80cd6ee10bb3"
+ "bids::example_func2highres.mat"
]
},
{
- "@id": "urn:13da9343-e2a6-4508-9d06-7e8628d176a4",
+ "@id": "urn:flirt-IzGlSqIc",
"Label": "flirt",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/flirt -ref standard -in example_func -out example_func2standard -applyxfm -init example_func2standard.mat -interp trilinear",
"Used": [
- "urn:8c230d32-2446-4dfb-9583-31f69475bd4e",
- "urn:972ae7c7-2673-4696-9362-ed2210c16011",
- "urn:e76c13e2-2635-44ea-9631-0f1dd0ed99d8"
+ "bids::example_func",
+ "bids::example_func2standard.mat",
+ "bids::standard"
]
},
{
- "@id": "urn:d1910e3d-571c-4a0a-8b04-922051d2f700",
+ "@id": "urn:convertx-NaXYQzXW",
"Label": "convert_xfm",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/convert_xfm -inverse -omat standard2example_func.mat example_func2standard.mat",
"Used": [
- "urn:8c230d32-2446-4dfb-9583-31f69475bd4e"
+ "bids::example_func2standard.mat"
]
},
{
- "@id": "urn:53f729e0-2ea7-4491-a1c0-5f1ab799f99a",
+ "@id": "urn:slicer-UQXUwp1F",
"Label": "slicer",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/slicer example_func2standard standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:d3f31eec-def0-413b-95a2-34b9a14d39b8",
- "urn:e76c13e2-2635-44ea-9631-0f1dd0ed99d8"
+ "bids::example_func2standard",
+ "bids::standard"
]
},
{
- "@id": "urn:05da50da-4c38-490d-939e-2529d5338e2b",
+ "@id": "urn:pngappen-XWpLEvlM",
"Label": "pngappend",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2standard1.png",
"Used": [
- "urn:27ca8d91-5360-4293-91fb-8ab8fb65ebf9",
- "urn:3a8bd22e-4fb4-4baf-b4e0-e6d37917798f",
- "urn:4e8380f4-779e-4fb0-8055-3853d04e3c3e",
- "urn:57a6d013-8c5a-4f73-903c-31102e6983f5",
- "urn:5fb0915d-c741-4a5b-802d-8b14cff8a199",
- "urn:6a224b53-f44c-4f61-b812-ea70fd0752b1",
- "urn:6ee4d50e-a3d9-4baa-8eca-fcc3e59e5f99",
- "urn:ae363fa1-5463-438c-952a-f4e2a0dfef11",
- "urn:b59e9cce-8a28-4ecc-b68a-079d48cca2b7",
- "urn:eb34f522-1fa9-4daa-acde-8c9c860d2868",
- "urn:fac605a0-fbab-47c9-bf38-7e7f3d8bacdb",
- "urn:fcf49bf1-869c-4a95-82c6-beca8a4ad40b"
+ "bids::sla.png",
+ "bids::slb.png",
+ "bids::slc.png",
+ "bids::sld.png",
+ "bids::sle.png",
+ "bids::slf.png",
+ "bids::slg.png",
+ "bids::slh.png",
+ "bids::sli.png",
+ "bids::slj.png",
+ "bids::slk.png",
+ "bids::sll.png"
]
},
{
- "@id": "urn:5352d93c-8554-4dd8-b154-4c8a7732ed7b",
+ "@id": "urn:slicer-gieR3uyT",
"Label": "slicer",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/slicer standard example_func2standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:d3f31eec-def0-413b-95a2-34b9a14d39b8",
- "urn:e76c13e2-2635-44ea-9631-0f1dd0ed99d8"
+ "bids::example_func2standard",
+ "bids::standard"
]
},
{
- "@id": "urn:f715da09-7169-4935-8a19-0e64acad6228",
+ "@id": "urn:pngappen-Q3DzJumP",
"Label": "pngappend",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2standard2.png",
"Used": [
- "urn:27ca8d91-5360-4293-91fb-8ab8fb65ebf9",
- "urn:3a8bd22e-4fb4-4baf-b4e0-e6d37917798f",
- "urn:4e8380f4-779e-4fb0-8055-3853d04e3c3e",
- "urn:57a6d013-8c5a-4f73-903c-31102e6983f5",
- "urn:5fb0915d-c741-4a5b-802d-8b14cff8a199",
- "urn:6a224b53-f44c-4f61-b812-ea70fd0752b1",
- "urn:6ee4d50e-a3d9-4baa-8eca-fcc3e59e5f99",
- "urn:ae363fa1-5463-438c-952a-f4e2a0dfef11",
- "urn:b59e9cce-8a28-4ecc-b68a-079d48cca2b7",
- "urn:eb34f522-1fa9-4daa-acde-8c9c860d2868",
- "urn:fac605a0-fbab-47c9-bf38-7e7f3d8bacdb",
- "urn:fcf49bf1-869c-4a95-82c6-beca8a4ad40b"
+ "bids::sla.png",
+ "bids::slb.png",
+ "bids::slc.png",
+ "bids::sld.png",
+ "bids::sle.png",
+ "bids::slf.png",
+ "bids::slg.png",
+ "bids::slh.png",
+ "bids::sli.png",
+ "bids::slj.png",
+ "bids::slk.png",
+ "bids::sll.png"
]
},
{
- "@id": "urn:706293e7-948d-45eb-98f1-39e4e201f4eb",
+ "@id": "urn:pngappen-SxqkKzF3",
"Label": "pngappend",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/usr/local/fsl/bin/pngappend example_func2standard1.png example_func2standard2.png example_func2standard.png",
"Used": [
- "urn:2b653326-eaf9-47ae-bb22-6ec2544f4982",
- "urn:aed85e52-689e-4126-982f-f3922723d4bc"
+ "bids::example_func2standard1.png",
+ "bids::example_func2standard2.png"
]
},
{
- "@id": "urn:7c6a5a4a-63e5-4786-b73c-f906e5120d91",
+ "@id": "urn:rm-7fETH355",
"Label": "rm",
- "AssociatedWith": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "AssociatedWith": "urn:fsl-KLLV16PQ",
"Command": "/bin/rm -f sl?.png example_func2standard2.png",
"Used": [
- "urn:aed85e52-689e-4126-982f-f3922723d4bc",
- "urn:bfc45329-a862-495e-998f-ce799762b913"
+ "bids::example_func2standard2.png",
+ "bids::sl?.png"
]
}
],
"Entities": [
{
- "@id": "urn:4b6c76de-2ef4-4b43-8d3c-e6c0e5003853",
+ "@id": "bids::/Users/cmaumet/Data/fsl_practicals/fsl_course_data/fmri/fmri_fluency/fmri",
"Label": "fmri",
"AtLocation": "/Users/cmaumet/Data/fsl_practicals/fsl_course_data/fmri/fmri_fluency/fmri",
"digest": {
@@ -763,43 +763,43 @@
}
},
{
- "@id": "urn:8992ddf0-b6d9-4da5-86ae-aae8b06bf498",
+ "@id": "bids::prefiltered_func_data",
"Label": "prefiltered_func_data",
"AtLocation": "prefiltered_func_data",
- "GeneratedBy": "urn:8c85596f-7fa2-43b1-8a9d-e343dd1250dc",
+ "GeneratedBy": "urn:fslmaths-b1MGvYNo",
"digest": {
"sha256": "2bea6005bace2adbea3534588b8c1b0d1759aa1af85b703b7f5bd2959c961a29"
}
},
{
- "@id": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "@id": "bids::example_func",
"Label": "example_func",
"AtLocation": "example_func",
- "GeneratedBy": "urn:6afdcda2-2b02-4320-acef-8b40a7b03680",
+ "GeneratedBy": "urn:fslroi-pEfBZwC1",
"digest": {
"sha256": "57841df382242a0e56f4fd1f340b30d4eb3bbd270342825da476367c640135e4"
}
},
{
- "@id": "urn:fbf7e4fe-124b-4f1f-8c16-6f23a9008267",
+ "@id": "bids::prefiltered_func_data_mcf",
"Label": "prefiltered_func_data_mcf",
"AtLocation": "prefiltered_func_data_mcf",
- "GeneratedBy": "urn:05ca7568-0ad0-495e-8456-fbc9ff878699",
+ "GeneratedBy": "urn:mcflirt-KeW71fTO",
"digest": {
"sha256": "83371e264d408de4f678b8182097b39c86bd0a618ca76af6d1dfee5db0903b78"
}
},
{
- "@id": "urn:d5b299e3-40d3-438b-86c6-f0cc41f05345",
+ "@id": "bids::mc",
"Label": "mc",
"AtLocation": "mc",
- "GeneratedBy": "urn:edc04ecc-b0d2-4ef2-9882-a31284993675",
+ "GeneratedBy": "urn:makedire-QsOZPp7d",
"digest": {
"sha256": "a1a8fa7b1d2bf5bc0a263e95f926d3d9b656d2572455245d46edf48e93744ffa"
}
},
{
- "@id": "urn:fa30e6eb-06b6-4084-8b84-2246196531dc",
+ "@id": "bids::prefiltered_func_data_mcf.mat",
"Label": "prefiltered_func_data_mcf.mat",
"AtLocation": "prefiltered_func_data_mcf.mat",
"digest": {
@@ -807,7 +807,7 @@
}
},
{
- "@id": "urn:579301fe-cc07-4b7e-9f44-f990d3d76bf5",
+ "@id": "bids::prefiltered_func_data_mcf.par",
"Label": "prefiltered_func_data_mcf.par",
"AtLocation": "prefiltered_func_data_mcf.par",
"digest": {
@@ -815,7 +815,7 @@
}
},
{
- "@id": "urn:a50b87fb-4dad-4045-af1b-5fb7218f58f6",
+ "@id": "bids::prefiltered_func_data_mcf_abs.rms",
"Label": "prefiltered_func_data_mcf_abs.rms",
"AtLocation": "prefiltered_func_data_mcf_abs.rms",
"digest": {
@@ -823,7 +823,7 @@
}
},
{
- "@id": "urn:925c8d49-ab58-4373-8b9b-57ee08f09074",
+ "@id": "bids::prefiltered_func_data_mcf_abs_mean.rms",
"Label": "prefiltered_func_data_mcf_abs_mean.rms",
"AtLocation": "prefiltered_func_data_mcf_abs_mean.rms",
"digest": {
@@ -831,7 +831,7 @@
}
},
{
- "@id": "urn:7389473f-485d-491b-8432-a4d07111e05e",
+ "@id": "bids::prefiltered_func_data_mcf_rel.rms",
"Label": "prefiltered_func_data_mcf_rel.rms",
"AtLocation": "prefiltered_func_data_mcf_rel.rms",
"digest": {
@@ -839,7 +839,7 @@
}
},
{
- "@id": "urn:00be7c67-3470-4109-aac0-ce3457fe672f",
+ "@id": "bids::prefiltered_func_data_mcf_rel_mean.rms",
"Label": "prefiltered_func_data_mcf_rel_mean.rms",
"AtLocation": "prefiltered_func_data_mcf_rel_mean.rms",
"digest": {
@@ -847,34 +847,34 @@
}
},
{
- "@id": "urn:8c7cfc61-2fa9-45fe-a568-dacccb6e4bd5",
+ "@id": "bids::mc",
"Label": "mc",
"AtLocation": "mc",
- "GeneratedBy": "urn:e0181246-8e96-4072-b1d0-fa45343c01a2",
+ "GeneratedBy": "urn:mv-iaHeHtFC",
"digest": {
"sha256": "a1a8fa7b1d2bf5bc0a263e95f926d3d9b656d2572455245d46edf48e93744ffa"
}
},
{
- "@id": "urn:b85e4dd6-61b9-4c63-85f1-76c2718a8fc2",
+ "@id": "bids::rot.png",
"Label": "rot.png",
"AtLocation": "rot.png",
- "GeneratedBy": "urn:859744a1-aec1-40a3-ad00-8006fdd1b111",
+ "GeneratedBy": "urn:fsltsplo-B4QqMADr",
"digest": {
"sha256": "b8776603f8865a358b2273847d21e63491e7c2e10567fb640608dd47ba721f29"
}
},
{
- "@id": "urn:776e5668-c60d-4388-8c68-0ed9953b0a58",
+ "@id": "bids::trans.png",
"Label": "trans.png",
"AtLocation": "trans.png",
- "GeneratedBy": "urn:bc2c5ca3-552a-4da0-9bd1-0c16a94c5ac2",
+ "GeneratedBy": "urn:fsltsplo-PBP7q6Mm",
"digest": {
"sha256": "496eac1d0ac15e80928780c73766c7791a1707291b2b9a6d1781c2f6a38de3cd"
}
},
{
- "@id": "urn:7b9b59ac-2c07-45fc-9bd2-6f3602b9c7d6",
+ "@id": "bids::prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"Label": "prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"AtLocation": "prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"digest": {
@@ -882,34 +882,34 @@
}
},
{
- "@id": "urn:f00f6f70-9f59-463a-9315-37ec75568f19",
+ "@id": "bids::disp.png",
"Label": "disp.png",
"AtLocation": "disp.png",
- "GeneratedBy": "urn:a8c06dac-29ad-4202-b47d-c3852118ca61",
+ "GeneratedBy": "urn:fsltsplo-FRGlfszX",
"digest": {
"sha256": "c4615e07e04f0c390d969482634cb62e81d47c818d2866ee866ec9c64a5350fd"
}
},
{
- "@id": "urn:2c359c35-45bf-4507-9103-a3cb62eb98ab",
+ "@id": "bids::mean_func",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:bcd8bccb-c962-4602-bf5f-650419dcf0f2",
+ "GeneratedBy": "urn:fslmaths-TFXrmtg1",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:40f0ba7c-6c5e-41e3-be4d-cb51edc55892",
+ "@id": "bids::mask",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:c4d758c0-3816-4dbd-b832-1268d95dba11",
+ "GeneratedBy": "urn:bet2-906V4kHT",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:7badca47-0d69-4d41-ab15-65dd48fbfb3c",
+ "@id": "bids::mask_mask",
"Label": "mask_mask",
"AtLocation": "mask_mask",
"digest": {
@@ -917,123 +917,115 @@
}
},
{
- "@id": "urn:26057a7a-635e-49cb-b254-4df7011e5db4",
+ "@id": "bids::mask",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:be53f424-1517-47d3-9eb0-815c5bd21f4f",
+ "GeneratedBy": "urn:immv-vs9RHb6O",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:f2efbcb4-3695-485f-8ac7-d1ef7a54cd5f",
+ "@id": "bids::prefiltered_func_data_bet",
"Label": "prefiltered_func_data_bet",
"AtLocation": "prefiltered_func_data_bet",
- "GeneratedBy": "urn:49db383a-f7ce-4b02-b18a-301f09f8ca2e",
+ "GeneratedBy": "urn:fslmaths-4fMxR2bm",
"digest": {
"sha256": "c01f21947b38d9886528dec14edf23dfb55304b7da67569fe93902472b286cf4"
}
},
{
- "@id": "urn:57a1e7f9-e61f-40a5-aba2-3dc9559d3f09",
+ "@id": "bids::mask",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:0f83ee71-21d4-4454-8c8e-38e6170a965d",
+ "GeneratedBy": "urn:fslmaths-ZT26rDzN",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:c7d2df71-a316-4e17-bddc-87b27b72082b",
+ "@id": "bids::mask",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:a44737d5-bbe8-45aa-bbda-e4e39c4fc2e4",
+ "GeneratedBy": "urn:fslmaths-x3vBn14T",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:f6ff0b38-f70a-4a10-b2da-eddaa63ba9d7",
+ "@id": "bids::prefiltered_func_data_thresh",
"Label": "prefiltered_func_data_thresh",
"AtLocation": "prefiltered_func_data_thresh",
- "GeneratedBy": "urn:f60325ef-133c-42ed-991d-cafc1d400a1c",
+ "GeneratedBy": "urn:fslmaths-Ug4rV82p",
"digest": {
"sha256": "c5c015a8df079b497bbce596808cbbdc09fb39411f490244de192dfa72d33640"
}
},
{
- "@id": "urn:bcc78824-4e5f-4dec-a981-c78823d20545",
+ "@id": "bids::mean_func",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:1f93c51d-0af7-428b-87d0-7e9cb9f08dc1",
+ "GeneratedBy": "urn:fslmaths-FtnR53jV",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:514b6380-1b32-4118-8264-87546493d9db",
+ "@id": "bids::prefiltered_func_data_smooth",
"Label": "prefiltered_func_data_smooth",
"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:0d20d783-5c33-47b9-acc0-d7c6c576fd63",
+ "GeneratedBy": "urn:susan-FiFaiCkb",
"digest": {
"sha256": "2a4901d885fce0b083c9f99364da8dcff184635e74ab011f53a68cfc6827b429"
}
},
{
- "@id": "urn:dd2943db-d18f-4c3b-b091-b2392fb26750",
+ "@id": "bids::prefiltered_func_data_smooth",
"Label": "prefiltered_func_data_smooth",
"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:bbc5cfa9-fc2a-4a19-b7cd-6eff9a5300b2",
+ "GeneratedBy": "urn:fslmaths-USD6zrsf",
"digest": {
"sha256": "2a4901d885fce0b083c9f99364da8dcff184635e74ab011f53a68cfc6827b429"
}
},
{
- "@id": "urn:9977a87f-a67e-46c5-9208-6d52284bb1ee",
+ "@id": "bids::prefiltered_func_data_intnorm",
"Label": "prefiltered_func_data_intnorm",
"AtLocation": "prefiltered_func_data_intnorm",
- "GeneratedBy": "urn:a88fe79f-9c31-48c7-a3fd-d9aa03416151",
+ "GeneratedBy": "urn:fslmaths-DFXryZ4N",
"digest": {
"sha256": "0698a276f6f0fdccfb06033926d333a176503a09aaa87b78384fbffbf1c54dee"
}
},
{
- "@id": "urn:20d47a60-b70e-40c7-8a9e-d71225be39f2",
- "Label": "227.142867456",
- "AtLocation": "227.142867456",
- "GeneratedBy": "urn:62757c28-bbaf-44ef-b41d-fba68148f8c4",
- "digest": {
- "sha256": "b1cf0f5d8383a1e910332b4d9862c7d8bbedd59af09169442e75308d07f87009"
- }
- },
- {
- "@id": "urn:2906ce55-4d86-46f2-b57b-d2e79a77c30c",
+ "@id": "bids::prefiltered_func_data_tempfilt",
"Label": "prefiltered_func_data_tempfilt",
"AtLocation": "prefiltered_func_data_tempfilt",
+ "GeneratedBy": "urn:fslmaths-YuhXjVaO",
"digest": {
"sha256": "a1836f4694e7ffdb50484626724602498c7b22b4f3cdd1e7d105efd336cbc8bd"
}
},
{
- "@id": "urn:b4ab62df-3021-4a35-890e-c262a04ac86d",
+ "@id": "bids::filtered_func_data",
"Label": "filtered_func_data",
"AtLocation": "filtered_func_data",
- "GeneratedBy": "urn:13e01b1e-8691-4c67-8b2f-3f8a6a3dc9ec",
+ "GeneratedBy": "urn:fslmaths-xst3I97I",
"digest": {
"sha256": "2a1854e3b48a54f88e063191e25159015a0afbd300d18a1cfda37b4b68a1ee69"
}
},
{
- "@id": "urn:c82523a5-fbd2-4815-82e4-409059edea30",
+ "@id": "bids::mean_func",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:876868d9-b90c-4dbe-b1c0-e8081a6b5783",
+ "GeneratedBy": "urn:fslmaths-YKjFeGPL",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:b1dfae7b-a755-4880-bb1b-2943bb5dabe6",
+ "@id": "bids::prefiltered_func_data*",
"Label": "prefiltered_func_data*",
"AtLocation": "prefiltered_func_data*",
"digest": {
@@ -1041,16 +1033,16 @@
}
},
{
- "@id": "urn:edc4d342-e3a2-4a70-9590-c7cd4293922d",
+ "@id": "bids::custom_timing_files",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:cf35254c-cfa1-47a4-b6fa-0bbfd48f1f2e",
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@@ -1058,22 +1050,22 @@
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@@ -1081,13 +1073,13 @@
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@@ -1095,16 +1087,16 @@
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@@ -1112,16 +1104,16 @@
}
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{
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@@ -1129,25 +1121,52 @@
}
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{
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@@ -1155,25 +1174,25 @@
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{
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@@ -1181,61 +1200,88 @@
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@@ -1243,16 +1289,16 @@
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@@ -1260,286 +1306,286 @@
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{
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- "GeneratedBy": "urn:43812cb6-b4d0-4133-9c67-ee4cc4b43261",
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- "GeneratedBy": "urn:83781569-a890-4a9e-ba7b-699412ca8c7b",
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@@ -1547,541 +1593,541 @@
}
},
{
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- "GeneratedBy": "urn:23b47ba8-6c77-47fa-8455-53b53de084b8",
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- "GeneratedBy": "urn:e9f64176-30cf-4e1d-9d99-1b0e3eb88593",
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{
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{
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diff --git a/examples/from_parsers/fsl/fsl_full_examples001_report_log.png b/examples/from_parsers/fsl/fsl_full_examples001_report_log.png
index 97fd2422b..9cc9cf216 100644
Binary files a/examples/from_parsers/fsl/fsl_full_examples001_report_log.png and b/examples/from_parsers/fsl/fsl_full_examples001_report_log.png differ
diff --git a/examples/from_parsers/fsl/fsl_gamma_basis_report_log.html b/examples/from_parsers/fsl/fsl_gamma_basis_report_log.html
index 504c2daec..e940a2265 100644
--- a/examples/from_parsers/fsl/fsl_gamma_basis_report_log.html
+++ b/examples/from_parsers/fsl/fsl_gamma_basis_report_log.html
@@ -35,20 +35,20 @@ Progress Report / Log
326910
Initialisation
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
Total original volumes = 104
/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1
Preprocessing:Stage 1
-/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90
+/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/example_func.nii.gz -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90
Option -F ( FEAT version parameter ) selected with argument "6.00"
Option -d ( output directory ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat"
Option -l ( logfile )input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/logs/feat2_pre"
Option -R ( html unwarping report ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/report_unwarp.html"
Option -r ( html registration report ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/report_reg.html"
Option -i ( main input ) input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/example_func.nii.gz"
-Option -h ( high-res structural image ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
+Option -h ( high-res structural image ) selected with argument "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
Option -w ( highres dof ) selected with argument "BBR"
Option -x ( highres search ) selected with argument "90"
Option -s ( standard image ) selected with argument "/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain"
@@ -59,10 +59,10 @@ Progress Report / Log
/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/reg
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head
did not find file: example_func2highres.mat. Generating transform.
@@ -128,9 +128,9 @@ Progress Report / Log
/bin/rm -rf prefiltered_func_data*
Stats
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
/usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con --fcon=design.fts
Log directory is: stats
diff --git a/examples/from_parsers/fsl/fsl_gamma_basis_report_log.jsonld b/examples/from_parsers/fsl/fsl_gamma_basis_report_log.jsonld
index 0541a1419..52eaa90b7 100644
--- a/examples/from_parsers/fsl/fsl_gamma_basis_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_gamma_basis_report_log.jsonld
@@ -4,1049 +4,1059 @@
"Records": {
"Software": [
{
- "@id": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:fsl-Ld1arblU",
"@type": "prov:SoftwareAgent",
"Label": "FSL",
- "Version": "xxx"
+ "Version": "xxx",
+ "AltIdentifier": "RRID:SCR_002823"
}
],
"Activities": [
{
- "@id": "urn:8b7ebf9b-55a0-4a1d-b503-719151eebc50",
+ "@id": "urn:fslmaths-qeUb1qc5",
"Label": "fslmaths",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
"Used": [
- "urn:cc8f8d80-4f02-496d-9a4a-e0e2bfbe3189"
+ "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold"
]
},
{
- "@id": "urn:74cebf5a-7236-4402-8dc4-8d5936bcc43c",
+ "@id": "urn:fslroi-VBxwwZY6",
"Label": "fslroi",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1",
"Used": [
- "urn:0924054c-0c39-4d36-b059-e742e85e493d"
+ "bids::prefiltered_func_data"
]
},
{
- "@id": "urn:e9a73030-0006-4ef8-95e3-5834de3078f3",
+ "@id": "urn:mainfeat-7FPDQFA3",
"Label": "mainfeatreg",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/example_func.nii.gz -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
"Used": [
- "urn:cb081815-8a6c-42f8-bb87-18c9e4cb7bc9",
- "urn:d2c7c8ce-aa21-4a64-a01f-9425bfa93b01",
- "urn:fadd4862-4c4b-4a39-ba35-666f29181e2c"
+ "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/example_func.nii.gz",
+ "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain",
+ "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
]
},
{
- "@id": "urn:3e26d898-d64e-4301-8def-9765c710bcdf",
+ "@id": "urn:makedire-lVc4z7Bv",
"Label": "Make directory",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/reg",
"Used": []
},
{
- "@id": "urn:1e662f78-13a4-474a-9645-9ee637aa9e4b",
+ "@id": "urn:fslmaths-DHqHCVuk",
"Label": "fslmaths",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
"Used": [
- "urn:cb081815-8a6c-42f8-bb87-18c9e4cb7bc9"
+ "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
]
},
{
- "@id": "urn:26a00968-1740-4b01-8330-41148ecff2f1",
+ "@id": "urn:fslmaths-hSsHK6sO",
"Label": "fslmaths",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
"Used": [
- "urn:e9aec74c-9fea-437a-8d93-0ae9789f2d8a"
+ "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w"
]
},
{
- "@id": "urn:42bc175e-636a-4d3f-8a84-ab0cec178f89",
+ "@id": "urn:epireg-PfcVzMiS",
"Label": "epi_reg",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres",
- "Used": []
+ "Used": [
+ "bids::example_func",
+ "bids::highres",
+ "bids::highres_head"
+ ]
},
{
- "@id": "urn:cb078c97-7316-4480-a77e-abf7f6853c4e",
+ "@id": "urn:convertx-WJotBeOj",
"Label": "convert_xfm",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat",
"Used": [
- "urn:5f05c7a5-2284-4cdf-b443-eaacdd73c3dc"
+ "bids::example_func2highres.mat"
]
},
{
- "@id": "urn:fa93e59f-1e2b-49fe-b6c1-2ea8c2665df1",
+ "@id": "urn:slicer-IvnNaijU",
"Label": "slicer",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:c48fddaa-6cf5-4453-b931-ef29776dbaad",
- "urn:c7e22265-242c-40b2-a6d4-3b6718af7d53"
+ "bids::example_func2highres",
+ "bids::highres"
]
},
{
- "@id": "urn:63dd083a-b6c0-4169-bdc1-5b4c478ae687",
+ "@id": "urn:pngappen-Hjp62Yc9",
"Label": "pngappend",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres1.png",
"Used": [
- "urn:12fad9c5-48eb-46f2-8071-7d08b1fb1098",
- "urn:2714f869-ac76-4842-8998-8d005cbe8b00",
- "urn:34dbf791-6f89-4a89-aee7-1908de2b5835",
- "urn:76125b99-5fb8-4a46-9b93-8ff9cd4e3e70",
- "urn:826557c4-b724-4e3c-bc51-cd7035d9eea8",
- "urn:835d8881-a887-40b8-9960-a4fc64ada68c",
- "urn:8bc12560-688d-456f-909d-dc9eda67b073",
- "urn:927af817-f93a-489f-a7f9-8042ef2bd242",
- "urn:bec98c26-9830-48d9-9ac8-1b988eb49dbf",
- "urn:c6b77905-a877-4bf7-bb02-8b2c581b45a6",
- "urn:c9b41c2e-95ef-41ff-ab0e-6ebafe11329d",
- "urn:dcb7674a-1e3c-411c-95d8-0e4fc5aab43e"
+ "bids::sla.png",
+ "bids::slb.png",
+ "bids::slc.png",
+ "bids::sld.png",
+ "bids::sle.png",
+ "bids::slf.png",
+ "bids::slg.png",
+ "bids::slh.png",
+ "bids::sli.png",
+ "bids::slj.png",
+ "bids::slk.png",
+ "bids::sll.png"
]
},
{
- "@id": "urn:a68d5032-c2be-4a84-ab5d-fbde9e657d5f",
+ "@id": "urn:slicer-4HjW8Tda",
"Label": "slicer",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:c48fddaa-6cf5-4453-b931-ef29776dbaad",
- "urn:c7e22265-242c-40b2-a6d4-3b6718af7d53"
+ "bids::example_func2highres",
+ "bids::highres"
]
},
{
- "@id": "urn:fc548620-4d3b-4aaf-a4d6-39a1641f8bcb",
+ "@id": "urn:pngappen-FqJ58gVR",
"Label": "pngappend",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres2.png",
"Used": [
- "urn:12fad9c5-48eb-46f2-8071-7d08b1fb1098",
- "urn:2714f869-ac76-4842-8998-8d005cbe8b00",
- "urn:34dbf791-6f89-4a89-aee7-1908de2b5835",
- "urn:76125b99-5fb8-4a46-9b93-8ff9cd4e3e70",
- "urn:826557c4-b724-4e3c-bc51-cd7035d9eea8",
- "urn:835d8881-a887-40b8-9960-a4fc64ada68c",
- "urn:8bc12560-688d-456f-909d-dc9eda67b073",
- "urn:927af817-f93a-489f-a7f9-8042ef2bd242",
- "urn:bec98c26-9830-48d9-9ac8-1b988eb49dbf",
- "urn:c6b77905-a877-4bf7-bb02-8b2c581b45a6",
- "urn:c9b41c2e-95ef-41ff-ab0e-6ebafe11329d",
- "urn:dcb7674a-1e3c-411c-95d8-0e4fc5aab43e"
+ "bids::sla.png",
+ "bids::slb.png",
+ "bids::slc.png",
+ "bids::sld.png",
+ "bids::sle.png",
+ "bids::slf.png",
+ "bids::slg.png",
+ "bids::slh.png",
+ "bids::sli.png",
+ "bids::slj.png",
+ "bids::slk.png",
+ "bids::sll.png"
]
},
{
- "@id": "urn:c77e6fc9-34cf-4f6e-b42e-3890d59a8e81",
+ "@id": "urn:pngappen-OAGXpflt",
"Label": "pngappend",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend example_func2highres1.png example_func2highres2.png example_func2highres.png",
"Used": [
- "urn:9fbead39-7891-43e5-8dc9-12d985617f2c",
- "urn:ce6239a0-e326-47c3-b7d0-1ee3963c36b4"
+ "bids::example_func2highres1.png",
+ "bids::example_func2highres2.png"
]
},
{
- "@id": "urn:6b72f628-1ec4-4a98-ae8a-929cba33bab5",
+ "@id": "urn:rm-ugjHnpxW",
"Label": "rm",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/bin/rm -f sl?.png example_func2highres2.png",
"Used": [
- "urn:9fbead39-7891-43e5-8dc9-12d985617f2c",
- "urn:ea755f41-a00d-4582-be8c-86b8d98cf377"
+ "bids::example_func2highres2.png",
+ "bids::sl?.png"
]
},
{
- "@id": "urn:84e58995-014d-4089-bad8-578e23399b07",
+ "@id": "urn:rm-SZJB2wRs",
"Label": "rm",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/bin/rm example_func2highres1.png",
"Used": [
- "urn:ce6239a0-e326-47c3-b7d0-1ee3963c36b4"
+ "bids::example_func2highres1.png"
]
},
{
- "@id": "urn:4335828e-9ce9-4fa0-85c2-4a0d18b4394c",
+ "@id": "urn:mcflirt-fSkOmPFv",
"Label": "mcflirt",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs -spline_final",
"Used": [
- "urn:0924054c-0c39-4d36-b059-e742e85e493d"
+ "bids::prefiltered_func_data"
]
},
{
- "@id": "urn:7556cc7a-14ba-46ba-a8f2-ba3d98f37993",
+ "@id": "urn:makedire-ykL6bIwa",
"Label": "Make directory",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/bin/mkdir -p mc",
"Used": []
},
{
- "@id": "urn:5dc549f4-647c-486e-8759-782021b9509f",
+ "@id": "urn:mv-r5PjOrob",
"Label": "mv",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc",
"Used": [
- "urn:1de485b9-a047-4a69-b2bf-8d71b7de8903",
- "urn:470281e3-3e60-4466-ae7f-99338ead202e",
- "urn:5a7b2004-f5c6-4f5b-ace8-adb7207782e0",
- "urn:5d2b1b83-5fd8-4230-8e74-13743ba69bb6",
- "urn:7383a9ee-eced-40b0-a8af-cac4cefc4d69",
- "urn:9f412ad3-5b63-4950-bbad-708aa07362fe"
+ "bids::prefiltered_func_data_mcf.mat",
+ "bids::prefiltered_func_data_mcf.par",
+ "bids::prefiltered_func_data_mcf_abs.rms",
+ "bids::prefiltered_func_data_mcf_abs_mean.rms",
+ "bids::prefiltered_func_data_mcf_rel.rms",
+ "bids::prefiltered_func_data_mcf_rel_mean.rms"
]
},
{
- "@id": "urn:cbfc8ec2-5355-4a4f-aaf8-dc161b588f7d",
+ "@id": "urn:fsltsplo-V40wbRN0",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png",
"Used": [
- "urn:470281e3-3e60-4466-ae7f-99338ead202e"
+ "bids::prefiltered_func_data_mcf.par"
]
},
{
- "@id": "urn:252514db-a544-4986-996e-fdaf40afdb46",
+ "@id": "urn:fsltsplo-S5OsKnAK",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png",
"Used": [
- "urn:470281e3-3e60-4466-ae7f-99338ead202e"
+ "bids::prefiltered_func_data_mcf.par"
]
},
{
- "@id": "urn:765995cc-ff2c-4b3d-ab06-620255e297ff",
+ "@id": "urn:fsltsplo-SEpWzzeB",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png",
"Used": [
- "urn:95e5d644-6386-44e3-aead-85ac9ac956a8"
+ "bids::prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms"
]
},
{
- "@id": "urn:a07b6f8c-7c19-4e7e-b155-24fb0168516e",
+ "@id": "urn:fslmaths-4R2qoFkh",
"Label": "fslmaths",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func",
"Used": [
- "urn:c00ec312-9c80-4217-b67b-1cf38581bceb"
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:93dba0ab-ccea-44d9-8dc3-a8e853cd4d31",
+ "@id": "urn:bet2-Y3qoaHaK",
"Label": "bet2",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/bet2 mean_func mask -f 0.3 -n -m",
"Used": [
- "urn:2c3ed292-748f-4a7d-9213-01e6c0b8164d"
+ "bids::mean_func"
]
},
{
- "@id": "urn:68476387-e9e1-4562-bd05-044521173b60",
+ "@id": "urn:immv-4kgkNuZh",
"Label": "immv",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/immv mask_mask mask",
"Used": [
- "urn:2f293ea8-ac23-4731-99a3-f243de258b39"
+ "bids::mask_mask"
]
},
{
- "@id": "urn:7eef4a4b-730b-4fea-b783-9403cf46b7fa",
+ "@id": "urn:fslmaths-96ZZNvFa",
"Label": "fslmaths",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet",
"Used": [
- "urn:8715ab85-5e53-496d-acb2-34021963c14a",
- "urn:c00ec312-9c80-4217-b67b-1cf38581bceb"
+ "bids::mask",
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:0c4d4783-701f-4c37-8ea8-410b00bee391",
+ "@id": "urn:fslstats-GBOY6eMl",
"Label": "fslstats",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_bet -p 2 -p 98",
"Used": [
- "urn:4e2824a4-208e-4109-98cd-d2aa9a90ede2"
+ "bids::prefiltered_func_data_bet"
]
},
{
- "@id": "urn:525029ed-c19f-49c3-ba6d-2d971b656318",
+ "@id": "urn:fslmaths-UGKt7EeQ",
"Label": "fslmaths",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_bet -thr 74.4585571 -Tmin -bin mask -odt char",
"Used": [
- "urn:4e2824a4-208e-4109-98cd-d2aa9a90ede2"
+ "bids::prefiltered_func_data_bet"
]
},
{
- "@id": "urn:8bdcd5fd-5c0d-49d3-bc53-e4f941f97875",
+ "@id": "urn:fslstats-q94UYRly",
"Label": "fslstats",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_mcf -k mask -p 50",
"Used": [
- "urn:c00ec312-9c80-4217-b67b-1cf38581bceb"
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:bd112a10-b4d7-4dc4-af3c-b22efb773c55",
+ "@id": "urn:fslmaths-xR0Ys5gM",
"Label": "fslmaths",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -dilF mask",
"Used": [
- "urn:8715ab85-5e53-496d-acb2-34021963c14a"
+ "bids::mask"
]
},
{
- "@id": "urn:2fc4ff83-2a26-4a10-80bc-0102aa6d6e94",
+ "@id": "urn:fslmaths-1w02UWwW",
"Label": "fslmaths",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh",
"Used": [
- "urn:8715ab85-5e53-496d-acb2-34021963c14a",
- "urn:c00ec312-9c80-4217-b67b-1cf38581bceb"
+ "bids::mask",
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:a63366cb-4305-471f-9c59-3eb80e99629e",
+ "@id": "urn:fslmaths-0JxcZLu8",
"Label": "fslmaths",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func",
"Used": [
- "urn:95fcf1df-0d61-4ca6-9267-40abe42fb652"
+ "bids::prefiltered_func_data_thresh"
]
},
{
- "@id": "urn:f0df4582-6ede-4262-af8a-21feda9b538b",
+ "@id": "urn:susan-TDeycXdk",
"Label": "susan",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/susan prefiltered_func_data_thresh 445.8289035 2.54777070064 3 1 1 mean_func 445.8289035 prefiltered_func_data_smooth",
"Used": [
- "urn:95fcf1df-0d61-4ca6-9267-40abe42fb652"
+ "bids::prefiltered_func_data_thresh"
]
},
{
- "@id": "urn:c96b85ef-9bad-41dc-a413-025a5563094d",
+ "@id": "urn:fslmaths-d80aVlfN",
"Label": "fslmaths",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth",
"Used": [
- "urn:8715ab85-5e53-496d-acb2-34021963c14a",
- "urn:a08509a8-7e5c-425e-b284-91fba26756e9"
+ "bids::mask",
+ "bids::prefiltered_func_data_smooth"
]
},
{
- "@id": "urn:133cc17d-bdb0-4a73-a87d-102c3a843276",
+ "@id": "urn:fslmaths-s0Y29iqz",
"Label": "fslmaths",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mul 16.8225970571 prefiltered_func_data_intnorm",
"Used": [
- "urn:a08509a8-7e5c-425e-b284-91fba26756e9"
+ "bids::prefiltered_func_data_smooth"
]
},
{
- "@id": "urn:96acc8d3-b1fb-411a-8a5e-0cd058d715e7",
+ "@id": "urn:fslmaths-JKhI0mGJ",
"Label": "fslmaths",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean",
"Used": [
- "urn:839d773c-d1ea-428c-980b-5c45cbd39a55"
+ "bids::prefiltered_func_data_intnorm"
]
},
{
- "@id": "urn:6bed399a-edb1-4db3-b058-05dc76a2f315",
+ "@id": "urn:fslmaths-TC3trTEP",
"Label": "fslmaths",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -bptf 15.0 -1 -add tempMean prefiltered_func_data_tempfilt",
"Used": [
- "urn:01e67382-f8f7-4229-91ba-20b303bf197e",
- "urn:839d773c-d1ea-428c-980b-5c45cbd39a55"
+ "bids::prefiltered_func_data_intnorm",
+ "bids::tempMean"
]
},
{
- "@id": "urn:b7e0e3c2-c7f2-4507-9981-68c0e7f497a8",
+ "@id": "urn:imrm-HwmXAUaU",
"Label": "imrm",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/imrm tempMean",
"Used": [
- "urn:01e67382-f8f7-4229-91ba-20b303bf197e"
+ "bids::tempMean"
]
},
{
- "@id": "urn:64c5f41e-349c-42dd-a27f-95f04499e42a",
+ "@id": "urn:fslmaths-tSgS8G2R",
"Label": "fslmaths",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data",
"Used": [
- "urn:9b63ff00-e57d-492c-9a6a-22e0bc8d0efd"
+ "bids::prefiltered_func_data_tempfilt"
]
},
{
- "@id": "urn:07f1d615-da56-4401-a194-3f2c26ee1978",
+ "@id": "urn:fslmaths-AhdmqdXD",
"Label": "fslmaths",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths filtered_func_data -Tmean mean_func",
"Used": [
- "urn:8c44dd51-35e1-4b89-8524-f882421e5782"
+ "bids::filtered_func_data"
]
},
{
- "@id": "urn:dcb5f57a-81cd-49cf-936d-37102a28864b",
+ "@id": "urn:rm-iMWORXue",
"Label": "rm",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/bin/rm -rf prefiltered_func_data*",
"Used": [
- "urn:6c3d4bab-9cb1-46cf-a0be-a4a89caec3cb"
+ "bids::prefiltered_func_data*"
]
},
{
- "@id": "urn:d0e0899e-adea-40d8-9ab3-eec5b6976039",
+ "@id": "urn:makedire-u1ksLVof",
"Label": "Make directory",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
- "@id": "urn:83cd1459-54f5-4567-bf38-85450c050b8a",
+ "@id": "urn:fslfixte-o8YA0I8P",
"Label": "fslFixText",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
"Used": [
- "urn:0e9519ef-e62c-48ff-9874-02d6bbe82cc7"
+ "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt"
]
},
{
- "@id": "urn:771a00ec-f716-4c32-b8e0-1d6bc6bd887b",
+ "@id": "urn:makedire-Xs7pKLaA",
"Label": "Make directory",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
- "@id": "urn:e8c59636-f0da-46b6-812b-0911a423417e",
+ "@id": "urn:fslfixte-ZTS63XMD",
"Label": "fslFixText",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
"Used": [
- "urn:51ef0d6d-7762-419d-9632-8d9387a31422"
+ "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt"
]
},
{
- "@id": "urn:29c83b1d-da8b-4533-8855-222e99990b85",
+ "@id": "urn:filmgls-jaruefJt",
"Label": "film_gls",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con --fcon=design.fts",
- "Used": []
+ "Used": [
+ "bids::design.con",
+ "bids::design.fts",
+ "bids::design.mat",
+ "bids::filtered_func_data",
+ "bids::stats"
+ ]
},
{
- "@id": "urn:7989ed26-c111-4c65-a7f2-c118f1201bff",
+ "@id": "urn:smoothes-s3pTDfVa",
"Label": "smoothest",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 98 -m mask -r stats/res4d > stats/smoothness",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 98 -m mask -r stats/res4d > stats/smoothness",
"Used": [
- "urn:8715ab85-5e53-496d-acb2-34021963c14a",
- "urn:c2986c0c-ed72-4122-9a88-1a28862e6651"
+ "bids::mask",
+ "bids::stats/res4d"
]
},
{
- "@id": "urn:0f339db7-b6d0-472c-86d9-935025f1e945",
+ "@id": "urn:fslmaths-n2qLbaoB",
"Label": "fslmaths",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1",
"Used": [
- "urn:71cb60e0-66dd-4d10-b2e8-2c188def3d27",
- "urn:8715ab85-5e53-496d-acb2-34021963c14a"
+ "bids::mask",
+ "bids::stats/zstat1"
]
},
{
- "@id": "urn:139dbd77-e2b9-4df8-a292-911d668ab165",
+ "@id": "urn:echo-C1H4DAmG",
"Label": "echo",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "echo 38352 > thresh_zstat1.vol",
"Used": []
},
{
- "@id": "urn:090659f4-2b0a-4c91-a339-d6eb664a39bd",
+ "@id": "urn:fslmaths-YBlEOore",
"Label": "fslmaths",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat2 -mas mask thresh_zstat2",
"Used": [
- "urn:1fc6cd3e-c4fe-4cdd-a175-20aec97b6157",
- "urn:8715ab85-5e53-496d-acb2-34021963c14a"
+ "bids::mask",
+ "bids::stats/zstat2"
]
},
{
- "@id": "urn:90161d09-6f0c-46e4-9d1c-a16798b445cf",
+ "@id": "urn:echo-Y0j456v8",
"Label": "echo",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "echo 38352 > thresh_zstat2.vol",
"Used": []
},
{
- "@id": "urn:ed331241-db7d-4bc0-8c44-35d1d4d65364",
+ "@id": "urn:fslmaths-KJE4C0bu",
"Label": "fslmaths",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat3 -mas mask thresh_zstat3",
"Used": [
- "urn:8715ab85-5e53-496d-acb2-34021963c14a",
- "urn:e97db26f-22a5-423d-ac55-e88ca7ffbfaf"
+ "bids::mask",
+ "bids::stats/zstat3"
]
},
{
- "@id": "urn:bb8e5ee7-88eb-4ae5-9ab0-cfcaabbfa556",
+ "@id": "urn:echo-qOxwR8Mo",
"Label": "echo",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "echo 38352 > thresh_zstat3.vol",
"Used": []
},
{
- "@id": "urn:dbd5fbb8-de1d-4d1f-958d-7bb195badc55",
+ "@id": "urn:fslmaths-E4jilCxt",
"Label": "fslmaths",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat4 -mas mask thresh_zstat4",
"Used": [
- "urn:21d25c7b-b33e-438b-8e59-6bf13beaa9de",
- "urn:8715ab85-5e53-496d-acb2-34021963c14a"
+ "bids::mask",
+ "bids::stats/zstat4"
]
},
{
- "@id": "urn:ad95a8e0-1090-4d6a-97da-f496eb5bb94d",
+ "@id": "urn:echo-3MOLIsgl",
"Label": "echo",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "echo 38352 > thresh_zstat4.vol",
"Used": []
},
{
- "@id": "urn:0f4d6eea-0d6c-4fec-8a2d-9fefb6752db1",
+ "@id": "urn:fslmaths-jPO5lIpX",
"Label": "fslmaths",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat5 -mas mask thresh_zstat5",
"Used": [
- "urn:6305398a-67f9-40b5-8456-ff711cd48892",
- "urn:8715ab85-5e53-496d-acb2-34021963c14a"
+ "bids::mask",
+ "bids::stats/zstat5"
]
},
{
- "@id": "urn:f4dc34ba-c07a-4a04-b16f-2778478dfb60",
+ "@id": "urn:echo-dT2QGlOX",
"Label": "echo",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "echo 38352 > thresh_zstat5.vol",
"Used": []
},
{
- "@id": "urn:9bbddc14-8c3b-4b30-87dd-6d3f0423692f",
+ "@id": "urn:fslmaths-na7pDpFB",
"Label": "fslmaths",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat6 -mas mask thresh_zstat6",
"Used": [
- "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
- "urn:8715ab85-5e53-496d-acb2-34021963c14a"
+ "bids::mask",
+ "bids::stats/zstat6"
]
},
{
- "@id": "urn:2a166a8b-0df5-48e7-885f-3dd1049a4a6e",
+ "@id": "urn:echo-4PcOAySz",
"Label": "echo",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "echo 38352 > thresh_zstat6.vol",
"Used": []
},
{
- "@id": "urn:8f8fe587-dd5a-43d2-9792-8b372f66297e",
+ "@id": "urn:fslmaths-clta5DMl",
"Label": "fslmaths",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zfstat1 -mas mask thresh_zfstat1",
"Used": [
- "urn:8715ab85-5e53-496d-acb2-34021963c14a",
- "urn:fac8ab5f-acb2-45d7-a176-6b27b1260cf1"
+ "bids::mask",
+ "bids::stats/zfstat1"
]
},
{
- "@id": "urn:29ae19fc-3f10-4560-b622-06a4f38fc36e",
+ "@id": "urn:echo-qn9VFNxL",
"Label": "echo",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "echo 38352 > thresh_zfstat1.vol",
"Used": []
},
{
- "@id": "urn:e744d76b-c5b8-44ba-a46a-d60b966b2cf2",
+ "@id": "urn:fslmaths-IhJIjkWO",
"Label": "fslmaths",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zfstat2 -mas mask thresh_zfstat2",
"Used": [
- "urn:12ce83c3-7028-4d69-afb7-ac47d8663d65",
- "urn:8715ab85-5e53-496d-acb2-34021963c14a"
+ "bids::mask",
+ "bids::stats/zfstat2"
]
},
{
- "@id": "urn:69730e52-a1bd-4eab-90f1-d16b1134d0e5",
+ "@id": "urn:echo-6pG3ZhNt",
"Label": "echo",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "echo 38352 > thresh_zfstat2.vol",
"Used": []
},
{
- "@id": "urn:66567581-ae6f-4fef-b90e-0c2e1b58c105",
+ "@id": "urn:ptoz-oLMyRlmj",
"Label": "ptoz",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:60c33d10-55ae-4161-b566-42216c3f0dc8",
+ "@id": "urn:cluster-JM4FT4fe",
"Label": "cluster",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -t 3.090232 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z --voxuncthresh -c stats/cope1 > cluster_zstat1.txt",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -t 3.090232 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z --voxuncthresh -c stats/cope1 > cluster_zstat1.txt",
"Used": [
- "urn:3e7ea993-af25-4097-bcde-e19282d42de7",
- "urn:7f26712f-542f-4cab-b485-c34d61c39b26"
+ "bids::stats/cope1",
+ "bids::thresh_zstat1"
]
},
{
- "@id": "urn:f9a6acf6-a5e0-4fff-9cd4-5518dd375af4",
+ "@id": "urn:cluster2-4gy3b7Dv",
"Label": "cluster2html",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat1",
"Used": [
- "urn:77014477-f46d-4f42-a5cc-62e47afe0b8c"
+ "bids::cluster_zstat1"
]
},
{
- "@id": "urn:8adaf97f-5454-4af6-b15e-0af7e42fb528",
+ "@id": "urn:ptoz-93BR4ond",
"Label": "ptoz",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:07a8d6a6-64b2-42fe-80b4-2b1eac1eb9e7",
+ "@id": "urn:cluster-eZtqBxsh",
"Label": "cluster",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat2 -t 3.090232 --othresh=thresh_zstat2 -o cluster_mask_zstat2 --connectivity=26 --olmax=lmax_zstat2.txt --scalarname=Z --voxuncthresh -c stats/cope2 > cluster_zstat2.txt",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat2 -t 3.090232 --othresh=thresh_zstat2 -o cluster_mask_zstat2 --connectivity=26 --olmax=lmax_zstat2.txt --scalarname=Z --voxuncthresh -c stats/cope2 > cluster_zstat2.txt",
"Used": [
- "urn:a3bdc092-1cb5-4795-9796-f21fd99a495e",
- "urn:d036abd4-f374-4ca5-83ad-1f151c63f354"
+ "bids::stats/cope2",
+ "bids::thresh_zstat2"
]
},
{
- "@id": "urn:50ceaff4-e70e-4882-a294-77ebc5bf71e9",
+ "@id": "urn:cluster2-i3XEGcsV",
"Label": "cluster2html",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat2",
"Used": [
- "urn:e784343f-88eb-4b8d-8447-9af21cf0b76a"
+ "bids::cluster_zstat2"
]
},
{
- "@id": "urn:41cbc35e-a5d8-4bb7-bc11-335f23d0d585",
+ "@id": "urn:ptoz-O2QqU30d",
"Label": "ptoz",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:cb7470f0-d59a-452e-ae07-d28403e45649",
+ "@id": "urn:cluster-f2RhlnID",
"Label": "cluster",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat3 -t 3.090232 --othresh=thresh_zstat3 -o cluster_mask_zstat3 --connectivity=26 --olmax=lmax_zstat3.txt --scalarname=Z --voxuncthresh -c stats/cope3 > cluster_zstat3.txt",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat3 -t 3.090232 --othresh=thresh_zstat3 -o cluster_mask_zstat3 --connectivity=26 --olmax=lmax_zstat3.txt --scalarname=Z --voxuncthresh -c stats/cope3 > cluster_zstat3.txt",
"Used": [
- "urn:6e408f66-20ca-482a-8005-ad8f3afa2a44",
- "urn:808246b0-cd67-4753-8f07-690754d4a9f8"
+ "bids::stats/cope3",
+ "bids::thresh_zstat3"
]
},
{
- "@id": "urn:02264add-1973-4141-8387-b33615c07ee2",
+ "@id": "urn:cluster2-eDt3axD4",
"Label": "cluster2html",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat3",
"Used": [
- "urn:876e299e-293c-40ca-9120-31b5a862d278"
+ "bids::cluster_zstat3"
]
},
{
- "@id": "urn:6110816b-7ef2-4df2-9454-12e5e7d9f8f3",
+ "@id": "urn:ptoz-dcSWGmgc",
"Label": "ptoz",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:925cff4d-fdf7-4657-9ec2-ce8b1557aaef",
+ "@id": "urn:cluster-HDbgeLZt",
"Label": "cluster",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat4 -t 3.090232 --othresh=thresh_zstat4 -o cluster_mask_zstat4 --connectivity=26 --olmax=lmax_zstat4.txt --scalarname=Z --voxuncthresh -c stats/cope4 > cluster_zstat4.txt",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat4 -t 3.090232 --othresh=thresh_zstat4 -o cluster_mask_zstat4 --connectivity=26 --olmax=lmax_zstat4.txt --scalarname=Z --voxuncthresh -c stats/cope4 > cluster_zstat4.txt",
"Used": [
- "urn:b3e44ae2-ba85-4258-8ca3-8f77ffce94c9",
- "urn:fd791b55-91e2-4377-905f-cdf0a2180274"
+ "bids::stats/cope4",
+ "bids::thresh_zstat4"
]
},
{
- "@id": "urn:f6036a07-8760-4628-bd77-3b22d8121ce4",
+ "@id": "urn:cluster2-FJInHTu7",
"Label": "cluster2html",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat4",
"Used": [
- "urn:9e3c0116-5947-4998-8e67-a79ab55a637f"
+ "bids::cluster_zstat4"
]
},
{
- "@id": "urn:f317f726-cdf5-4537-8121-e7d5cd0b8427",
+ "@id": "urn:ptoz-PLRJwxPm",
"Label": "ptoz",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:ab3c4e2c-eac4-499d-83f7-ac40b11b2893",
+ "@id": "urn:cluster-RlEhegMp",
"Label": "cluster",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat5 -t 3.090232 --othresh=thresh_zstat5 -o cluster_mask_zstat5 --connectivity=26 --olmax=lmax_zstat5.txt --scalarname=Z --voxuncthresh -c stats/cope5 > cluster_zstat5.txt",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat5 -t 3.090232 --othresh=thresh_zstat5 -o cluster_mask_zstat5 --connectivity=26 --olmax=lmax_zstat5.txt --scalarname=Z --voxuncthresh -c stats/cope5 > cluster_zstat5.txt",
"Used": [
- "urn:241de80c-b8e2-43b3-be20-f4200ac54a29",
- "urn:fd665767-b5b2-4d60-a6e6-23c46cdfdc3c"
+ "bids::stats/cope5",
+ "bids::thresh_zstat5"
]
},
{
- "@id": "urn:11e8ed87-b70c-4982-96a9-a139509bc82e",
+ "@id": "urn:cluster2-TS1gkeXO",
"Label": "cluster2html",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat5",
"Used": [
- "urn:7de17507-bdc9-4002-bf2d-2815ea50a192"
+ "bids::cluster_zstat5"
]
},
{
- "@id": "urn:932a5b83-fa80-448a-a1c3-dedfd1901952",
+ "@id": "urn:ptoz-jBncOG5N",
"Label": "ptoz",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:78841fc2-5796-4cc5-9c0e-afab1681ff6b",
+ "@id": "urn:cluster-ef7ehgcK",
"Label": "cluster",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat6 -t 3.090232 --othresh=thresh_zstat6 -o cluster_mask_zstat6 --connectivity=26 --olmax=lmax_zstat6.txt --scalarname=Z --voxuncthresh -c stats/cope6 > cluster_zstat6.txt",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat6 -t 3.090232 --othresh=thresh_zstat6 -o cluster_mask_zstat6 --connectivity=26 --olmax=lmax_zstat6.txt --scalarname=Z --voxuncthresh -c stats/cope6 > cluster_zstat6.txt",
"Used": [
- "urn:9636addd-4ce7-45df-a999-e6e6136f6bd5",
- "urn:9b654366-a76d-4764-b5c9-25583871e422"
+ "bids::stats/cope6",
+ "bids::thresh_zstat6"
]
},
{
- "@id": "urn:00752b92-e109-448b-997f-b3ea8196cd92",
+ "@id": "urn:cluster2-y8dpnA3u",
"Label": "cluster2html",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat6",
"Used": [
- "urn:f4788744-9fd7-46ff-ab58-b82a497af808"
+ "bids::cluster_zstat6"
]
},
{
- "@id": "urn:65fc4b87-9264-42a7-9b71-53ce3afb9822",
+ "@id": "urn:ptoz-ARjYR1mH",
"Label": "ptoz",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:5c4343d6-8bff-477b-9505-6886037bf8fa",
+ "@id": "urn:cluster-l1k6btTJ",
"Label": "cluster",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zfstat1 -t 3.090232 --othresh=thresh_zfstat1 -o cluster_mask_zfstat1 --connectivity=26 --olmax=lmax_zfstat1.txt --scalarname=Z --voxuncthresh > cluster_zfstat1.txt",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zfstat1 -t 3.090232 --othresh=thresh_zfstat1 -o cluster_mask_zfstat1 --connectivity=26 --olmax=lmax_zfstat1.txt --scalarname=Z --voxuncthresh > cluster_zfstat1.txt",
"Used": [
- "urn:8e8371ea-1da5-42d5-87e9-39e5dbce47ae"
+ "bids::thresh_zfstat1"
]
},
{
- "@id": "urn:9bc6ddb2-0e44-4319-9930-3448025da245",
+ "@id": "urn:cluster2-LnaUBQbQ",
"Label": "cluster2html",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zfstat1",
"Used": [
- "urn:30c8cd54-1653-4cff-86ea-7ad669b107a4"
+ "bids::cluster_zfstat1"
]
},
{
- "@id": "urn:0f413d1b-22ea-42e5-9d8f-a8ed53c5e448",
+ "@id": "urn:ptoz-FsDdgUhs",
"Label": "ptoz",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:df900226-398d-422c-963e-eee25dd764b6",
+ "@id": "urn:cluster-24hfHD40",
"Label": "cluster",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zfstat2 -t 3.090232 --othresh=thresh_zfstat2 -o cluster_mask_zfstat2 --connectivity=26 --olmax=lmax_zfstat2.txt --scalarname=Z --voxuncthresh > cluster_zfstat2.txt",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zfstat2 -t 3.090232 --othresh=thresh_zfstat2 -o cluster_mask_zfstat2 --connectivity=26 --olmax=lmax_zfstat2.txt --scalarname=Z --voxuncthresh > cluster_zfstat2.txt",
"Used": [
- "urn:5e13557d-67b9-492a-80c9-23771d8429e4"
+ "bids::thresh_zfstat2"
]
},
{
- "@id": "urn:0c1e9eef-fa09-4004-ba3d-9269e91e41ed",
+ "@id": "urn:cluster2-ZjVOQLu5",
"Label": "cluster2html",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
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"Used": [
- "urn:81217ec8-dd0d-414e-bb72-4f7b170531f9"
+ "bids::cluster_zfstat2"
]
},
{
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- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
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"Used": [
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+ "bids::thresh_zstat1"
]
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{
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"Used": [
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+ "bids::thresh_zstat2"
]
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{
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- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
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+ "bids::thresh_zstat3"
]
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+ "bids::thresh_zstat4"
]
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+ "bids::thresh_zstat5"
]
},
{
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"Label": "fslstats",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
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"Used": [
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+ "bids::thresh_zstat6"
]
},
{
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"Label": "fslstats",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
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"Used": [
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+ "bids::thresh_zfstat1"
]
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{
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"Label": "fslstats",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
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"Used": [
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+ "bids::thresh_zfstat2"
]
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"Used": []
},
{
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- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
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"Used": [
- "urn:b51f6a09-3f73-4fb2-85a4-d4686faec93e"
+ "bids::rendered_thresh_zstat1"
]
},
{
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+ "@id": "urn:cp-qc6GeWl1",
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- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
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"Used": [
- "urn:e0483247-a008-491a-8bb4-5b7c9e14dc17"
+ "bids::/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif"
]
},
{
- "@id": "urn:a9e05bff-7f86-441f-aea4-2b1431340600",
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+ "AssociatedWith": "urn:fsl-Ld1arblU",
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"Used": []
},
{
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"Label": "slicer",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
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"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat2 -A 750 rendered_thresh_zstat2.png",
"Used": [
- "urn:f015120b-6635-4636-8f4e-0bc4e2972782"
+ "bids::rendered_thresh_zstat2"
]
},
{
- "@id": "urn:f150c860-a320-4b6a-bffb-3296f4a0d6df",
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"Label": "overlay",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
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"Used": []
},
{
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"Used": [
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+ "bids::rendered_thresh_zstat3"
]
},
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"Used": []
},
{
- "@id": "urn:8f306cc1-f996-42e7-9d77-2467d960872b",
+ "@id": "urn:slicer-bbTTWKvI",
"Label": "slicer",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
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"Used": [
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+ "bids::rendered_thresh_zstat4"
]
},
{
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+ "@id": "urn:overlay-IzdEsoLz",
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- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
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"Used": []
},
{
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+ "@id": "urn:slicer-2HP5rM9A",
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- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
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+ "bids::rendered_thresh_zstat5"
]
},
{
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+ "@id": "urn:overlay-LtsDrMgV",
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+ "AssociatedWith": "urn:fsl-Ld1arblU",
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"Used": []
},
{
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"Used": [
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+ "bids::rendered_thresh_zstat6"
]
},
{
- "@id": "urn:1b1ff05f-85fe-4337-80e1-7a9b9cde64fc",
+ "@id": "urn:overlay-q6aDo9iF",
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+ "AssociatedWith": "urn:fsl-Ld1arblU",
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},
{
- "@id": "urn:592a3b92-acfc-4483-a533-fe9b09f9012d",
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- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
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"Used": [
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+ "bids::rendered_thresh_zfstat1"
]
},
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+ "@id": "urn:overlay-0BQ508sk",
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"Used": []
},
{
- "@id": "urn:ef48de35-484e-4f6e-bccc-353b7247adc5",
+ "@id": "urn:slicer-L7n6t8V4",
"Label": "slicer",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
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"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zfstat2 -A 750 rendered_thresh_zfstat2.png",
"Used": [
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+ "bids::rendered_thresh_zfstat2"
]
},
{
- "@id": "urn:76a2a86f-3b5d-43d4-a38a-337f94d822dd",
+ "@id": "urn:makedire-aJnJKcVD",
"Label": "Make directory",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "mkdir -p tsplot",
"Used": []
},
{
- "@id": "urn:fdcb6c32-a4be-4021-b672-192113a2f992",
+ "@id": "urn:tsplot-omt5Es95",
"Label": "tsplot",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:fsl-Ld1arblU",
"Command": "/usr/local/packages/fsl-5.0.10/bin/tsplot . -f filtered_func_data -o tsplot",
"Used": []
}
],
"Entities": [
{
- "@id": "urn:cc8f8d80-4f02-496d-9a4a-e0e2bfbe3189",
+ "@id": "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold",
"Label": "sub-01_task-tonecounting_bold",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold",
+ "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold",
"digest": {
- "sha256": "028adf00daa36e78f06a61dcd3cb3526cd8564c1284e80516ab5520701324ac1"
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}
},
{
- "@id": "urn:0924054c-0c39-4d36-b059-e742e85e493d",
+ "@id": "bids::prefiltered_func_data",
"Label": "prefiltered_func_data",
"AtLocation": "prefiltered_func_data",
- "GeneratedBy": "urn:8b7ebf9b-55a0-4a1d-b503-719151eebc50",
+ "GeneratedBy": "urn:fslmaths-qeUb1qc5",
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}
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{
- "@id": "urn:8b3bbb39-0aea-4201-97f0-045c3f5022a9",
+ "@id": "bids::example_func",
"Label": "example_func",
"AtLocation": "example_func",
- "GeneratedBy": "urn:74cebf5a-7236-4402-8dc4-8d5936bcc43c",
+ "GeneratedBy": "urn:fslroi-VBxwwZY6",
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+ "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/example_func.nii.gz",
"Label": "example_func.nii.gz",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/example_func.nii.gz",
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@@ -1054,15 +1064,15 @@
}
},
{
- "@id": "urn:cb081815-8a6c-42f8-bb87-18c9e4cb7bc9",
+ "@id": "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
"Label": "sub-01_T1w_brain",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
+ "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
"digest": {
- "sha256": "ccb9a4d1def67002e358c45bd912034053ffc221ab52c2a19aa55f72c3236279"
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}
},
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- "@id": "urn:d2c7c8ce-aa21-4a64-a01f-9425bfa93b01",
+ "@id": "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain",
"Label": "MNI152_T1_2mm_brain",
"AtLocation": "/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain",
"digest": {
@@ -1070,45 +1080,57 @@
}
},
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- "@id": "urn:7c045668-7bf9-44d6-8e7b-bfa797641a7b",
+ "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat",
"Label": "fsl_gamma_basis.feat",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat",
- "GeneratedBy": "urn:e9a73030-0006-4ef8-95e3-5834de3078f3"
+ "GeneratedBy": "urn:mainfeat-7FPDQFA3"
},
{
- "@id": "urn:d6a983fb-16fb-45a7-be11-a76b4e20cd8b",
+ "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/reg",
"Label": "reg",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/reg",
- "GeneratedBy": "urn:3e26d898-d64e-4301-8def-9765c710bcdf",
+ "GeneratedBy": "urn:makedire-lVc4z7Bv",
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{
- "@id": "urn:c7e22265-242c-40b2-a6d4-3b6718af7d53",
+ "@id": "bids::highres",
"Label": "highres",
"AtLocation": "highres",
- "GeneratedBy": "urn:1e662f78-13a4-474a-9645-9ee637aa9e4b",
+ "GeneratedBy": "urn:fslmaths-DHqHCVuk",
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+ "@id": "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
"Label": "sub-01_T1w",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
+ "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
"digest": {
- "sha256": "3be6c69338e200d2a286a56cd9a0030539cf50201f412c910ade833e18354d27"
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},
{
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- "Label": "",
- "AtLocation": "",
- "GeneratedBy": "urn:26a00968-1740-4b01-8330-41148ecff2f1"
+ "@id": "bids::highres_head",
+ "Label": "highres_head",
+ "AtLocation": "highres_head",
+ "GeneratedBy": "urn:fslmaths-hSsHK6sO",
+ "digest": {
+ "sha256": "590f180bade23162ef1567a5a61d86ee93155e4c7dc59c04c8ac5d6b7a20ea51"
+ }
+ },
+ {
+ "@id": "bids::example_func2highres",
+ "Label": "example_func2highres",
+ "AtLocation": "example_func2highres",
+ "GeneratedBy": "urn:epireg-PfcVzMiS",
+ "digest": {
+ "sha256": "00c021d82b83d2dc562c77f76528ece0f7425d4982f292f22021467afce1ba59"
+ }
},
{
- "@id": "urn:5f05c7a5-2284-4cdf-b443-eaacdd73c3dc",
+ "@id": "bids::example_func2highres.mat",
"Label": "example_func2highres.mat",
"AtLocation": "example_func2highres.mat",
"digest": {
@@ -1116,267 +1138,259 @@
}
},
{
- "@id": "urn:6b7b084a-b2b2-475f-920a-c985e82cda62",
+ "@id": "bids::highres2example_func.mat",
"Label": "highres2example_func.mat",
"AtLocation": "highres2example_func.mat",
- "GeneratedBy": "urn:cb078c97-7316-4480-a77e-abf7f6853c4e",
+ "GeneratedBy": "urn:convertx-WJotBeOj",
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}
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- "AtLocation": "example_func2highres",
- "digest": {
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- }
- },
- {
- "@id": "urn:826557c4-b724-4e3c-bc51-cd7035d9eea8",
+ "@id": "bids::sla.png",
"Label": "sla.png",
"AtLocation": "sla.png",
- "GeneratedBy": "urn:fa93e59f-1e2b-49fe-b6c1-2ea8c2665df1",
+ "GeneratedBy": "urn:slicer-IvnNaijU",
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}
},
{
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"Label": "slb.png",
"AtLocation": "slb.png",
- "GeneratedBy": "urn:fa93e59f-1e2b-49fe-b6c1-2ea8c2665df1",
+ "GeneratedBy": "urn:slicer-IvnNaijU",
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}
},
{
- "@id": "urn:c9b41c2e-95ef-41ff-ab0e-6ebafe11329d",
+ "@id": "bids::slc.png",
"Label": "slc.png",
"AtLocation": "slc.png",
- "GeneratedBy": "urn:fa93e59f-1e2b-49fe-b6c1-2ea8c2665df1",
+ "GeneratedBy": "urn:slicer-IvnNaijU",
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}
},
{
- "@id": "urn:927af817-f93a-489f-a7f9-8042ef2bd242",
+ "@id": "bids::sld.png",
"Label": "sld.png",
"AtLocation": "sld.png",
- "GeneratedBy": "urn:fa93e59f-1e2b-49fe-b6c1-2ea8c2665df1",
+ "GeneratedBy": "urn:slicer-IvnNaijU",
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}
},
{
- "@id": "urn:2714f869-ac76-4842-8998-8d005cbe8b00",
+ "@id": "bids::sle.png",
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"AtLocation": "sle.png",
- "GeneratedBy": "urn:fa93e59f-1e2b-49fe-b6c1-2ea8c2665df1",
+ "GeneratedBy": "urn:slicer-IvnNaijU",
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}
},
{
- "@id": "urn:c6b77905-a877-4bf7-bb02-8b2c581b45a6",
+ "@id": "bids::slf.png",
"Label": "slf.png",
"AtLocation": "slf.png",
- "GeneratedBy": "urn:fa93e59f-1e2b-49fe-b6c1-2ea8c2665df1",
+ "GeneratedBy": "urn:slicer-IvnNaijU",
"digest": {
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}
},
{
- "@id": "urn:8bc12560-688d-456f-909d-dc9eda67b073",
+ "@id": "bids::slg.png",
"Label": "slg.png",
"AtLocation": "slg.png",
- "GeneratedBy": "urn:fa93e59f-1e2b-49fe-b6c1-2ea8c2665df1",
+ "GeneratedBy": "urn:slicer-IvnNaijU",
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}
},
{
- "@id": "urn:76125b99-5fb8-4a46-9b93-8ff9cd4e3e70",
+ "@id": "bids::slh.png",
"Label": "slh.png",
"AtLocation": "slh.png",
- "GeneratedBy": "urn:fa93e59f-1e2b-49fe-b6c1-2ea8c2665df1",
+ "GeneratedBy": "urn:slicer-IvnNaijU",
"digest": {
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}
},
{
- "@id": "urn:835d8881-a887-40b8-9960-a4fc64ada68c",
+ "@id": "bids::sli.png",
"Label": "sli.png",
"AtLocation": "sli.png",
- "GeneratedBy": "urn:fa93e59f-1e2b-49fe-b6c1-2ea8c2665df1",
+ "GeneratedBy": "urn:slicer-IvnNaijU",
"digest": {
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}
},
{
- "@id": "urn:12fad9c5-48eb-46f2-8071-7d08b1fb1098",
+ "@id": "bids::slj.png",
"Label": "slj.png",
"AtLocation": "slj.png",
- "GeneratedBy": "urn:fa93e59f-1e2b-49fe-b6c1-2ea8c2665df1",
+ "GeneratedBy": "urn:slicer-IvnNaijU",
"digest": {
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}
},
{
- "@id": "urn:bec98c26-9830-48d9-9ac8-1b988eb49dbf",
+ "@id": "bids::slk.png",
"Label": "slk.png",
"AtLocation": "slk.png",
- "GeneratedBy": "urn:fa93e59f-1e2b-49fe-b6c1-2ea8c2665df1",
+ "GeneratedBy": "urn:slicer-IvnNaijU",
"digest": {
"sha256": "c540df2ed1d697609b08bd955a2ca31f3aeca3395c403edd9b036be63682eb64"
}
},
{
- "@id": "urn:34dbf791-6f89-4a89-aee7-1908de2b5835",
+ "@id": "bids::sll.png",
"Label": "sll.png",
"AtLocation": "sll.png",
- "GeneratedBy": "urn:fa93e59f-1e2b-49fe-b6c1-2ea8c2665df1",
+ "GeneratedBy": "urn:slicer-IvnNaijU",
"digest": {
"sha256": "0b9c965bbea7bb7d1f251ea0f2973f485727fbbc91357e30aee25ff9869f5009"
}
},
{
- "@id": "urn:ce6239a0-e326-47c3-b7d0-1ee3963c36b4",
+ "@id": "bids::example_func2highres1.png",
"Label": "example_func2highres1.png",
"AtLocation": "example_func2highres1.png",
- "GeneratedBy": "urn:63dd083a-b6c0-4169-bdc1-5b4c478ae687",
+ "GeneratedBy": "urn:pngappen-Hjp62Yc9",
"digest": {
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}
},
{
- "@id": "urn:65393bc8-f970-412f-9ce9-6614d4d6200a",
+ "@id": "bids::sla.png",
"Label": "sla.png",
"AtLocation": "sla.png",
- "GeneratedBy": "urn:a68d5032-c2be-4a84-ab5d-fbde9e657d5f",
+ "GeneratedBy": "urn:slicer-4HjW8Tda",
"digest": {
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}
},
{
- "@id": "urn:c65ad0ab-2625-4563-8b53-45bd217dfa41",
+ "@id": "bids::slb.png",
"Label": "slb.png",
"AtLocation": "slb.png",
- "GeneratedBy": "urn:a68d5032-c2be-4a84-ab5d-fbde9e657d5f",
+ "GeneratedBy": "urn:slicer-4HjW8Tda",
"digest": {
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}
},
{
- "@id": "urn:aad4164b-37cd-491c-964b-2a23d48dfe04",
+ "@id": "bids::slc.png",
"Label": "slc.png",
"AtLocation": "slc.png",
- "GeneratedBy": "urn:a68d5032-c2be-4a84-ab5d-fbde9e657d5f",
+ "GeneratedBy": "urn:slicer-4HjW8Tda",
"digest": {
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}
},
{
- "@id": "urn:1afe2e30-81b6-43e6-97ee-869c7c2e8a2b",
+ "@id": "bids::sld.png",
"Label": "sld.png",
"AtLocation": "sld.png",
- "GeneratedBy": "urn:a68d5032-c2be-4a84-ab5d-fbde9e657d5f",
+ "GeneratedBy": "urn:slicer-4HjW8Tda",
"digest": {
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}
},
{
- "@id": "urn:ccd6be76-9e7a-48e0-b962-3d8488e16e65",
+ "@id": "bids::sle.png",
"Label": "sle.png",
"AtLocation": "sle.png",
- "GeneratedBy": "urn:a68d5032-c2be-4a84-ab5d-fbde9e657d5f",
+ "GeneratedBy": "urn:slicer-4HjW8Tda",
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}
},
{
- "@id": "urn:bc74ef1e-f1ed-42f8-8a16-b6b53a79c64e",
+ "@id": "bids::slf.png",
"Label": "slf.png",
"AtLocation": "slf.png",
- "GeneratedBy": "urn:a68d5032-c2be-4a84-ab5d-fbde9e657d5f",
+ "GeneratedBy": "urn:slicer-4HjW8Tda",
"digest": {
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}
},
{
- "@id": "urn:9f3489e8-3177-45d1-a55e-0af7bb8c0eab",
+ "@id": "bids::slg.png",
"Label": "slg.png",
"AtLocation": "slg.png",
- "GeneratedBy": "urn:a68d5032-c2be-4a84-ab5d-fbde9e657d5f",
+ "GeneratedBy": "urn:slicer-4HjW8Tda",
"digest": {
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}
},
{
- "@id": "urn:8197e7e1-580a-4d2f-8865-764f9d032b4d",
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"Label": "slh.png",
"AtLocation": "slh.png",
- "GeneratedBy": "urn:a68d5032-c2be-4a84-ab5d-fbde9e657d5f",
+ "GeneratedBy": "urn:slicer-4HjW8Tda",
"digest": {
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}
},
{
- "@id": "urn:8219f30c-b029-404f-8ee3-680e7b1dd0c7",
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"AtLocation": "sli.png",
- "GeneratedBy": "urn:a68d5032-c2be-4a84-ab5d-fbde9e657d5f",
+ "GeneratedBy": "urn:slicer-4HjW8Tda",
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}
},
{
- "@id": "urn:f23ebd7e-7168-4959-80be-49956f5b7329",
+ "@id": "bids::slj.png",
"Label": "slj.png",
"AtLocation": "slj.png",
- "GeneratedBy": "urn:a68d5032-c2be-4a84-ab5d-fbde9e657d5f",
+ "GeneratedBy": "urn:slicer-4HjW8Tda",
"digest": {
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}
},
{
- "@id": "urn:a50e4d44-5998-469b-bdd7-e58dc42e9c39",
+ "@id": "bids::slk.png",
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"AtLocation": "slk.png",
- "GeneratedBy": "urn:a68d5032-c2be-4a84-ab5d-fbde9e657d5f",
+ "GeneratedBy": "urn:slicer-4HjW8Tda",
"digest": {
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}
},
{
- "@id": "urn:2b9671d2-998a-4437-8282-c857b0bf8b84",
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"AtLocation": "sll.png",
- "GeneratedBy": "urn:a68d5032-c2be-4a84-ab5d-fbde9e657d5f",
+ "GeneratedBy": "urn:slicer-4HjW8Tda",
"digest": {
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}
},
{
- "@id": "urn:9fbead39-7891-43e5-8dc9-12d985617f2c",
+ "@id": "bids::example_func2highres2.png",
"Label": "example_func2highres2.png",
"AtLocation": "example_func2highres2.png",
- "GeneratedBy": "urn:fc548620-4d3b-4aaf-a4d6-39a1641f8bcb",
+ "GeneratedBy": "urn:pngappen-FqJ58gVR",
"digest": {
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}
},
{
- "@id": "urn:84e80130-5c98-46ec-ad2f-28ae98a0c8f4",
+ "@id": "bids::example_func2highres.png",
"Label": "example_func2highres.png",
"AtLocation": "example_func2highres.png",
- "GeneratedBy": "urn:c77e6fc9-34cf-4f6e-b42e-3890d59a8e81",
+ "GeneratedBy": "urn:pngappen-OAGXpflt",
"digest": {
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}
},
{
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+ "@id": "bids::sl?.png",
"Label": "sl?.png",
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"digest": {
@@ -1384,25 +1398,25 @@
}
},
{
- "@id": "urn:c00ec312-9c80-4217-b67b-1cf38581bceb",
+ "@id": "bids::prefiltered_func_data_mcf",
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"AtLocation": "prefiltered_func_data_mcf",
- "GeneratedBy": "urn:4335828e-9ce9-4fa0-85c2-4a0d18b4394c",
+ "GeneratedBy": "urn:mcflirt-fSkOmPFv",
"digest": {
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}
},
{
- "@id": "urn:3320ef3f-df08-4280-abfe-5bb489fd6a0f",
+ "@id": "bids::mc",
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"AtLocation": "mc",
- "GeneratedBy": "urn:7556cc7a-14ba-46ba-a8f2-ba3d98f37993",
+ "GeneratedBy": "urn:makedire-ykL6bIwa",
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}
},
{
- "@id": "urn:9f412ad3-5b63-4950-bbad-708aa07362fe",
+ "@id": "bids::prefiltered_func_data_mcf.mat",
"Label": "prefiltered_func_data_mcf.mat",
"AtLocation": "prefiltered_func_data_mcf.mat",
"digest": {
@@ -1410,7 +1424,7 @@
}
},
{
- "@id": "urn:470281e3-3e60-4466-ae7f-99338ead202e",
+ "@id": "bids::prefiltered_func_data_mcf.par",
"Label": "prefiltered_func_data_mcf.par",
"AtLocation": "prefiltered_func_data_mcf.par",
"digest": {
@@ -1418,7 +1432,7 @@
}
},
{
- "@id": "urn:1de485b9-a047-4a69-b2bf-8d71b7de8903",
+ "@id": "bids::prefiltered_func_data_mcf_abs.rms",
"Label": "prefiltered_func_data_mcf_abs.rms",
"AtLocation": "prefiltered_func_data_mcf_abs.rms",
"digest": {
@@ -1426,7 +1440,7 @@
}
},
{
- "@id": "urn:5a7b2004-f5c6-4f5b-ace8-adb7207782e0",
+ "@id": "bids::prefiltered_func_data_mcf_abs_mean.rms",
"Label": "prefiltered_func_data_mcf_abs_mean.rms",
"AtLocation": "prefiltered_func_data_mcf_abs_mean.rms",
"digest": {
@@ -1434,7 +1448,7 @@
}
},
{
- "@id": "urn:7383a9ee-eced-40b0-a8af-cac4cefc4d69",
+ "@id": "bids::prefiltered_func_data_mcf_rel.rms",
"Label": "prefiltered_func_data_mcf_rel.rms",
"AtLocation": "prefiltered_func_data_mcf_rel.rms",
"digest": {
@@ -1442,7 +1456,7 @@
}
},
{
- "@id": "urn:5d2b1b83-5fd8-4230-8e74-13743ba69bb6",
+ "@id": "bids::prefiltered_func_data_mcf_rel_mean.rms",
"Label": "prefiltered_func_data_mcf_rel_mean.rms",
"AtLocation": "prefiltered_func_data_mcf_rel_mean.rms",
"digest": {
@@ -1450,34 +1464,34 @@
}
},
{
- "@id": "urn:692db7c4-53fe-4a91-9834-ef4c246fcd14",
+ "@id": "bids::mc",
"Label": "mc",
"AtLocation": "mc",
- "GeneratedBy": "urn:5dc549f4-647c-486e-8759-782021b9509f",
+ "GeneratedBy": "urn:mv-r5PjOrob",
"digest": {
"sha256": "a1a8fa7b1d2bf5bc0a263e95f926d3d9b656d2572455245d46edf48e93744ffa"
}
},
{
- "@id": "urn:1e30c693-6f40-49df-b6e7-cbc1b79a9ab6",
+ "@id": "bids::rot.png",
"Label": "rot.png",
"AtLocation": "rot.png",
- "GeneratedBy": "urn:cbfc8ec2-5355-4a4f-aaf8-dc161b588f7d",
+ "GeneratedBy": "urn:fsltsplo-V40wbRN0",
"digest": {
"sha256": "b8776603f8865a358b2273847d21e63491e7c2e10567fb640608dd47ba721f29"
}
},
{
- "@id": "urn:ee3d8f5f-b513-4b0c-b42b-3ab7434d558f",
+ "@id": "bids::trans.png",
"Label": "trans.png",
"AtLocation": "trans.png",
- "GeneratedBy": "urn:252514db-a544-4986-996e-fdaf40afdb46",
+ "GeneratedBy": "urn:fsltsplo-S5OsKnAK",
"digest": {
"sha256": "496eac1d0ac15e80928780c73766c7791a1707291b2b9a6d1781c2f6a38de3cd"
}
},
{
- "@id": "urn:95e5d644-6386-44e3-aead-85ac9ac956a8",
+ "@id": "bids::prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"Label": "prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"AtLocation": "prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"digest": {
@@ -1485,34 +1499,34 @@
}
},
{
- "@id": "urn:0f469813-3e5f-475c-a372-f4c2eccfb6a5",
+ "@id": "bids::disp.png",
"Label": "disp.png",
"AtLocation": "disp.png",
- "GeneratedBy": "urn:765995cc-ff2c-4b3d-ab06-620255e297ff",
+ "GeneratedBy": "urn:fsltsplo-SEpWzzeB",
"digest": {
"sha256": "c4615e07e04f0c390d969482634cb62e81d47c818d2866ee866ec9c64a5350fd"
}
},
{
- "@id": "urn:2c3ed292-748f-4a7d-9213-01e6c0b8164d",
+ "@id": "bids::mean_func",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:a07b6f8c-7c19-4e7e-b155-24fb0168516e",
+ "GeneratedBy": "urn:fslmaths-4R2qoFkh",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:8715ab85-5e53-496d-acb2-34021963c14a",
+ "@id": "bids::mask",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:93dba0ab-ccea-44d9-8dc3-a8e853cd4d31",
+ "GeneratedBy": "urn:bet2-Y3qoaHaK",
"digest": {
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}
},
{
- "@id": "urn:2f293ea8-ac23-4731-99a3-f243de258b39",
+ "@id": "bids::mask_mask",
"Label": "mask_mask",
"AtLocation": "mask_mask",
"digest": {
@@ -1520,132 +1534,124 @@
}
},
{
- "@id": "urn:45d1bc03-4935-4ded-ac0f-a0179cf4517a",
+ "@id": "bids::mask",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:68476387-e9e1-4562-bd05-044521173b60",
+ "GeneratedBy": "urn:immv-4kgkNuZh",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:4e2824a4-208e-4109-98cd-d2aa9a90ede2",
+ "@id": "bids::prefiltered_func_data_bet",
"Label": "prefiltered_func_data_bet",
"AtLocation": "prefiltered_func_data_bet",
- "GeneratedBy": "urn:7eef4a4b-730b-4fea-b783-9403cf46b7fa",
+ "GeneratedBy": "urn:fslmaths-96ZZNvFa",
"digest": {
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}
},
{
- "@id": "urn:a7c9b9ca-942e-49c6-92df-d191822f78ad",
+ "@id": "bids::mask",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:525029ed-c19f-49c3-ba6d-2d971b656318",
+ "GeneratedBy": "urn:fslmaths-UGKt7EeQ",
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}
},
{
- "@id": "urn:9bfa1c28-4a98-4831-a854-82969c939da3",
+ "@id": "bids::mask",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:bd112a10-b4d7-4dc4-af3c-b22efb773c55",
+ "GeneratedBy": "urn:fslmaths-xR0Ys5gM",
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}
},
{
- "@id": "urn:95fcf1df-0d61-4ca6-9267-40abe42fb652",
+ "@id": "bids::prefiltered_func_data_thresh",
"Label": "prefiltered_func_data_thresh",
"AtLocation": "prefiltered_func_data_thresh",
- "GeneratedBy": "urn:2fc4ff83-2a26-4a10-80bc-0102aa6d6e94",
+ "GeneratedBy": "urn:fslmaths-1w02UWwW",
"digest": {
"sha256": "c5c015a8df079b497bbce596808cbbdc09fb39411f490244de192dfa72d33640"
}
},
{
- "@id": "urn:4994ee96-8a5f-4514-9409-283aac70c4aa",
+ "@id": "bids::mean_func",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:a63366cb-4305-471f-9c59-3eb80e99629e",
+ "GeneratedBy": "urn:fslmaths-0JxcZLu8",
"digest": {
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}
},
{
- "@id": "urn:a08509a8-7e5c-425e-b284-91fba26756e9",
+ "@id": "bids::prefiltered_func_data_smooth",
"Label": "prefiltered_func_data_smooth",
"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:f0df4582-6ede-4262-af8a-21feda9b538b",
+ "GeneratedBy": "urn:susan-TDeycXdk",
"digest": {
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}
},
{
- "@id": "urn:21662e29-fc09-4b5e-8c02-31ca30ee9d23",
+ "@id": "bids::prefiltered_func_data_smooth",
"Label": "prefiltered_func_data_smooth",
"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:c96b85ef-9bad-41dc-a413-025a5563094d",
+ "GeneratedBy": "urn:fslmaths-d80aVlfN",
"digest": {
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}
},
{
- "@id": "urn:839d773c-d1ea-428c-980b-5c45cbd39a55",
+ "@id": "bids::prefiltered_func_data_intnorm",
"Label": "prefiltered_func_data_intnorm",
"AtLocation": "prefiltered_func_data_intnorm",
- "GeneratedBy": "urn:133cc17d-bdb0-4a73-a87d-102c3a843276",
+ "GeneratedBy": "urn:fslmaths-s0Y29iqz",
"digest": {
"sha256": "0698a276f6f0fdccfb06033926d333a176503a09aaa87b78384fbffbf1c54dee"
}
},
{
- "@id": "urn:01e67382-f8f7-4229-91ba-20b303bf197e",
+ "@id": "bids::tempMean",
"Label": "tempMean",
"AtLocation": "tempMean",
- "GeneratedBy": "urn:96acc8d3-b1fb-411a-8a5e-0cd058d715e7",
+ "GeneratedBy": "urn:fslmaths-JKhI0mGJ",
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"sha256": "1a01513c76bc17516b60df315a1922789ce79d72e66e105fbf2723df9cb1b038"
}
},
{
- "@id": "urn:25f83831-8237-4bcf-a95d-c1c43b678e9a",
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- }
- },
- {
- "@id": "urn:9b63ff00-e57d-492c-9a6a-22e0bc8d0efd",
+ "@id": "bids::prefiltered_func_data_tempfilt",
"Label": "prefiltered_func_data_tempfilt",
"AtLocation": "prefiltered_func_data_tempfilt",
+ "GeneratedBy": "urn:fslmaths-TC3trTEP",
"digest": {
"sha256": "a1836f4694e7ffdb50484626724602498c7b22b4f3cdd1e7d105efd336cbc8bd"
}
},
{
- "@id": "urn:8c44dd51-35e1-4b89-8524-f882421e5782",
+ "@id": "bids::filtered_func_data",
"Label": "filtered_func_data",
"AtLocation": "filtered_func_data",
- "GeneratedBy": "urn:64c5f41e-349c-42dd-a27f-95f04499e42a",
+ "GeneratedBy": "urn:fslmaths-tSgS8G2R",
"digest": {
"sha256": "2a1854e3b48a54f88e063191e25159015a0afbd300d18a1cfda37b4b68a1ee69"
}
},
{
- "@id": "urn:9b37749a-3351-487a-8ae2-eb5aca1a5d50",
+ "@id": "bids::mean_func",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:07f1d615-da56-4401-a194-3f2c26ee1978",
+ "GeneratedBy": "urn:fslmaths-AhdmqdXD",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:6c3d4bab-9cb1-46cf-a0be-a4a89caec3cb",
+ "@id": "bids::prefiltered_func_data*",
"Label": "prefiltered_func_data*",
"AtLocation": "prefiltered_func_data*",
"digest": {
@@ -1653,232 +1659,264 @@
}
},
{
- "@id": "urn:87e6336f-0546-4d51-8158-72b17abf6e90",
+ "@id": "bids::custom_timing_files",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:d0e0899e-adea-40d8-9ab3-eec5b6976039",
+ "GeneratedBy": "urn:makedire-u1ksLVof",
"digest": {
"sha256": "1d7e19792328d5040f2f9fb3c15d59de90fc771785f81c67039a043bd5f2ed20"
}
},
{
- "@id": "urn:0e9519ef-e62c-48ff-9874-02d6bbe82cc7",
+ "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
"Label": "sub-01_tone_counting.txt",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
+ "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
"digest": {
- "sha256": "c120d27b9d5d81a91be0e55f5cb880b2cb7de6c655554d9c15c9c04c6232ea8e"
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}
},
{
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+ "@id": "bids::custom_timing_files/ev1.txt",
"Label": "ev1.txt",
"AtLocation": "custom_timing_files/ev1.txt",
- "GeneratedBy": "urn:83cd1459-54f5-4567-bf38-85450c050b8a"
+ "GeneratedBy": "urn:fslfixte-o8YA0I8P"
},
{
- "@id": "urn:db065346-363d-4ba1-826a-e17bbdd3fcaf",
+ "@id": "bids::custom_timing_files",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:771a00ec-f716-4c32-b8e0-1d6bc6bd887b",
+ "GeneratedBy": "urn:makedire-Xs7pKLaA",
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}
},
{
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+ "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
"Label": "sub-01_tone_counting_probe.txt",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
+ "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
"digest": {
- "sha256": "f09eeb82fa0be8e8759a5269403f36ec2b7dbf2c5b6caba1f0f985cc6cb3f703"
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},
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+ "@id": "bids::custom_timing_files/ev2.txt",
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"AtLocation": "custom_timing_files/ev2.txt",
- "GeneratedBy": "urn:e8c59636-f0da-46b6-812b-0911a423417e"
+ "GeneratedBy": "urn:fslfixte-ZTS63XMD"
},
{
- "@id": "urn:c2986c0c-ed72-4122-9a88-1a28862e6651",
- "Label": "res4d",
- "AtLocation": "stats/res4d",
+ "@id": "bids::stats",
+ "Label": "stats",
+ "AtLocation": "stats",
"digest": {
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{
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- "Label": "smoothness",
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- "GeneratedBy": "urn:7989ed26-c111-4c65-a7f2-c118f1201bff",
+ "@id": "bids::design.mat",
+ "Label": "design.mat",
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"digest": {
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{
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+ "@id": "bids::design.con",
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"digest": {
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},
{
- "@id": "urn:3e7ea993-af25-4097-bcde-e19282d42de7",
+ "@id": "bids::design.fts",
+ "Label": "design.fts",
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+ {
+ "@id": "bids::stats",
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+ "AtLocation": "stats",
+ "GeneratedBy": "urn:filmgls-jaruefJt",
+ "digest": {
+ "sha256": "a9f3e135372514a16d11a8038262b3eff94ccd69a9b35c4724b2759cfc944a07"
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+ {
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+ "AtLocation": "stats/res4d"
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+ {
+ "@id": "bids::stats/smoothness",
+ "Label": "smoothness",
+ "AtLocation": "stats/smoothness",
+ "GeneratedBy": "urn:smoothes-s3pTDfVa"
+ },
+ {
+ "@id": "bids::stats/zstat1",
+ "Label": "zstat1",
+ "AtLocation": "stats/zstat1"
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+ {
+ "@id": "bids::thresh_zstat1",
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"AtLocation": "thresh_zstat1",
- "GeneratedBy": "urn:0f339db7-b6d0-472c-86d9-935025f1e945",
+ "GeneratedBy": "urn:fslmaths-n2qLbaoB",
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},
{
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- "digest": {
- "sha256": "b6b265908257e91648f7007e172c3ba159d9231b0acfce7fbf48d754f8cfe52c"
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+ "AtLocation": "stats/zstat2"
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{
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+ "@id": "bids::thresh_zstat2",
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"AtLocation": "thresh_zstat2",
- "GeneratedBy": "urn:090659f4-2b0a-4c91-a339-d6eb664a39bd",
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},
{
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- "digest": {
- "sha256": "2375921a9294c98b426a10611f5bf5998097ae3798c731661bd4b66b4114e300"
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+ "AtLocation": "stats/zstat3"
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{
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+ "@id": "bids::thresh_zstat3",
"Label": "thresh_zstat3",
"AtLocation": "thresh_zstat3",
- "GeneratedBy": "urn:ed331241-db7d-4bc0-8c44-35d1d4d65364",
+ "GeneratedBy": "urn:fslmaths-KJE4C0bu",
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}
},
{
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- "digest": {
- "sha256": "0d0e991aafff027ab2303c1d026384120c4ab1862bb6c02220e064924bfe873f"
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+ "AtLocation": "stats/zstat4"
},
{
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+ "@id": "bids::thresh_zstat4",
"Label": "thresh_zstat4",
"AtLocation": "thresh_zstat4",
- "GeneratedBy": "urn:dbd5fbb8-de1d-4d1f-958d-7bb195badc55",
+ "GeneratedBy": "urn:fslmaths-E4jilCxt",
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}
},
{
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- "digest": {
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+ "AtLocation": "stats/zstat5"
},
{
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+ "@id": "bids::thresh_zstat5",
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"AtLocation": "thresh_zstat5",
- "GeneratedBy": "urn:0f4d6eea-0d6c-4fec-8a2d-9fefb6752db1",
+ "GeneratedBy": "urn:fslmaths-jPO5lIpX",
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}
},
{
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- "digest": {
- "sha256": "e8c2089e7e85be38a4844163a63204937f06dc01f353e6117874cff0858f53b4"
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+ "AtLocation": "stats/zstat6"
},
{
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+ "@id": "bids::thresh_zstat6",
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"AtLocation": "thresh_zstat6",
- "GeneratedBy": "urn:9bbddc14-8c3b-4b30-87dd-6d3f0423692f",
+ "GeneratedBy": "urn:fslmaths-na7pDpFB",
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}
},
{
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+ "@id": "bids::stats/zfstat1",
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- "digest": {
- "sha256": "7411c38cb93415865a53b21dc0427506ed7994230aca73062e72251f77549cb9"
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+ "AtLocation": "stats/zfstat1"
},
{
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+ "@id": "bids::thresh_zfstat1",
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"AtLocation": "thresh_zfstat1",
- "GeneratedBy": "urn:8f8fe587-dd5a-43d2-9792-8b372f66297e",
+ "GeneratedBy": "urn:fslmaths-clta5DMl",
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}
},
{
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+ "@id": "bids::stats/zfstat2",
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- "digest": {
- "sha256": "bb4ff282a5f3cb0f071d986283a23ffd3ec4aee0180437f0cceed465ca29c4ea"
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+ "AtLocation": "stats/zfstat2"
},
{
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+ "@id": "bids::thresh_zfstat2",
"Label": "thresh_zfstat2",
"AtLocation": "thresh_zfstat2",
- "GeneratedBy": "urn:e744d76b-c5b8-44ba-a46a-d60b966b2cf2",
+ "GeneratedBy": "urn:fslmaths-IhJIjkWO",
"digest": {
"sha256": "c298297997e4640c4c2d803314ca8cee706d302781975cdc53946aa6ca0d69c1"
}
},
{
- "@id": "urn:7f26712f-542f-4cab-b485-c34d61c39b26",
+ "@id": "bids::stats/cope1",
"Label": "cope1",
- "AtLocation": "stats/cope1",
- "digest": {
- "sha256": "bf3b603569da6dbe3d6f0e8667d346f3ac943c9d01d2fc9743ce17abeb1547fb"
- }
+ "AtLocation": "stats/cope1"
},
{
- "@id": "urn:26f9a9dc-3402-4c47-b515-59febac8369e",
+ "@id": "bids::cluster_mask_zstat1",
"Label": "cluster_mask_zstat1",
"AtLocation": "cluster_mask_zstat1",
- "GeneratedBy": "urn:60c33d10-55ae-4161-b566-42216c3f0dc8",
+ "GeneratedBy": "urn:cluster-JM4FT4fe",
"digest": {
"sha256": "b28c170e33d2917cac55183786616a9e976e5e7f30dc7c8666341f12ed6d0277"
}
},
{
- "@id": "urn:68d1f283-8c1c-4996-96d0-8bd367625bef",
+ "@id": "bids::thresh_zstat1",
+ "Label": "thresh_zstat1",
+ "AtLocation": "thresh_zstat1",
+ "GeneratedBy": "urn:cluster-JM4FT4fe",
+ "digest": {
+ "sha256": "662e7ba670e124d15bb3cc18b818868f76604578034b524c8882f35fc5db413f"
+ }
+ },
+ {
+ "@id": "bids::lmax_zstat1.txt",
+ "Label": "lmax_zstat1.txt",
+ "AtLocation": "lmax_zstat1.txt",
+ "GeneratedBy": "urn:cluster-JM4FT4fe",
+ "digest": {
+ "sha256": "d44ee21719775397a1a95ede6778d25404b50e8bd259dbdf02d2fde635fc81a5"
+ }
+ },
+ {
+ "@id": "bids::stats/cope1",
"Label": "cope1",
"AtLocation": "stats/cope1",
- "GeneratedBy": "urn:60c33d10-55ae-4161-b566-42216c3f0dc8",
+ "GeneratedBy": "urn:cluster-JM4FT4fe"
+ },
+ {
+ "@id": "bids::cluster_zstat1.txt",
+ "Label": "cluster_zstat1.txt",
+ "AtLocation": "cluster_zstat1.txt",
+ "GeneratedBy": "urn:cluster-JM4FT4fe",
"digest": {
- "sha256": "bf3b603569da6dbe3d6f0e8667d346f3ac943c9d01d2fc9743ce17abeb1547fb"
+ "sha256": "b06695ff4f0a8158fa439b1ddf224b58d344606d400885c177390d09506e8e4c"
}
},
{
- "@id": "urn:77014477-f46d-4f42-a5cc-62e47afe0b8c",
+ "@id": "bids::cluster_zstat1",
"Label": "cluster_zstat1",
"AtLocation": "cluster_zstat1",
"digest": {
@@ -1886,33 +1924,54 @@
}
},
{
- "@id": "urn:d036abd4-f374-4ca5-83ad-1f151c63f354",
+ "@id": "bids::stats/cope2",
"Label": "cope2",
- "AtLocation": "stats/cope2",
- "digest": {
- "sha256": "5f073baabd78c1c473fed55b511738f0ffe30d9fc1f23352a16ec058daacd88c"
- }
+ "AtLocation": "stats/cope2"
},
{
- "@id": "urn:52b1e261-fec0-4e34-a356-90ad7d4e1234",
+ "@id": "bids::cluster_mask_zstat2",
"Label": "cluster_mask_zstat2",
"AtLocation": "cluster_mask_zstat2",
- "GeneratedBy": "urn:07a8d6a6-64b2-42fe-80b4-2b1eac1eb9e7",
+ "GeneratedBy": "urn:cluster-eZtqBxsh",
"digest": {
"sha256": "b88bb3cd4d809827a5c0a45cb4f6aac570cb25b7e056d5986d81d879548da121"
}
},
{
- "@id": "urn:c65011b8-5ce9-4ef5-8fc3-3bbfe50987ab",
+ "@id": "bids::thresh_zstat2",
+ "Label": "thresh_zstat2",
+ "AtLocation": "thresh_zstat2",
+ "GeneratedBy": "urn:cluster-eZtqBxsh",
+ "digest": {
+ "sha256": "fe707ed68d72f4376668be45a2030f2d00fa81534a3e95bf92b6a499fa8595bd"
+ }
+ },
+ {
+ "@id": "bids::lmax_zstat2.txt",
+ "Label": "lmax_zstat2.txt",
+ "AtLocation": "lmax_zstat2.txt",
+ "GeneratedBy": "urn:cluster-eZtqBxsh",
+ "digest": {
+ "sha256": "23ca5266a11743c7252c1758989cf555126dd598ae07080cf11f0a7c9e8a988b"
+ }
+ },
+ {
+ "@id": "bids::stats/cope2",
"Label": "cope2",
"AtLocation": "stats/cope2",
- "GeneratedBy": "urn:07a8d6a6-64b2-42fe-80b4-2b1eac1eb9e7",
+ "GeneratedBy": "urn:cluster-eZtqBxsh"
+ },
+ {
+ "@id": "bids::cluster_zstat2.txt",
+ "Label": "cluster_zstat2.txt",
+ "AtLocation": "cluster_zstat2.txt",
+ "GeneratedBy": "urn:cluster-eZtqBxsh",
"digest": {
- "sha256": "5f073baabd78c1c473fed55b511738f0ffe30d9fc1f23352a16ec058daacd88c"
+ "sha256": "05b4675c829a96e029b38d828f0160bb2299d2d76d7c1248cd45119f0c6c9c2e"
}
},
{
- "@id": "urn:e784343f-88eb-4b8d-8447-9af21cf0b76a",
+ "@id": "bids::cluster_zstat2",
"Label": "cluster_zstat2",
"AtLocation": "cluster_zstat2",
"digest": {
@@ -1920,33 +1979,54 @@
}
},
{
- "@id": "urn:6e408f66-20ca-482a-8005-ad8f3afa2a44",
+ "@id": "bids::stats/cope3",
"Label": "cope3",
- "AtLocation": "stats/cope3",
- "digest": {
- "sha256": "4f5e165fb3b62e5ef5397e9f93b4572ba23f3ffe3c9f118e8a2a9cba52e2fe0e"
- }
+ "AtLocation": "stats/cope3"
},
{
- "@id": "urn:4dd470c8-0988-4c71-a5f7-fece23acbed2",
+ "@id": "bids::cluster_mask_zstat3",
"Label": "cluster_mask_zstat3",
"AtLocation": "cluster_mask_zstat3",
- "GeneratedBy": "urn:cb7470f0-d59a-452e-ae07-d28403e45649",
+ "GeneratedBy": "urn:cluster-f2RhlnID",
"digest": {
"sha256": "fac31b7cc91c4dbb519375fa9238cfde00689381b0783d7e3b623a937b9f51d0"
}
},
{
- "@id": "urn:8e0a645d-cbe1-4326-91da-cb1ea26a5356",
+ "@id": "bids::thresh_zstat3",
+ "Label": "thresh_zstat3",
+ "AtLocation": "thresh_zstat3",
+ "GeneratedBy": "urn:cluster-f2RhlnID",
+ "digest": {
+ "sha256": "d0f88769369dc8215d7373817e8f9a48482b508bb9deb2ca29904069bb23f484"
+ }
+ },
+ {
+ "@id": "bids::lmax_zstat3.txt",
+ "Label": "lmax_zstat3.txt",
+ "AtLocation": "lmax_zstat3.txt",
+ "GeneratedBy": "urn:cluster-f2RhlnID",
+ "digest": {
+ "sha256": "9786cf311d8427bc717d3d91faa64a67cb151e8e40043e6cc30e896b724f55f2"
+ }
+ },
+ {
+ "@id": "bids::stats/cope3",
"Label": "cope3",
"AtLocation": "stats/cope3",
- "GeneratedBy": "urn:cb7470f0-d59a-452e-ae07-d28403e45649",
+ "GeneratedBy": "urn:cluster-f2RhlnID"
+ },
+ {
+ "@id": "bids::cluster_zstat3.txt",
+ "Label": "cluster_zstat3.txt",
+ "AtLocation": "cluster_zstat3.txt",
+ "GeneratedBy": "urn:cluster-f2RhlnID",
"digest": {
- "sha256": "4f5e165fb3b62e5ef5397e9f93b4572ba23f3ffe3c9f118e8a2a9cba52e2fe0e"
+ "sha256": "edeacd33c60c6b43daae0c296f32ca021cca90824ee868b061f1ac10758f807f"
}
},
{
- "@id": "urn:876e299e-293c-40ca-9120-31b5a862d278",
+ "@id": "bids::cluster_zstat3",
"Label": "cluster_zstat3",
"AtLocation": "cluster_zstat3",
"digest": {
@@ -1954,33 +2034,54 @@
}
},
{
- "@id": "urn:fd791b55-91e2-4377-905f-cdf0a2180274",
+ "@id": "bids::stats/cope4",
"Label": "cope4",
- "AtLocation": "stats/cope4",
- "digest": {
- "sha256": "b6f8f8cfc79a9728843c597031f0d708ffe70f4865e3ec6456482bcf5e988347"
- }
+ "AtLocation": "stats/cope4"
},
{
- "@id": "urn:97807332-c0ef-40d8-9cf2-95a4f8b109cc",
+ "@id": "bids::cluster_mask_zstat4",
"Label": "cluster_mask_zstat4",
"AtLocation": "cluster_mask_zstat4",
- "GeneratedBy": "urn:925cff4d-fdf7-4657-9ec2-ce8b1557aaef",
+ "GeneratedBy": "urn:cluster-HDbgeLZt",
"digest": {
"sha256": "236c7040f9f44c5f102ed2cc3fad96a03bcdf369e764ef6bfea5b18d75e9abb5"
}
},
{
- "@id": "urn:48a6c19e-309b-418e-bd45-f0f33dfb3cb1",
+ "@id": "bids::thresh_zstat4",
+ "Label": "thresh_zstat4",
+ "AtLocation": "thresh_zstat4",
+ "GeneratedBy": "urn:cluster-HDbgeLZt",
+ "digest": {
+ "sha256": "7d0ee58ccf12389afd32deb44a620da2bd1f2ebfa70a72c43328055de692ff98"
+ }
+ },
+ {
+ "@id": "bids::lmax_zstat4.txt",
+ "Label": "lmax_zstat4.txt",
+ "AtLocation": "lmax_zstat4.txt",
+ "GeneratedBy": "urn:cluster-HDbgeLZt",
+ "digest": {
+ "sha256": "c31dc754223bbb903bd61dba85d63351ee87a98fd3d85c41857ef5532ef4771b"
+ }
+ },
+ {
+ "@id": "bids::stats/cope4",
"Label": "cope4",
"AtLocation": "stats/cope4",
- "GeneratedBy": "urn:925cff4d-fdf7-4657-9ec2-ce8b1557aaef",
+ "GeneratedBy": "urn:cluster-HDbgeLZt"
+ },
+ {
+ "@id": "bids::cluster_zstat4.txt",
+ "Label": "cluster_zstat4.txt",
+ "AtLocation": "cluster_zstat4.txt",
+ "GeneratedBy": "urn:cluster-HDbgeLZt",
"digest": {
- "sha256": "b6f8f8cfc79a9728843c597031f0d708ffe70f4865e3ec6456482bcf5e988347"
+ "sha256": "36023a0bbbc9d81db1bcfe7a8ba3f1b8bc08aaccbf36ce7f87149e71ec1ada18"
}
},
{
- "@id": "urn:9e3c0116-5947-4998-8e67-a79ab55a637f",
+ "@id": "bids::cluster_zstat4",
"Label": "cluster_zstat4",
"AtLocation": "cluster_zstat4",
"digest": {
@@ -1988,33 +2089,54 @@
}
},
{
- "@id": "urn:fd665767-b5b2-4d60-a6e6-23c46cdfdc3c",
+ "@id": "bids::stats/cope5",
"Label": "cope5",
- "AtLocation": "stats/cope5",
- "digest": {
- "sha256": "cce90c23c0b7646ad6ed60fe900a84c9a92a151e90e51a3c8d5bf609e48e7e37"
- }
+ "AtLocation": "stats/cope5"
},
{
- "@id": "urn:0f140c41-9200-4788-864b-b308f1f6bbba",
+ "@id": "bids::cluster_mask_zstat5",
"Label": "cluster_mask_zstat5",
"AtLocation": "cluster_mask_zstat5",
- "GeneratedBy": "urn:ab3c4e2c-eac4-499d-83f7-ac40b11b2893",
+ "GeneratedBy": "urn:cluster-RlEhegMp",
"digest": {
"sha256": "c017022e8f02a206ba703043a7cca57d23cbb1327fe198615792ef86a6d9e088"
}
},
{
- "@id": "urn:e6be6791-8da7-4e56-b1a5-b8192775becc",
+ "@id": "bids::thresh_zstat5",
+ "Label": "thresh_zstat5",
+ "AtLocation": "thresh_zstat5",
+ "GeneratedBy": "urn:cluster-RlEhegMp",
+ "digest": {
+ "sha256": "1f5c0f183460f4e90178ce2e1778cf74f2b9cbb163602d06d7b10023caef88c9"
+ }
+ },
+ {
+ "@id": "bids::lmax_zstat5.txt",
+ "Label": "lmax_zstat5.txt",
+ "AtLocation": "lmax_zstat5.txt",
+ "GeneratedBy": "urn:cluster-RlEhegMp",
+ "digest": {
+ "sha256": "55fb936b12b71c757ae751dfaceff30903c3123b845bcc970ecc0ba368327b09"
+ }
+ },
+ {
+ "@id": "bids::stats/cope5",
"Label": "cope5",
"AtLocation": "stats/cope5",
- "GeneratedBy": "urn:ab3c4e2c-eac4-499d-83f7-ac40b11b2893",
+ "GeneratedBy": "urn:cluster-RlEhegMp"
+ },
+ {
+ "@id": "bids::cluster_zstat5.txt",
+ "Label": "cluster_zstat5.txt",
+ "AtLocation": "cluster_zstat5.txt",
+ "GeneratedBy": "urn:cluster-RlEhegMp",
"digest": {
- "sha256": "cce90c23c0b7646ad6ed60fe900a84c9a92a151e90e51a3c8d5bf609e48e7e37"
+ "sha256": "746bb0d80cbb53398541ef3f3569938147e76afb366f7f0025e8345555d68398"
}
},
{
- "@id": "urn:7de17507-bdc9-4002-bf2d-2815ea50a192",
+ "@id": "bids::cluster_zstat5",
"Label": "cluster_zstat5",
"AtLocation": "cluster_zstat5",
"digest": {
@@ -2022,33 +2144,54 @@
}
},
{
- "@id": "urn:9636addd-4ce7-45df-a999-e6e6136f6bd5",
+ "@id": "bids::stats/cope6",
"Label": "cope6",
- "AtLocation": "stats/cope6",
- "digest": {
- "sha256": "f45749b02e0f09e62c96d79da8d85078fec9357d695e8bc30eba2e0c0658fedb"
- }
+ "AtLocation": "stats/cope6"
},
{
- "@id": "urn:9784fc8e-7627-4dbb-8abc-886296d00f0e",
+ "@id": "bids::cluster_mask_zstat6",
"Label": "cluster_mask_zstat6",
"AtLocation": "cluster_mask_zstat6",
- "GeneratedBy": "urn:78841fc2-5796-4cc5-9c0e-afab1681ff6b",
+ "GeneratedBy": "urn:cluster-ef7ehgcK",
"digest": {
"sha256": "b443499c0537a51d05605fa88d988683ccda5aedfeb1959b3a465864cfc16476"
}
},
{
- "@id": "urn:1a01b370-3827-4cae-a220-12911e53e9c2",
+ "@id": "bids::thresh_zstat6",
+ "Label": "thresh_zstat6",
+ "AtLocation": "thresh_zstat6",
+ "GeneratedBy": "urn:cluster-ef7ehgcK",
+ "digest": {
+ "sha256": "9e3f489bd3068058a3f61a8aaaa0cc5b9ea4f4180ecff380d03a899d0cf3a976"
+ }
+ },
+ {
+ "@id": "bids::lmax_zstat6.txt",
+ "Label": "lmax_zstat6.txt",
+ "AtLocation": "lmax_zstat6.txt",
+ "GeneratedBy": "urn:cluster-ef7ehgcK",
+ "digest": {
+ "sha256": "86452e07a97ac3c734b682c22f48a73f197406ca27612c24957906f42fcb7ae2"
+ }
+ },
+ {
+ "@id": "bids::stats/cope6",
"Label": "cope6",
"AtLocation": "stats/cope6",
- "GeneratedBy": "urn:78841fc2-5796-4cc5-9c0e-afab1681ff6b",
+ "GeneratedBy": "urn:cluster-ef7ehgcK"
+ },
+ {
+ "@id": "bids::cluster_zstat6.txt",
+ "Label": "cluster_zstat6.txt",
+ "AtLocation": "cluster_zstat6.txt",
+ "GeneratedBy": "urn:cluster-ef7ehgcK",
"digest": {
- "sha256": "f45749b02e0f09e62c96d79da8d85078fec9357d695e8bc30eba2e0c0658fedb"
+ "sha256": "418a2201d5616ec9ebd662eea9ce8eadaff7350b370832f524ff1c4928aa932e"
}
},
{
- "@id": "urn:f4788744-9fd7-46ff-ab58-b82a497af808",
+ "@id": "bids::cluster_zstat6",
"Label": "cluster_zstat6",
"AtLocation": "cluster_zstat6",
"digest": {
@@ -2056,16 +2199,43 @@
}
},
{
- "@id": "urn:9f50245f-1c7a-46b8-ad97-1b9ddd842bd1",
+ "@id": "bids::cluster_mask_zfstat1",
"Label": "cluster_mask_zfstat1",
"AtLocation": "cluster_mask_zfstat1",
- "GeneratedBy": "urn:5c4343d6-8bff-477b-9505-6886037bf8fa",
+ "GeneratedBy": "urn:cluster-l1k6btTJ",
"digest": {
"sha256": "3523a5abe83ae8c76dd74f74632bc34163aac475152d48a6b79f37eca7dfe022"
}
},
{
- "@id": "urn:30c8cd54-1653-4cff-86ea-7ad669b107a4",
+ "@id": "bids::thresh_zfstat1",
+ "Label": "thresh_zfstat1",
+ "AtLocation": "thresh_zfstat1",
+ "GeneratedBy": "urn:cluster-l1k6btTJ",
+ "digest": {
+ "sha256": "e4e927e247bdf8ff3b58b41cbb9db7643b27df1f7578c506950eb4b1ca2d0031"
+ }
+ },
+ {
+ "@id": "bids::lmax_zfstat1.txt",
+ "Label": "lmax_zfstat1.txt",
+ "AtLocation": "lmax_zfstat1.txt",
+ "GeneratedBy": "urn:cluster-l1k6btTJ",
+ "digest": {
+ "sha256": "f6140171309069ed9586f94b07f187a4bbea683c429dc6a5558047a484c5e8a1"
+ }
+ },
+ {
+ "@id": "bids::cluster_zfstat1.txt",
+ "Label": "cluster_zfstat1.txt",
+ "AtLocation": "cluster_zfstat1.txt",
+ "GeneratedBy": "urn:cluster-l1k6btTJ",
+ "digest": {
+ "sha256": "0b5d4fcb253267ddae2859bc1226696992a2f6db2dba10d35c80399bd51477d4"
+ }
+ },
+ {
+ "@id": "bids::cluster_zfstat1",
"Label": "cluster_zfstat1",
"AtLocation": "cluster_zfstat1",
"digest": {
@@ -2073,16 +2243,43 @@
}
},
{
- "@id": "urn:2b597991-b55c-470b-93e4-7495b66a06e7",
+ "@id": "bids::cluster_mask_zfstat2",
"Label": "cluster_mask_zfstat2",
"AtLocation": "cluster_mask_zfstat2",
- "GeneratedBy": "urn:df900226-398d-422c-963e-eee25dd764b6",
+ "GeneratedBy": "urn:cluster-24hfHD40",
"digest": {
"sha256": "962ef7014f226d586c47fb23ebcde5968e55a03f06dae8514b358579d8457e7a"
}
},
{
- "@id": "urn:81217ec8-dd0d-414e-bb72-4f7b170531f9",
+ "@id": "bids::thresh_zfstat2",
+ "Label": "thresh_zfstat2",
+ "AtLocation": "thresh_zfstat2",
+ "GeneratedBy": "urn:cluster-24hfHD40",
+ "digest": {
+ "sha256": "c298297997e4640c4c2d803314ca8cee706d302781975cdc53946aa6ca0d69c1"
+ }
+ },
+ {
+ "@id": "bids::lmax_zfstat2.txt",
+ "Label": "lmax_zfstat2.txt",
+ "AtLocation": "lmax_zfstat2.txt",
+ "GeneratedBy": "urn:cluster-24hfHD40",
+ "digest": {
+ "sha256": "00212684d755543487d676533c59ad32790c5df6ec82c71143d2a3e634c48427"
+ }
+ },
+ {
+ "@id": "bids::cluster_zfstat2.txt",
+ "Label": "cluster_zfstat2.txt",
+ "AtLocation": "cluster_zfstat2.txt",
+ "GeneratedBy": "urn:cluster-24hfHD40",
+ "digest": {
+ "sha256": "aebb5170ab0ff6dc4d5357af34587a0007aa2156e6c6920f18444bc4528f9b7c"
+ }
+ },
+ {
+ "@id": "bids::cluster_zfstat2",
"Label": "cluster_zfstat2",
"AtLocation": "cluster_zfstat2",
"digest": {
@@ -2090,25 +2287,25 @@
}
},
{
- "@id": "urn:b51f6a09-3f73-4fb2-85a4-d4686faec93e",
+ "@id": "bids::rendered_thresh_zstat1",
"Label": "rendered_thresh_zstat1",
"AtLocation": "rendered_thresh_zstat1",
- "GeneratedBy": "urn:261dc1bd-062a-45f8-aaf6-940102b64247",
+ "GeneratedBy": "urn:overlay-X86Egc5m",
"digest": {
"sha256": "de5b9d44d95f4252f491eb45c76a0ae2b4d2c75b58664fc0df7d9153810c0bf6"
}
},
{
- "@id": "urn:d4632aff-3cc6-4d05-9e3d-3a245046d540",
+ "@id": "bids::rendered_thresh_zstat1.png",
"Label": "rendered_thresh_zstat1.png",
"AtLocation": "rendered_thresh_zstat1.png",
- "GeneratedBy": "urn:e27ae9b4-0f62-4c4e-9c20-049a703eee03",
+ "GeneratedBy": "urn:slicer-TrwKgGLm",
"digest": {
"sha256": "15d6a8bf7a902df8c5feeb7468a3d0caacf9eb3067c0840c2f4763f5e2301527"
}
},
{
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@@ -2116,154 +2313,154 @@
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"AtLocation": "rendered_thresh_zstat3.png",
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"AtLocation": "rendered_thresh_zstat4.png",
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"AtLocation": "rendered_thresh_zstat5.png",
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diff --git a/examples/from_parsers/fsl/fsl_gamma_basis_report_log.png b/examples/from_parsers/fsl/fsl_gamma_basis_report_log.png
index 4632bb2f7..45542a081 100644
Binary files a/examples/from_parsers/fsl/fsl_gamma_basis_report_log.png and b/examples/from_parsers/fsl/fsl_gamma_basis_report_log.png differ
diff --git a/examples/from_parsers/fsl/fsl_gaussian_report_log.html b/examples/from_parsers/fsl/fsl_gaussian_report_log.html
index 614e75ee0..18b4e2700 100644
--- a/examples/from_parsers/fsl/fsl_gaussian_report_log.html
+++ b/examples/from_parsers/fsl/fsl_gaussian_report_log.html
@@ -35,20 +35,20 @@ Progress Report / Log
326915
Initialisation
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
Total original volumes = 104
/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1
Preprocessing:Stage 1
-/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90
+/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/example_func.nii.gz -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90
Option -F ( FEAT version parameter ) selected with argument "6.00"
Option -d ( output directory ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat"
Option -l ( logfile )input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/logs/feat2_pre"
Option -R ( html unwarping report ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/report_unwarp.html"
Option -r ( html registration report ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/report_reg.html"
Option -i ( main input ) input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/example_func.nii.gz"
-Option -h ( high-res structural image ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
+Option -h ( high-res structural image ) selected with argument "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
Option -w ( highres dof ) selected with argument "BBR"
Option -x ( highres search ) selected with argument "90"
Option -s ( standard image ) selected with argument "/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain"
@@ -59,10 +59,10 @@ Progress Report / Log
/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/reg
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head
did not find file: example_func2highres.mat. Generating transform.
@@ -128,9 +128,9 @@ Progress Report / Log
/bin/rm -rf prefiltered_func_data*
Stats
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
/usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con
Log directory is: stats
diff --git a/examples/from_parsers/fsl/fsl_gaussian_report_log.jsonld b/examples/from_parsers/fsl/fsl_gaussian_report_log.jsonld
index 089a79c8c..272584db1 100644
--- a/examples/from_parsers/fsl/fsl_gaussian_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_gaussian_report_log.jsonld
@@ -4,643 +4,652 @@
"Records": {
"Software": [
{
- "@id": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:fsl-LlDJMBmv",
"@type": "prov:SoftwareAgent",
"Label": "FSL",
- "Version": "xxx"
+ "Version": "xxx",
+ "AltIdentifier": "RRID:SCR_002823"
}
],
"Activities": [
{
- "@id": "urn:f88935b4-f79e-4b80-98b6-0842df6f8e9c",
+ "@id": "urn:fslmaths-c40EgfsR",
"Label": "fslmaths",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
"Used": [
- "urn:1abb6b74-47f8-4ecd-bf39-ce9eb36d5274"
+ "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold"
]
},
{
- "@id": "urn:ca984797-be7e-42b0-9135-ca32141717b4",
+ "@id": "urn:fslroi-BT8jJF5g",
"Label": "fslroi",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1",
"Used": [
- "urn:ad48371d-a0aa-40e9-87c1-3d835c7d9bc4"
+ "bids::prefiltered_func_data"
]
},
{
- "@id": "urn:fde13367-6de1-4a55-9b52-eba74f0cd730",
+ "@id": "urn:mainfeat-tikUw4Yc",
"Label": "mainfeatreg",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/example_func.nii.gz -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
"Used": [
- "urn:2bafc123-f535-4eb0-9d99-98ffd606e387",
- "urn:98b37057-a7c5-41c7-a584-2b9af6c287bb",
- "urn:dd7dba6e-c651-4e36-82aa-19b93d86be8b"
+ "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/example_func.nii.gz",
+ "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain",
+ "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
]
},
{
- "@id": "urn:a0e060d4-45b1-40c4-85c6-7e89e9ead411",
+ "@id": "urn:makedire-4q5WpPKB",
"Label": "Make directory",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gaussian.feat/reg",
"Used": []
},
{
- "@id": "urn:868a5cd1-12a1-444b-be3a-5bc2304b75a4",
+ "@id": "urn:fslmaths-aZ0oYGeF",
"Label": "fslmaths",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
"Used": [
- "urn:dd7dba6e-c651-4e36-82aa-19b93d86be8b"
+ "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
]
},
{
- "@id": "urn:68e68da7-bcca-452f-b6f2-f83c35290e9e",
+ "@id": "urn:fslmaths-sOsEVkdS",
"Label": "fslmaths",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
"Used": [
- "urn:5c5526d3-9ff7-428e-91db-935ee6ff422f"
+ "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w"
]
},
{
- "@id": "urn:8ff96632-d4d4-4fff-9a73-a76e6a9c355e",
+ "@id": "urn:epireg-NXkPO3x2",
"Label": "epi_reg",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres",
- "Used": []
+ "Used": [
+ "bids::example_func",
+ "bids::highres",
+ "bids::highres_head"
+ ]
},
{
- "@id": "urn:5ea01a67-f03a-40ce-a834-16e5a65b6c5c",
+ "@id": "urn:convertx-a0Vf86Tw",
"Label": "convert_xfm",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat",
"Used": [
- "urn:926d02b6-a8ff-4d5b-b823-8b030b3526b2"
+ "bids::example_func2highres.mat"
]
},
{
- "@id": "urn:5a78e128-92b4-4fb3-a38b-559576fcda4c",
+ "@id": "urn:slicer-wUSva9lv",
"Label": "slicer",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:1dc3fde5-282a-415a-bdae-7d2dbcda22f7",
- "urn:2a0541ac-72b1-43f5-929b-fbbb9aae72ee"
+ "bids::example_func2highres",
+ "bids::highres"
]
},
{
- "@id": "urn:b58a4b95-7e2c-42ca-8cf1-12c9a3e329fa",
+ "@id": "urn:pngappen-fbEh7nJR",
"Label": "pngappend",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres1.png",
"Used": [
- "urn:0874b92d-50eb-4f06-aa11-1b4c1a3d7f25",
- "urn:14f993bf-a7b7-4eb8-b904-564e770d919b",
- "urn:2627df04-74d6-48a9-8477-97f0d80b5479",
- "urn:3264d870-df93-44d9-b00d-1e80a6a58e24",
- "urn:439b451c-3b96-4949-ad1d-5c2dff6aba46",
- "urn:71f4a784-5e42-413d-a991-c4aa0bda779d",
- "urn:a300eddf-c764-4425-9145-adeb4ae34f9e",
- "urn:a571a087-7a6a-4a92-bc68-41edb558da5c",
- "urn:a9593a39-5119-468e-96b2-5047fbc8492a",
- "urn:c8d4dbf8-7fd9-4758-a617-722459e3fa10",
- "urn:d9762ba0-28f1-4f2b-8d48-d26a5b51e993",
- "urn:eee94271-3a18-4576-818c-4513e34e6363"
+ "bids::sla.png",
+ "bids::slb.png",
+ "bids::slc.png",
+ "bids::sld.png",
+ "bids::sle.png",
+ "bids::slf.png",
+ "bids::slg.png",
+ "bids::slh.png",
+ "bids::sli.png",
+ "bids::slj.png",
+ "bids::slk.png",
+ "bids::sll.png"
]
},
{
- "@id": "urn:51ef7764-16ea-49aa-bae7-90739e3a6643",
+ "@id": "urn:slicer-xGVl3dhc",
"Label": "slicer",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:1dc3fde5-282a-415a-bdae-7d2dbcda22f7",
- "urn:2a0541ac-72b1-43f5-929b-fbbb9aae72ee"
+ "bids::example_func2highres",
+ "bids::highres"
]
},
{
- "@id": "urn:824f0992-a9ac-41bc-adc9-0af7ddf3a550",
+ "@id": "urn:pngappen-C0NWHKHZ",
"Label": "pngappend",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres2.png",
"Used": [
- "urn:0874b92d-50eb-4f06-aa11-1b4c1a3d7f25",
- "urn:14f993bf-a7b7-4eb8-b904-564e770d919b",
- "urn:2627df04-74d6-48a9-8477-97f0d80b5479",
- "urn:3264d870-df93-44d9-b00d-1e80a6a58e24",
- "urn:439b451c-3b96-4949-ad1d-5c2dff6aba46",
- "urn:71f4a784-5e42-413d-a991-c4aa0bda779d",
- "urn:a300eddf-c764-4425-9145-adeb4ae34f9e",
- "urn:a571a087-7a6a-4a92-bc68-41edb558da5c",
- "urn:a9593a39-5119-468e-96b2-5047fbc8492a",
- "urn:c8d4dbf8-7fd9-4758-a617-722459e3fa10",
- "urn:d9762ba0-28f1-4f2b-8d48-d26a5b51e993",
- "urn:eee94271-3a18-4576-818c-4513e34e6363"
+ "bids::sla.png",
+ "bids::slb.png",
+ "bids::slc.png",
+ "bids::sld.png",
+ "bids::sle.png",
+ "bids::slf.png",
+ "bids::slg.png",
+ "bids::slh.png",
+ "bids::sli.png",
+ "bids::slj.png",
+ "bids::slk.png",
+ "bids::sll.png"
]
},
{
- "@id": "urn:6fd69f94-a903-4b36-8c44-b3836dc86b5e",
+ "@id": "urn:pngappen-JPfO5AdL",
"Label": "pngappend",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend example_func2highres1.png example_func2highres2.png example_func2highres.png",
"Used": [
- "urn:33ada915-fc3b-480d-9981-cb1e137f6c75",
- "urn:72dce464-30aa-4ee0-a144-88999ef0598b"
+ "bids::example_func2highres1.png",
+ "bids::example_func2highres2.png"
]
},
{
- "@id": "urn:07827d93-865e-4420-b4b5-bcbf69f12d6b",
+ "@id": "urn:rm-rHzvu8Pm",
"Label": "rm",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/bin/rm -f sl?.png example_func2highres2.png",
"Used": [
- "urn:72dce464-30aa-4ee0-a144-88999ef0598b",
- "urn:bf8771f2-a6ca-4308-a241-70cae05127e9"
+ "bids::example_func2highres2.png",
+ "bids::sl?.png"
]
},
{
- "@id": "urn:b190365e-a81a-49de-8516-a4ec5f695a35",
+ "@id": "urn:rm-oZgZdvYj",
"Label": "rm",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/bin/rm example_func2highres1.png",
"Used": [
- "urn:33ada915-fc3b-480d-9981-cb1e137f6c75"
+ "bids::example_func2highres1.png"
]
},
{
- "@id": "urn:768b07e6-4c61-4e15-be15-27eb66dc108a",
+ "@id": "urn:mcflirt-9iSyFXGh",
"Label": "mcflirt",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs -spline_final",
"Used": [
- "urn:ad48371d-a0aa-40e9-87c1-3d835c7d9bc4"
+ "bids::prefiltered_func_data"
]
},
{
- "@id": "urn:325a2bfd-6837-4b92-822d-3b697d0883a6",
+ "@id": "urn:makedire-VSGQwlhb",
"Label": "Make directory",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/bin/mkdir -p mc",
"Used": []
},
{
- "@id": "urn:0139ed04-010d-414f-8907-5d6163b567ea",
+ "@id": "urn:mv-a1clMa7z",
"Label": "mv",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc",
"Used": [
- "urn:3e6964e1-0ce4-4cae-b165-83f556a2a6e4",
- "urn:51085d5c-9272-48b6-8298-868f86ac98e5",
- "urn:695fc232-c43b-47af-9cef-3c948b5bfcff",
- "urn:793001e3-092c-46bb-b006-638851f60f1e",
- "urn:90ae9a95-aa81-4c49-a5ba-b7a37d554b7f",
- "urn:cd76fc5a-b376-4723-bac8-111eaaa24083"
+ "bids::prefiltered_func_data_mcf.mat",
+ "bids::prefiltered_func_data_mcf.par",
+ "bids::prefiltered_func_data_mcf_abs.rms",
+ "bids::prefiltered_func_data_mcf_abs_mean.rms",
+ "bids::prefiltered_func_data_mcf_rel.rms",
+ "bids::prefiltered_func_data_mcf_rel_mean.rms"
]
},
{
- "@id": "urn:6029fd2b-6341-4c78-9c8f-ed8b23999598",
+ "@id": "urn:fsltsplo-0AK42d62",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png",
"Used": [
- "urn:793001e3-092c-46bb-b006-638851f60f1e"
+ "bids::prefiltered_func_data_mcf.par"
]
},
{
- "@id": "urn:322ef859-6275-4576-b46c-c4b1de5333f5",
+ "@id": "urn:fsltsplo-D2384XzX",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png",
"Used": [
- "urn:793001e3-092c-46bb-b006-638851f60f1e"
+ "bids::prefiltered_func_data_mcf.par"
]
},
{
- "@id": "urn:9ab1f065-b1b1-4d54-a405-59ef938a5da1",
+ "@id": "urn:fsltsplo-oFlR7AKx",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png",
"Used": [
- "urn:58295d4c-36e1-499e-8a3a-181a424b6142"
+ "bids::prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms"
]
},
{
- "@id": "urn:3dc068ee-1ef5-4ee5-bb1b-e1c8b3c87c91",
+ "@id": "urn:fslmaths-t17JOD8i",
"Label": "fslmaths",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func",
"Used": [
- "urn:ca79b157-4377-4949-9689-0d2ab409a269"
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "@id": "urn:bet2-RLQM3p76",
"Label": "bet2",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/bet2 mean_func mask -f 0.3 -n -m",
"Used": [
- "urn:9d1898a7-03e2-445f-8756-faeb5bec2948"
+ "bids::mean_func"
]
},
{
- "@id": "urn:6442d6c7-861e-47b6-a7ec-869397d3fd3c",
+ "@id": "urn:immv-gwbMDqAA",
"Label": "immv",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/immv mask_mask mask",
"Used": [
- "urn:3c8f1e80-b4dc-4d12-b22c-ac616848f9ae"
+ "bids::mask_mask"
]
},
{
- "@id": "urn:057be9c0-35ac-49f8-a62a-d3917a8736cf",
+ "@id": "urn:fslmaths-t2aHVzoS",
"Label": "fslmaths",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet",
"Used": [
- "urn:ca79b157-4377-4949-9689-0d2ab409a269",
- "urn:f68ab65b-7eba-43ac-9558-ac93d8a9627f"
+ "bids::mask",
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:b7aa1492-f271-4938-ba63-83b2832e399d",
+ "@id": "urn:fslstats-iN2bHXNs",
"Label": "fslstats",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_bet -p 2 -p 98",
"Used": [
- "urn:f8ad3805-7098-4b47-bba8-e210230c5e80"
+ "bids::prefiltered_func_data_bet"
]
},
{
- "@id": "urn:a5fc0d33-b76e-4555-a307-ff6b719128b6",
+ "@id": "urn:fslmaths-8BSfMD2j",
"Label": "fslmaths",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_bet -thr 74.4585571 -Tmin -bin mask -odt char",
"Used": [
- "urn:f8ad3805-7098-4b47-bba8-e210230c5e80"
+ "bids::prefiltered_func_data_bet"
]
},
{
- "@id": "urn:40782800-0f18-44eb-927b-9a18f874c562",
+ "@id": "urn:fslstats-24U2euPv",
"Label": "fslstats",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_mcf -k mask -p 50",
"Used": [
- "urn:ca79b157-4377-4949-9689-0d2ab409a269"
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:90a887ab-a8a3-45b6-87c3-d33000ccc882",
+ "@id": "urn:fslmaths-9SKMjmJH",
"Label": "fslmaths",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -dilF mask",
"Used": [
- "urn:f68ab65b-7eba-43ac-9558-ac93d8a9627f"
+ "bids::mask"
]
},
{
- "@id": "urn:82533282-c050-4033-8227-7a8e5d1dcc98",
+ "@id": "urn:fslmaths-LT5qFn1b",
"Label": "fslmaths",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh",
"Used": [
- "urn:ca79b157-4377-4949-9689-0d2ab409a269",
- "urn:f68ab65b-7eba-43ac-9558-ac93d8a9627f"
+ "bids::mask",
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:9f95d75b-2960-4442-b622-cfa279765332",
+ "@id": "urn:fslmaths-w1OidnBM",
"Label": "fslmaths",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func",
"Used": [
- "urn:e77609bf-fd45-4ea1-ad95-08171ed97abb"
+ "bids::prefiltered_func_data_thresh"
]
},
{
- "@id": "urn:dcf9ddaa-39ea-47a9-be3b-8b2af995f141",
+ "@id": "urn:susan-6PHMBnDq",
"Label": "susan",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/susan prefiltered_func_data_thresh 445.8289035 2.54777070064 3 1 1 mean_func 445.8289035 prefiltered_func_data_smooth",
"Used": [
- "urn:e77609bf-fd45-4ea1-ad95-08171ed97abb"
+ "bids::prefiltered_func_data_thresh"
]
},
{
- "@id": "urn:34a6ccc1-c1a9-4abc-9c95-3c421aed66d5",
+ "@id": "urn:fslmaths-AtC5PthI",
"Label": "fslmaths",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth",
"Used": [
- "urn:525db306-486b-4f71-9290-dbb1682ab1f7",
- "urn:f68ab65b-7eba-43ac-9558-ac93d8a9627f"
+ "bids::mask",
+ "bids::prefiltered_func_data_smooth"
]
},
{
- "@id": "urn:23b3a8fd-1d9d-4840-b592-ff7a5854e10b",
+ "@id": "urn:fslmaths-2DRcnfmM",
"Label": "fslmaths",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mul 16.8225970571 prefiltered_func_data_intnorm",
"Used": [
- "urn:525db306-486b-4f71-9290-dbb1682ab1f7"
+ "bids::prefiltered_func_data_smooth"
]
},
{
- "@id": "urn:af12b69b-fe39-4e11-90eb-ebe03f5f448a",
+ "@id": "urn:fslmaths-6z0BIKxs",
"Label": "fslmaths",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean",
"Used": [
- "urn:a4dbd220-cd2c-47f5-af17-d530c580025b"
+ "bids::prefiltered_func_data_intnorm"
]
},
{
- "@id": "urn:e777f8b9-880c-4a71-ad01-43f3f0abbeee",
+ "@id": "urn:fslmaths-mTFxCyoQ",
"Label": "fslmaths",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -bptf 15.0 -1 -add tempMean prefiltered_func_data_tempfilt",
"Used": [
- "urn:a4dbd220-cd2c-47f5-af17-d530c580025b",
- "urn:bf94ded8-b9a7-437d-9389-d428f2666053"
+ "bids::prefiltered_func_data_intnorm",
+ "bids::tempMean"
]
},
{
- "@id": "urn:bc3e53a0-c4c7-497a-9f5f-a6a01ce571da",
+ "@id": "urn:imrm-OTEd4jdX",
"Label": "imrm",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/imrm tempMean",
"Used": [
- "urn:bf94ded8-b9a7-437d-9389-d428f2666053"
+ "bids::tempMean"
]
},
{
- "@id": "urn:2bfbbd04-1c3c-497c-bb68-6aec82246c3b",
+ "@id": "urn:fslmaths-vC7x32pX",
"Label": "fslmaths",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data",
"Used": [
- "urn:0557adb8-317b-43b3-9a7c-cc92bc076ae4"
+ "bids::prefiltered_func_data_tempfilt"
]
},
{
- "@id": "urn:af083328-c044-4b96-ab22-8eb5fc590cd5",
+ "@id": "urn:fslmaths-htzC3QnL",
"Label": "fslmaths",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths filtered_func_data -Tmean mean_func",
"Used": [
- "urn:46e4ccb6-9f24-41af-a5f0-3d0c94cad925"
+ "bids::filtered_func_data"
]
},
{
- "@id": "urn:a2a332d5-28ed-4942-8b86-a35a27e8bddb",
+ "@id": "urn:rm-6K7QbTxg",
"Label": "rm",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/bin/rm -rf prefiltered_func_data*",
"Used": [
- "urn:68954e54-5941-4ec9-ac55-7d2e944fbb74"
+ "bids::prefiltered_func_data*"
]
},
{
- "@id": "urn:565d6945-cf43-4637-91dd-959ef59fd94f",
+ "@id": "urn:makedire-ddWcoA2E",
"Label": "Make directory",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
- "@id": "urn:beae7e86-fb11-4df3-84b4-4666debc7e5f",
+ "@id": "urn:fslfixte-pdQxZQAo",
"Label": "fslFixText",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
"Used": [
- "urn:a593e27f-7e1a-44ef-85cc-4712ba305740"
+ "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt"
]
},
{
- "@id": "urn:2b244cf4-5e67-41c2-bf50-4eab48c53424",
+ "@id": "urn:makedire-MvIqyL0b",
"Label": "Make directory",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
- "@id": "urn:23a6da3c-5123-4785-9953-2811110cbadd",
+ "@id": "urn:fslfixte-8AM2FS0p",
"Label": "fslFixText",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
"Used": [
- "urn:0aaa9b00-90b6-4f7c-bef2-5e46efd3abe5"
+ "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt"
]
},
{
- "@id": "urn:f330816b-b82a-4d29-83cd-78e2d6e6a680",
+ "@id": "urn:filmgls-J1GidVef",
"Label": "film_gls",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con",
- "Used": []
+ "Used": [
+ "bids::design.con",
+ "bids::design.mat",
+ "bids::filtered_func_data",
+ "bids::stats"
+ ]
},
{
- "@id": "urn:1ea5f0a6-5c3a-4f1c-a8b2-2471344253bc",
+ "@id": "urn:smoothes-VGJzmzTv",
"Label": "smoothest",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 102 -m mask -r stats/res4d > stats/smoothness",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 102 -m mask -r stats/res4d > stats/smoothness",
"Used": [
- "urn:16abfbc5-89b6-4a8d-bcb3-5216a6cca934",
- "urn:f68ab65b-7eba-43ac-9558-ac93d8a9627f"
+ "bids::mask",
+ "bids::stats/res4d"
]
},
{
- "@id": "urn:87b39aea-7485-4ccb-be46-cf814c21fc7b",
+ "@id": "urn:fslmaths-K3fmTMnl",
"Label": "fslmaths",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1",
"Used": [
- "urn:e654e524-4ecb-49e1-844a-6cfd6bf2cda9",
- "urn:f68ab65b-7eba-43ac-9558-ac93d8a9627f"
+ "bids::mask",
+ "bids::stats/zstat1"
]
},
{
- "@id": "urn:a2e9a27e-e4fc-454e-a015-e4591a0003df",
+ "@id": "urn:echo-jVwSVYtg",
"Label": "echo",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "echo 38352 > thresh_zstat1.vol",
"Used": []
},
{
- "@id": "urn:ac9e2bcd-cb54-40e8-a68c-9962174801f5",
+ "@id": "urn:fslmaths-u2VVZ7tv",
"Label": "fslmaths",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat2 -mas mask thresh_zstat2",
"Used": [
- "urn:a68b66ec-2367-4d43-8664-e02dd673998a",
- "urn:f68ab65b-7eba-43ac-9558-ac93d8a9627f"
+ "bids::mask",
+ "bids::stats/zstat2"
]
},
{
- "@id": "urn:c62bd1a0-c919-4b92-8fce-570a872cf405",
+ "@id": "urn:echo-HA8f2GFE",
"Label": "echo",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "echo 38352 > thresh_zstat2.vol",
"Used": []
},
{
- "@id": "urn:74423947-e686-4ba8-9fbf-1df2c6f63d5b",
+ "@id": "urn:ptoz-bRHfLZiR",
"Label": "ptoz",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:14fea31e-6012-42ea-b435-728cb9bb44ae",
+ "@id": "urn:cluster-1qGG2rFS",
"Label": "cluster",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -t 3.090232 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z --voxuncthresh -c stats/cope1 > cluster_zstat1.txt",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -t 3.090232 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z --voxuncthresh -c stats/cope1 > cluster_zstat1.txt",
"Used": [
- "urn:8306f482-d9ff-4eb9-b0b1-67182a7af916",
- "urn:f0ecf845-76ce-4699-8ae5-ba0bb2ad4118"
+ "bids::stats/cope1",
+ "bids::thresh_zstat1"
]
},
{
- "@id": "urn:095384b1-8649-42be-85d8-93f6790e8498",
+ "@id": "urn:cluster2-AbLpC1LT",
"Label": "cluster2html",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat1",
"Used": [
- "urn:542d59dc-af4e-49b0-b3a0-9512a2ecf64d"
+ "bids::cluster_zstat1"
]
},
{
- "@id": "urn:614e1d98-68ea-4037-959c-218caac702b4",
+ "@id": "urn:ptoz-oUD5u0y9",
"Label": "ptoz",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:36bd51f7-6a7b-4972-9e3f-128f1e3bc200",
+ "@id": "urn:cluster-pIRYl9sN",
"Label": "cluster",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat2 -t 3.090232 --othresh=thresh_zstat2 -o cluster_mask_zstat2 --connectivity=26 --olmax=lmax_zstat2.txt --scalarname=Z --voxuncthresh -c stats/cope2 > cluster_zstat2.txt",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat2 -t 3.090232 --othresh=thresh_zstat2 -o cluster_mask_zstat2 --connectivity=26 --olmax=lmax_zstat2.txt --scalarname=Z --voxuncthresh -c stats/cope2 > cluster_zstat2.txt",
"Used": [
- "urn:bba20b2d-4d4a-4190-8d90-d76d8a736f06",
- "urn:ea8a00b5-0155-4e66-b452-2ccbd7fd3940"
+ "bids::stats/cope2",
+ "bids::thresh_zstat2"
]
},
{
- "@id": "urn:cd0c6bf0-a4e1-4661-91d7-3ac3a921f611",
+ "@id": "urn:cluster2-iHy49U0U",
"Label": "cluster2html",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat2",
"Used": [
- "urn:073168b5-b593-4406-9b08-d95f08b1cd1e"
+ "bids::cluster_zstat2"
]
},
{
- "@id": "urn:99bfb3b9-63a3-4d93-9388-84dd8aaba7b3",
+ "@id": "urn:fslstats-68QurBZC",
"Label": "fslstats",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat1 -l 0.0001 -R 2>/dev/null",
"Used": [
- "urn:f0ecf845-76ce-4699-8ae5-ba0bb2ad4118"
+ "bids::thresh_zstat1"
]
},
{
- "@id": "urn:cd2192eb-05ca-4a36-b7f3-02f2de727f03",
+ "@id": "urn:fslstats-KGQicDB8",
"Label": "fslstats",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat2 -l 0.0001 -R 2>/dev/null",
"Used": [
- "urn:ea8a00b5-0155-4e66-b452-2ccbd7fd3940"
+ "bids::thresh_zstat2"
]
},
{
- "@id": "urn:99294797-5ac2-4a26-ac54-35efb70dd070",
+ "@id": "urn:overlay-K259t49U",
"Label": "overlay",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat1 3.090259 7.129133 rendered_thresh_zstat1",
"Used": []
},
{
- "@id": "urn:66264a2d-510c-4b43-ba0b-f808d8aa1fbf",
+ "@id": "urn:slicer-4gEMZuYv",
"Label": "slicer",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat1 -A 750 rendered_thresh_zstat1.png",
"Used": [
- "urn:a7f17246-55db-4911-bfc2-1c25c8cbd171"
+ "bids::rendered_thresh_zstat1"
]
},
{
- "@id": "urn:c9f93d13-28f2-4940-8f5b-e03bcf9f67a7",
+ "@id": "urn:cp-klo2wOQo",
"Label": "cp",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/bin/cp /usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif .ramp.gif",
"Used": [
- "urn:5f9b6c63-f114-4763-a153-e4ba8a4c510e"
+ "bids::/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif"
]
},
{
- "@id": "urn:01ddd7c2-68e7-46d1-a2f0-0754251c9b70",
+ "@id": "urn:overlay-HXXKsGWM",
"Label": "overlay",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat2 3.090259 7.129133 rendered_thresh_zstat2",
"Used": []
},
{
- "@id": "urn:af6179ab-9c22-4d4a-bf0e-222d6c572bb8",
+ "@id": "urn:slicer-lHD16dgj",
"Label": "slicer",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat2 -A 750 rendered_thresh_zstat2.png",
"Used": [
- "urn:fe55b2a7-0de1-499d-a868-a5dc04c73443"
+ "bids::rendered_thresh_zstat2"
]
},
{
- "@id": "urn:30eff423-d391-4db7-a391-898d50dc8e92",
+ "@id": "urn:makedire-wmAJGONO",
"Label": "Make directory",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "mkdir -p tsplot",
"Used": []
},
{
- "@id": "urn:1c858060-3800-44dc-bcab-8a540f7d215c",
+ "@id": "urn:tsplot-a71eZBwo",
"Label": "tsplot",
- "AssociatedWith": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "AssociatedWith": "urn:fsl-LlDJMBmv",
"Command": "/usr/local/packages/fsl-5.0.10/bin/tsplot . -f filtered_func_data -o tsplot",
"Used": []
}
],
"Entities": [
{
- "@id": "urn:1abb6b74-47f8-4ecd-bf39-ce9eb36d5274",
+ "@id": "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold",
"Label": "sub-01_task-tonecounting_bold",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold",
+ "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold",
"digest": {
- "sha256": "028adf00daa36e78f06a61dcd3cb3526cd8564c1284e80516ab5520701324ac1"
+ "sha256": "33501604ae140e58832facff473a9578d5a549403bdbec53107d2b3eaab898ee"
}
},
{
- "@id": "urn:ad48371d-a0aa-40e9-87c1-3d835c7d9bc4",
+ "@id": "bids::prefiltered_func_data",
"Label": "prefiltered_func_data",
"AtLocation": "prefiltered_func_data",
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@@ -664,45 +673,57 @@
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@@ -710,267 +731,259 @@
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@@ -978,25 +991,25 @@
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+ "@id": "bids::mc",
"Label": "mc",
"AtLocation": "mc",
- "GeneratedBy": "urn:325a2bfd-6837-4b92-822d-3b697d0883a6",
+ "GeneratedBy": "urn:makedire-VSGQwlhb",
"digest": {
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}
},
{
- "@id": "urn:cd76fc5a-b376-4723-bac8-111eaaa24083",
+ "@id": "bids::prefiltered_func_data_mcf.mat",
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"AtLocation": "prefiltered_func_data_mcf.mat",
"digest": {
@@ -1004,7 +1017,7 @@
}
},
{
- "@id": "urn:793001e3-092c-46bb-b006-638851f60f1e",
+ "@id": "bids::prefiltered_func_data_mcf.par",
"Label": "prefiltered_func_data_mcf.par",
"AtLocation": "prefiltered_func_data_mcf.par",
"digest": {
@@ -1012,7 +1025,7 @@
}
},
{
- "@id": "urn:695fc232-c43b-47af-9cef-3c948b5bfcff",
+ "@id": "bids::prefiltered_func_data_mcf_abs.rms",
"Label": "prefiltered_func_data_mcf_abs.rms",
"AtLocation": "prefiltered_func_data_mcf_abs.rms",
"digest": {
@@ -1020,7 +1033,7 @@
}
},
{
- "@id": "urn:51085d5c-9272-48b6-8298-868f86ac98e5",
+ "@id": "bids::prefiltered_func_data_mcf_abs_mean.rms",
"Label": "prefiltered_func_data_mcf_abs_mean.rms",
"AtLocation": "prefiltered_func_data_mcf_abs_mean.rms",
"digest": {
@@ -1028,7 +1041,7 @@
}
},
{
- "@id": "urn:3e6964e1-0ce4-4cae-b165-83f556a2a6e4",
+ "@id": "bids::prefiltered_func_data_mcf_rel.rms",
"Label": "prefiltered_func_data_mcf_rel.rms",
"AtLocation": "prefiltered_func_data_mcf_rel.rms",
"digest": {
@@ -1036,7 +1049,7 @@
}
},
{
- "@id": "urn:90ae9a95-aa81-4c49-a5ba-b7a37d554b7f",
+ "@id": "bids::prefiltered_func_data_mcf_rel_mean.rms",
"Label": "prefiltered_func_data_mcf_rel_mean.rms",
"AtLocation": "prefiltered_func_data_mcf_rel_mean.rms",
"digest": {
@@ -1044,34 +1057,34 @@
}
},
{
- "@id": "urn:6310131e-c904-4128-a310-bcd85a930896",
+ "@id": "bids::mc",
"Label": "mc",
"AtLocation": "mc",
- "GeneratedBy": "urn:0139ed04-010d-414f-8907-5d6163b567ea",
+ "GeneratedBy": "urn:mv-a1clMa7z",
"digest": {
"sha256": "a1a8fa7b1d2bf5bc0a263e95f926d3d9b656d2572455245d46edf48e93744ffa"
}
},
{
- "@id": "urn:e743a0bb-478d-4238-aedf-b1620721c88b",
+ "@id": "bids::rot.png",
"Label": "rot.png",
"AtLocation": "rot.png",
- "GeneratedBy": "urn:6029fd2b-6341-4c78-9c8f-ed8b23999598",
+ "GeneratedBy": "urn:fsltsplo-0AK42d62",
"digest": {
"sha256": "b8776603f8865a358b2273847d21e63491e7c2e10567fb640608dd47ba721f29"
}
},
{
- "@id": "urn:6670247b-4942-4a7a-a1fa-31c4d3f24695",
+ "@id": "bids::trans.png",
"Label": "trans.png",
"AtLocation": "trans.png",
- "GeneratedBy": "urn:322ef859-6275-4576-b46c-c4b1de5333f5",
+ "GeneratedBy": "urn:fsltsplo-D2384XzX",
"digest": {
"sha256": "496eac1d0ac15e80928780c73766c7791a1707291b2b9a6d1781c2f6a38de3cd"
}
},
{
- "@id": "urn:58295d4c-36e1-499e-8a3a-181a424b6142",
+ "@id": "bids::prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"Label": "prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"AtLocation": "prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"digest": {
@@ -1079,34 +1092,34 @@
}
},
{
- "@id": "urn:b1cfd1b0-2ccc-4359-b62c-14e43afb5b18",
+ "@id": "bids::disp.png",
"Label": "disp.png",
"AtLocation": "disp.png",
- "GeneratedBy": "urn:9ab1f065-b1b1-4d54-a405-59ef938a5da1",
+ "GeneratedBy": "urn:fsltsplo-oFlR7AKx",
"digest": {
"sha256": "c4615e07e04f0c390d969482634cb62e81d47c818d2866ee866ec9c64a5350fd"
}
},
{
- "@id": "urn:9d1898a7-03e2-445f-8756-faeb5bec2948",
+ "@id": "bids::mean_func",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:3dc068ee-1ef5-4ee5-bb1b-e1c8b3c87c91",
+ "GeneratedBy": "urn:fslmaths-t17JOD8i",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:f68ab65b-7eba-43ac-9558-ac93d8a9627f",
+ "@id": "bids::mask",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "GeneratedBy": "urn:bet2-RLQM3p76",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:3c8f1e80-b4dc-4d12-b22c-ac616848f9ae",
+ "@id": "bids::mask_mask",
"Label": "mask_mask",
"AtLocation": "mask_mask",
"digest": {
@@ -1114,132 +1127,124 @@
}
},
{
- "@id": "urn:01916163-39ab-406b-a4ad-fe365cf6bf5e",
+ "@id": "bids::mask",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:6442d6c7-861e-47b6-a7ec-869397d3fd3c",
+ "GeneratedBy": "urn:immv-gwbMDqAA",
"digest": {
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}
},
{
- "@id": "urn:f8ad3805-7098-4b47-bba8-e210230c5e80",
+ "@id": "bids::prefiltered_func_data_bet",
"Label": "prefiltered_func_data_bet",
"AtLocation": "prefiltered_func_data_bet",
- "GeneratedBy": "urn:057be9c0-35ac-49f8-a62a-d3917a8736cf",
+ "GeneratedBy": "urn:fslmaths-t2aHVzoS",
"digest": {
"sha256": "c01f21947b38d9886528dec14edf23dfb55304b7da67569fe93902472b286cf4"
}
},
{
- "@id": "urn:1f493787-989c-4c06-97df-d5dde83c5dcf",
+ "@id": "bids::mask",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:a5fc0d33-b76e-4555-a307-ff6b719128b6",
+ "GeneratedBy": "urn:fslmaths-8BSfMD2j",
"digest": {
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}
},
{
- "@id": "urn:ac927f49-4167-4dc0-b0da-d215e9262d89",
+ "@id": "bids::mask",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:90a887ab-a8a3-45b6-87c3-d33000ccc882",
+ "GeneratedBy": "urn:fslmaths-9SKMjmJH",
"digest": {
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}
},
{
- "@id": "urn:e77609bf-fd45-4ea1-ad95-08171ed97abb",
+ "@id": "bids::prefiltered_func_data_thresh",
"Label": "prefiltered_func_data_thresh",
"AtLocation": "prefiltered_func_data_thresh",
- "GeneratedBy": "urn:82533282-c050-4033-8227-7a8e5d1dcc98",
+ "GeneratedBy": "urn:fslmaths-LT5qFn1b",
"digest": {
"sha256": "c5c015a8df079b497bbce596808cbbdc09fb39411f490244de192dfa72d33640"
}
},
{
- "@id": "urn:f18b385c-ae9d-432e-a000-11b8fcc937f0",
+ "@id": "bids::mean_func",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:9f95d75b-2960-4442-b622-cfa279765332",
+ "GeneratedBy": "urn:fslmaths-w1OidnBM",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:525db306-486b-4f71-9290-dbb1682ab1f7",
+ "@id": "bids::prefiltered_func_data_smooth",
"Label": "prefiltered_func_data_smooth",
"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:dcf9ddaa-39ea-47a9-be3b-8b2af995f141",
+ "GeneratedBy": "urn:susan-6PHMBnDq",
"digest": {
"sha256": "2a4901d885fce0b083c9f99364da8dcff184635e74ab011f53a68cfc6827b429"
}
},
{
- "@id": "urn:555bcac3-727b-420f-be4c-d8e506e33ce6",
+ "@id": "bids::prefiltered_func_data_smooth",
"Label": "prefiltered_func_data_smooth",
"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:34a6ccc1-c1a9-4abc-9c95-3c421aed66d5",
+ "GeneratedBy": "urn:fslmaths-AtC5PthI",
"digest": {
"sha256": "2a4901d885fce0b083c9f99364da8dcff184635e74ab011f53a68cfc6827b429"
}
},
{
- "@id": "urn:a4dbd220-cd2c-47f5-af17-d530c580025b",
+ "@id": "bids::prefiltered_func_data_intnorm",
"Label": "prefiltered_func_data_intnorm",
"AtLocation": "prefiltered_func_data_intnorm",
- "GeneratedBy": "urn:23b3a8fd-1d9d-4840-b592-ff7a5854e10b",
+ "GeneratedBy": "urn:fslmaths-2DRcnfmM",
"digest": {
"sha256": "0698a276f6f0fdccfb06033926d333a176503a09aaa87b78384fbffbf1c54dee"
}
},
{
- "@id": "urn:bf94ded8-b9a7-437d-9389-d428f2666053",
+ "@id": "bids::tempMean",
"Label": "tempMean",
"AtLocation": "tempMean",
- "GeneratedBy": "urn:af12b69b-fe39-4e11-90eb-ebe03f5f448a",
+ "GeneratedBy": "urn:fslmaths-6z0BIKxs",
"digest": {
"sha256": "1a01513c76bc17516b60df315a1922789ce79d72e66e105fbf2723df9cb1b038"
}
},
{
- "@id": "urn:c73caae5-64c6-4d21-8599-9e670b9bfb9b",
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- "digest": {
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- }
- },
- {
- "@id": "urn:0557adb8-317b-43b3-9a7c-cc92bc076ae4",
+ "@id": "bids::prefiltered_func_data_tempfilt",
"Label": "prefiltered_func_data_tempfilt",
"AtLocation": "prefiltered_func_data_tempfilt",
+ "GeneratedBy": "urn:fslmaths-mTFxCyoQ",
"digest": {
"sha256": "a1836f4694e7ffdb50484626724602498c7b22b4f3cdd1e7d105efd336cbc8bd"
}
},
{
- "@id": "urn:46e4ccb6-9f24-41af-a5f0-3d0c94cad925",
+ "@id": "bids::filtered_func_data",
"Label": "filtered_func_data",
"AtLocation": "filtered_func_data",
- "GeneratedBy": "urn:2bfbbd04-1c3c-497c-bb68-6aec82246c3b",
+ "GeneratedBy": "urn:fslmaths-vC7x32pX",
"digest": {
"sha256": "2a1854e3b48a54f88e063191e25159015a0afbd300d18a1cfda37b4b68a1ee69"
}
},
{
- "@id": "urn:8cc3c85c-f86e-4cbf-a49d-309ec01af2ec",
+ "@id": "bids::mean_func",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:af083328-c044-4b96-ab22-8eb5fc590cd5",
+ "GeneratedBy": "urn:fslmaths-htzC3QnL",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:68954e54-5941-4ec9-ac55-7d2e944fbb74",
+ "@id": "bids::prefiltered_func_data*",
"Label": "prefiltered_func_data*",
"AtLocation": "prefiltered_func_data*",
"digest": {
@@ -1247,130 +1252,172 @@
}
},
{
- "@id": "urn:f1adcdf3-1142-44e9-91b5-d5e17469c02e",
+ "@id": "bids::custom_timing_files",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:565d6945-cf43-4637-91dd-959ef59fd94f",
+ "GeneratedBy": "urn:makedire-ddWcoA2E",
"digest": {
"sha256": "1d7e19792328d5040f2f9fb3c15d59de90fc771785f81c67039a043bd5f2ed20"
}
},
{
- "@id": "urn:a593e27f-7e1a-44ef-85cc-4712ba305740",
+ "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
"Label": "sub-01_tone_counting.txt",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
+ "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
"digest": {
- "sha256": "c120d27b9d5d81a91be0e55f5cb880b2cb7de6c655554d9c15c9c04c6232ea8e"
+ "sha256": "165398224a205d2fc0b19354e15d9b085c6d81e333b69c4697b7894a2549be0b"
}
},
{
- "@id": "urn:7b9e73d4-ce1b-4f85-90c1-720b737aecf6",
+ "@id": "bids::custom_timing_files/ev1.txt",
"Label": "ev1.txt",
"AtLocation": "custom_timing_files/ev1.txt",
- "GeneratedBy": "urn:beae7e86-fb11-4df3-84b4-4666debc7e5f"
+ "GeneratedBy": "urn:fslfixte-pdQxZQAo"
},
{
- "@id": "urn:848d10fa-989f-4a16-9db9-e9f346013291",
+ "@id": "bids::custom_timing_files",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:2b244cf4-5e67-41c2-bf50-4eab48c53424",
+ "GeneratedBy": "urn:makedire-MvIqyL0b",
"digest": {
"sha256": "1d7e19792328d5040f2f9fb3c15d59de90fc771785f81c67039a043bd5f2ed20"
}
},
{
- "@id": "urn:0aaa9b00-90b6-4f7c-bef2-5e46efd3abe5",
+ "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
"Label": "sub-01_tone_counting_probe.txt",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
+ "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
"digest": {
- "sha256": "f09eeb82fa0be8e8759a5269403f36ec2b7dbf2c5b6caba1f0f985cc6cb3f703"
+ "sha256": "8b912293767f1a5e082311f6aaf0c44fc91fe45b0f2ae7f80e368bc2f4c2918a"
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},
{
- "@id": "urn:dbc11716-e865-4e0f-9e6b-70c3603b6f2c",
+ "@id": "bids::custom_timing_files/ev2.txt",
"Label": "ev2.txt",
"AtLocation": "custom_timing_files/ev2.txt",
- "GeneratedBy": "urn:23a6da3c-5123-4785-9953-2811110cbadd"
+ "GeneratedBy": "urn:fslfixte-8AM2FS0p"
},
{
- "@id": "urn:16abfbc5-89b6-4a8d-bcb3-5216a6cca934",
- "Label": "res4d",
- "AtLocation": "stats/res4d",
+ "@id": "bids::stats",
+ "Label": "stats",
+ "AtLocation": "stats",
"digest": {
- "sha256": "8845286f36caedf891a02afddc4175ea46f18f830b59a8c5026962184a530699"
+ "sha256": "a9f3e135372514a16d11a8038262b3eff94ccd69a9b35c4724b2759cfc944a07"
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},
{
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- "Label": "smoothness",
- "AtLocation": "stats/smoothness",
- "GeneratedBy": "urn:1ea5f0a6-5c3a-4f1c-a8b2-2471344253bc",
+ "@id": "bids::design.mat",
+ "Label": "design.mat",
+ "AtLocation": "design.mat",
"digest": {
- "sha256": "67b0aaf95a257beff60d331b56265034807ca51e67e2d312d481d5835ef0b1d0"
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{
- "@id": "urn:e654e524-4ecb-49e1-844a-6cfd6bf2cda9",
- "Label": "zstat1",
- "AtLocation": "stats/zstat1",
+ "@id": "bids::design.con",
+ "Label": "design.con",
+ "AtLocation": "design.con",
"digest": {
- "sha256": "70ae47cee1ea1d3f1f6f8aa7ac51f2641cb2fcb745dfd8cc54a389346e6fa094"
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},
{
- "@id": "urn:f0ecf845-76ce-4699-8ae5-ba0bb2ad4118",
+ "@id": "bids::stats",
+ "Label": "stats",
+ "AtLocation": "stats",
+ "GeneratedBy": "urn:filmgls-J1GidVef",
+ "digest": {
+ "sha256": "a9f3e135372514a16d11a8038262b3eff94ccd69a9b35c4724b2759cfc944a07"
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+ {
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+ "Label": "res4d",
+ "AtLocation": "stats/res4d"
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+ {
+ "@id": "bids::stats/smoothness",
+ "Label": "smoothness",
+ "AtLocation": "stats/smoothness",
+ "GeneratedBy": "urn:smoothes-VGJzmzTv"
+ },
+ {
+ "@id": "bids::stats/zstat1",
+ "Label": "zstat1",
+ "AtLocation": "stats/zstat1"
+ },
+ {
+ "@id": "bids::thresh_zstat1",
"Label": "thresh_zstat1",
"AtLocation": "thresh_zstat1",
- "GeneratedBy": "urn:87b39aea-7485-4ccb-be46-cf814c21fc7b",
+ "GeneratedBy": "urn:fslmaths-K3fmTMnl",
"digest": {
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}
},
{
- "@id": "urn:a68b66ec-2367-4d43-8664-e02dd673998a",
+ "@id": "bids::stats/zstat2",
"Label": "zstat2",
- "AtLocation": "stats/zstat2",
- "digest": {
- "sha256": "b6b265908257e91648f7007e172c3ba159d9231b0acfce7fbf48d754f8cfe52c"
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+ "AtLocation": "stats/zstat2"
},
{
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+ "@id": "bids::thresh_zstat2",
"Label": "thresh_zstat2",
"AtLocation": "thresh_zstat2",
- "GeneratedBy": "urn:ac9e2bcd-cb54-40e8-a68c-9962174801f5",
+ "GeneratedBy": "urn:fslmaths-u2VVZ7tv",
"digest": {
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}
},
{
- "@id": "urn:8306f482-d9ff-4eb9-b0b1-67182a7af916",
+ "@id": "bids::stats/cope1",
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- "AtLocation": "stats/cope1",
- "digest": {
- "sha256": "bf3b603569da6dbe3d6f0e8667d346f3ac943c9d01d2fc9743ce17abeb1547fb"
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+ "AtLocation": "stats/cope1"
},
{
- "@id": "urn:8713b1e0-13ad-450b-904d-babd44c29b53",
+ "@id": "bids::cluster_mask_zstat1",
"Label": "cluster_mask_zstat1",
"AtLocation": "cluster_mask_zstat1",
- "GeneratedBy": "urn:14fea31e-6012-42ea-b435-728cb9bb44ae",
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+ "GeneratedBy": "urn:cluster-1qGG2rFS"
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"AtLocation": "cluster_zstat1",
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@@ -1378,33 +1425,54 @@
}
},
{
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- "digest": {
- "sha256": "5f073baabd78c1c473fed55b511738f0ffe30d9fc1f23352a16ec058daacd88c"
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+ "AtLocation": "stats/cope2"
},
{
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"AtLocation": "cluster_mask_zstat2",
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{
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+ "Label": "thresh_zstat2",
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"Label": "cope2",
"AtLocation": "stats/cope2",
- "GeneratedBy": "urn:36bd51f7-6a7b-4972-9e3f-128f1e3bc200",
+ "GeneratedBy": "urn:cluster-pIRYl9sN"
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}
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{
- "@id": "urn:073168b5-b593-4406-9b08-d95f08b1cd1e",
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"AtLocation": "cluster_zstat2",
"digest": {
@@ -1412,25 +1480,25 @@
}
},
{
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"AtLocation": "rendered_thresh_zstat1",
- "GeneratedBy": "urn:99294797-5ac2-4a26-ac54-35efb70dd070",
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"AtLocation": "rendered_thresh_zstat1.png",
- "GeneratedBy": "urn:66264a2d-510c-4b43-ba0b-f808d8aa1fbf",
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{
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"digest": {
@@ -1438,46 +1506,46 @@
}
},
{
- "@id": "urn:ec283808-c37d-4153-868a-acac76f311bf",
+ "@id": "bids::.ramp.gif",
"Label": ".ramp.gif",
"AtLocation": ".ramp.gif",
- "GeneratedBy": "urn:c9f93d13-28f2-4940-8f5b-e03bcf9f67a7",
+ "GeneratedBy": "urn:cp-klo2wOQo",
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"Label": "rendered_thresh_zstat2",
"AtLocation": "rendered_thresh_zstat2",
- "GeneratedBy": "urn:01ddd7c2-68e7-46d1-a2f0-0754251c9b70",
+ "GeneratedBy": "urn:overlay-HXXKsGWM",
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{
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+ "@id": "bids::rendered_thresh_zstat2.png",
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"AtLocation": "rendered_thresh_zstat2.png",
- "GeneratedBy": "urn:af6179ab-9c22-4d4a-bf0e-222d6c572bb8",
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}
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{
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+ "@id": "bids::tsplot",
"Label": "tsplot",
"AtLocation": "tsplot",
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+ "GeneratedBy": "urn:makedire-wmAJGONO",
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},
{
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+ "@id": "bids::tsplot",
"Label": "tsplot",
"AtLocation": "tsplot",
- "GeneratedBy": "urn:1c858060-3800-44dc-bcab-8a540f7d215c",
+ "GeneratedBy": "urn:tsplot-a71eZBwo",
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diff --git a/examples/from_parsers/fsl/fsl_gaussian_report_log.png b/examples/from_parsers/fsl/fsl_gaussian_report_log.png
index 756d7bad3..485bb37e5 100644
Binary files a/examples/from_parsers/fsl/fsl_gaussian_report_log.png and b/examples/from_parsers/fsl/fsl_gaussian_report_log.png differ
diff --git a/examples/from_parsers/fsl/fsl_group_btw_report_log.jsonld b/examples/from_parsers/fsl/fsl_group_btw_report_log.jsonld
index 69822ddfc..0c1695fb2 100644
--- a/examples/from_parsers/fsl/fsl_group_btw_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_group_btw_report_log.jsonld
@@ -4,437 +4,437 @@
"Records": {
"Software": [
{
- "@id": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:fsl-AZ1kWvHX",
"@type": "prov:SoftwareAgent",
"Label": "FSL",
- "Version": "xxx"
+ "Version": "xxx",
+ "AltIdentifier": "RRID:SCR_002823"
}
],
"Activities": [
{
- "@id": "urn:21b70068-0e68-4cfa-afd4-f6103efb8b83",
+ "@id": "urn:featrega-taLbN7kR",
"Label": "featregapply",
- "AssociatedWith": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
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"Used": []
},
{
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"Label": "featregapply",
- "AssociatedWith": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
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"Used": []
},
{
- "@id": "urn:15bea182-294d-4fe1-9350-ae103cb0dddb",
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"Label": "featregapply",
- "AssociatedWith": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
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"Used": []
},
{
- "@id": "urn:e8466eba-cc73-4e2d-a3e9-9df243ee1687",
+ "@id": "urn:featrega-zLqqWQIB",
"Label": "featregapply",
- "AssociatedWith": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
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"Used": []
},
{
- "@id": "urn:7328a639-5800-430e-9d20-d0c7d77f0daa",
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- "AssociatedWith": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
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},
{
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},
{
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},
{
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"Used": []
},
{
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{
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},
{
- "@id": "urn:fe6b1502-266f-4d26-84fb-040ce6fc2a3d",
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{
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"Used": []
},
{
- "@id": "urn:c0202a60-50f5-4497-b5d0-e6fb9ceead1d",
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{
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"Used": []
},
{
- "@id": "urn:1756ff39-a0cf-41b2-a7c8-d940ea52eaab",
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},
{
- "@id": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
+ "@id": "urn:fslmaths-xAVI0ILB",
"Label": "fslmaths",
- "AssociatedWith": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
+ "AssociatedWith": "urn:fsl-AZ1kWvHX",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths bg_image -inm 1000 -Tmean bg_image -odt float",
"Used": [
- "urn:b2625755-9228-4f29-9cdc-9e2e311271b4"
+ "bids::bg_image"
]
},
{
- "@id": "urn:496fc0fe-61c9-4f9f-9f38-fda4fc784cd0",
+ "@id": "urn:fslmerge-2F6G7rII",
"Label": "fslmerge",
- "AssociatedWith": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmerge -t mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/mask",
+ "AssociatedWith": "urn:fsl-AZ1kWvHX",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmerge -t mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/mask /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/mask",
"Used": []
},
{
- "@id": "urn:b6285a9f-3c3b-4835-8421-b287dd391f8a",
+ "@id": "urn:makedire-74G7oRAv",
"Label": "Make directory",
- "AssociatedWith": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
+ "AssociatedWith": "urn:fsl-AZ1kWvHX",
"Command": "mkdir -p inputreg",
"Used": []
},
{
- "@id": "urn:57e2f46d-dd77-4e80-91e3-0ca1293cc9eb",
+ "@id": "urn:fslmaths-GzWzykG0",
"Label": "fslmaths",
- "AssociatedWith": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
+ "AssociatedWith": "urn:fsl-AZ1kWvHX",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ../mask -mul 14 -Tmean masksum -odt short",
"Used": [
- "urn:98687417-079d-459f-ab4a-89047b25a9ea"
+ "bids::mask"
]
},
{
- "@id": "urn:7d63f25f-d6b3-4cdc-8adb-96dd6839ae99",
+ "@id": "urn:fslmaths-8xYEeypD",
"Label": "fslmaths",
- "AssociatedWith": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
+ "AssociatedWith": "urn:fsl-AZ1kWvHX",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths masksum -thr 14 -add masksum masksum",
"Used": [
- "urn:26845403-e157-4c37-9a6e-c1eeaeae3b18"
+ "bids::masksum"
]
},
{
- "@id": "urn:4c12c01c-24cf-4949-ba38-a94c7331e0ec",
+ "@id": "urn:overlay-ncDkuQ1G",
"Label": "overlay",
- "AssociatedWith": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
+ "AssociatedWith": "urn:fsl-AZ1kWvHX",
"Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 0 0 -c ../bg_image -a masksum 0.9 28 masksum_overlay",
"Used": []
},
{
- "@id": "urn:a8fe7655-9fee-499e-892a-e6bdb67b388b",
+ "@id": "urn:slicer-uWTpbMIs",
"Label": "slicer",
- "AssociatedWith": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
+ "AssociatedWith": "urn:fsl-AZ1kWvHX",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer masksum_overlay -S 2 750 masksum_overlay.png",
"Used": [
- "urn:7fc2e81a-11c5-4b76-920d-9f1edce0cf30"
+ "bids::masksum_overlay"
]
},
{
- "@id": "urn:1f300416-cb44-4146-9f15-9c00172b67c2",
+ "@id": "urn:fslmaths-MqM50oOn",
"Label": "fslmaths",
- "AssociatedWith": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
+ "AssociatedWith": "urn:fsl-AZ1kWvHX",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths masksum -mul 0 maskunique",
"Used": [
- "urn:26845403-e157-4c37-9a6e-c1eeaeae3b18"
+ "bids::masksum"
]
},
{
- "@id": "urn:ee1dc8c2-1f47-49cd-be91-a9401a7b67e3",
+ "@id": "urn:fslmaths-ttzGVzPh",
"Label": "fslmaths",
- "AssociatedWith": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
+ "AssociatedWith": "urn:fsl-AZ1kWvHX",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/mask -mul -1 -add 1 -mul 1 -add maskunique maskunique",
"Used": [
- "urn:35b33c51-06cd-4fc3-9a42-dc5335988375",
- "urn:f5e2dc55-f182-4797-a887-a3ef2bcdffbb"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:106c67ad-3cda-4b75-9642-0d563c02bba6",
+ "@id": "urn:fslmaths-ZzO3yLZn",
"Label": "fslmaths",
- "AssociatedWith": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
+ "AssociatedWith": "urn:fsl-AZ1kWvHX",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/mask -mul -1 -add 1 -mul 2 -add maskunique maskunique",
"Used": [
- "urn:2b724579-87a4-402f-aeb6-403c1971174d",
- "urn:f5e2dc55-f182-4797-a887-a3ef2bcdffbb"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:ce5318f7-cbe7-499e-bbb5-4ad119b79e07",
+ "@id": "urn:fslmaths-rgVzb0P7",
"Label": "fslmaths",
- "AssociatedWith": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
+ "AssociatedWith": "urn:fsl-AZ1kWvHX",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/mask -mul -1 -add 1 -mul 3 -add maskunique maskunique",
"Used": [
- "urn:521fc7ba-4582-4997-8637-e76a4c3b4be8",
- "urn:f5e2dc55-f182-4797-a887-a3ef2bcdffbb"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:3990b2ab-c24a-4737-a70a-2d9e95fae845",
+ "@id": "urn:fslmaths-jjTUJlby",
"Label": "fslmaths",
- "AssociatedWith": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
+ "AssociatedWith": "urn:fsl-AZ1kWvHX",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/mask -mul -1 -add 1 -mul 4 -add maskunique maskunique",
"Used": [
- "urn:c4f4cc11-80af-41f1-af25-079c326a068c",
- "urn:f5e2dc55-f182-4797-a887-a3ef2bcdffbb"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:eb1300ed-f917-4b8d-be12-a9b6917ab7c7",
+ "@id": "urn:fslmaths-CICGEO6f",
"Label": "fslmaths",
- "AssociatedWith": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
+ "AssociatedWith": "urn:fsl-AZ1kWvHX",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/mask -mul -1 -add 1 -mul 5 -add maskunique maskunique",
"Used": [
- "urn:9c2c6c31-e6f6-4773-a202-95c36cda8dc2",
- "urn:f5e2dc55-f182-4797-a887-a3ef2bcdffbb"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:59c6504b-32b9-4a78-88ba-e3e3e4518c34",
+ "@id": "urn:fslmaths-03CGMMoO",
"Label": "fslmaths",
- "AssociatedWith": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
+ "AssociatedWith": "urn:fsl-AZ1kWvHX",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/mask -mul -1 -add 1 -mul 6 -add maskunique maskunique",
"Used": [
- "urn:43f6af6c-9154-48de-a5ff-3d6037e27b5b",
- "urn:f5e2dc55-f182-4797-a887-a3ef2bcdffbb"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:2cc59175-6303-4cd7-9c05-77a398e2fc83",
+ "@id": "urn:fslmaths-UHAOAQx9",
"Label": "fslmaths",
- "AssociatedWith": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
+ "AssociatedWith": "urn:fsl-AZ1kWvHX",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/mask -mul -1 -add 1 -mul 7 -add maskunique maskunique",
"Used": [
- "urn:49c149bd-506d-43dc-a748-105569e82a6a",
- "urn:f5e2dc55-f182-4797-a887-a3ef2bcdffbb"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:b51b4e36-1b3d-46c2-94e0-75cc74a1bda8",
+ "@id": "urn:fslmaths-z870NCtH",
"Label": "fslmaths",
- "AssociatedWith": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
+ "AssociatedWith": "urn:fsl-AZ1kWvHX",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/mask -mul -1 -add 1 -mul 8 -add maskunique maskunique",
"Used": [
- "urn:8bd0fa0e-165e-4ade-b4bf-ecf95fcbb251",
- "urn:f5e2dc55-f182-4797-a887-a3ef2bcdffbb"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:2b56fc0d-dbd7-46b0-a6b9-e669e98c5221",
+ "@id": "urn:fslmaths-1RPdsfVd",
"Label": "fslmaths",
- "AssociatedWith": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
+ "AssociatedWith": "urn:fsl-AZ1kWvHX",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/mask -mul -1 -add 1 -mul 9 -add maskunique maskunique",
"Used": [
- "urn:79a6464c-ebf6-464b-a23c-0825fe2219d4",
- "urn:f5e2dc55-f182-4797-a887-a3ef2bcdffbb"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:8fdab540-bd37-46a4-99a9-1dfbd560ff1f",
+ "@id": "urn:fslmaths-F4G8zuWD",
"Label": "fslmaths",
- "AssociatedWith": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
+ "AssociatedWith": "urn:fsl-AZ1kWvHX",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/mask -mul -1 -add 1 -mul 10 -add maskunique maskunique",
"Used": [
- "urn:4f73c006-9fd9-4d4f-aa02-9fa910e1b0c1",
- "urn:f5e2dc55-f182-4797-a887-a3ef2bcdffbb"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:8fd7a49f-cd5e-4f2d-be62-ddacac0dc6a8",
+ "@id": "urn:fslmaths-LXmFBqUt",
"Label": "fslmaths",
- "AssociatedWith": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
+ "AssociatedWith": "urn:fsl-AZ1kWvHX",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/mask -mul -1 -add 1 -mul 11 -add maskunique maskunique",
"Used": [
- "urn:a776bbd5-c892-4326-8d84-4c7f41f01d09",
- "urn:f5e2dc55-f182-4797-a887-a3ef2bcdffbb"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:75586543-bccc-41f5-aaf9-bf36873ef23b",
+ "@id": "urn:fslmaths-9a4825SK",
"Label": "fslmaths",
- "AssociatedWith": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
+ "AssociatedWith": "urn:fsl-AZ1kWvHX",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/mask -mul -1 -add 1 -mul 12 -add maskunique maskunique",
"Used": [
- "urn:4e9893aa-8897-4a5f-91bb-0b1547dfe62f",
- "urn:f5e2dc55-f182-4797-a887-a3ef2bcdffbb"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:724dea6a-6896-4486-b16c-a7e098c1866e",
+ "@id": "urn:fslmaths-lhUJMGSX",
"Label": "fslmaths",
- "AssociatedWith": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
+ "AssociatedWith": "urn:fsl-AZ1kWvHX",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/mask -mul -1 -add 1 -mul 13 -add maskunique maskunique",
"Used": [
- "urn:cd6ea8cc-feea-4766-bde3-eec92e872133",
- "urn:f5e2dc55-f182-4797-a887-a3ef2bcdffbb"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:f5874f15-2dae-4e97-a34f-7eda960d9655",
+ "@id": "urn:fslmaths-8d7sRdMJ",
"Label": "fslmaths",
- "AssociatedWith": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
+ "AssociatedWith": "urn:fsl-AZ1kWvHX",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/mask -mul -1 -add 1 -mul 14 -add maskunique maskunique",
"Used": [
- "urn:6a66a71e-7be2-4194-a6da-82730ee2ada8",
- "urn:f5e2dc55-f182-4797-a887-a3ef2bcdffbb"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:38049568-e433-4b10-990c-85b8dae900a9",
+ "@id": "urn:fslmaths-PbaO1I2Q",
"Label": "fslmaths",
- "AssociatedWith": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
+ "AssociatedWith": "urn:fsl-AZ1kWvHX",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths masksum -thr 13 -uthr 13 -bin -mul maskunique maskunique",
"Used": [
- "urn:26845403-e157-4c37-9a6e-c1eeaeae3b18",
- "urn:f5e2dc55-f182-4797-a887-a3ef2bcdffbb"
+ "bids::masksum",
+ "bids::maskunique"
]
},
{
- "@id": "urn:b0983ddd-77c6-48b2-96ad-529163046e5d",
+ "@id": "urn:overlay-54oJrhOb",
"Label": "overlay",
- "AssociatedWith": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
+ "AssociatedWith": "urn:fsl-AZ1kWvHX",
"Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 0 0 ../bg_image -a maskunique 0.9 14 maskunique_overlay",
"Used": []
},
{
- "@id": "urn:6af22b2c-914b-4caa-bead-4f1717d17c43",
+ "@id": "urn:slicer-NsXw0tcg",
"Label": "slicer",
- "AssociatedWith": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
+ "AssociatedWith": "urn:fsl-AZ1kWvHX",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer maskunique_overlay -S 2 750 maskunique_overlay.png",
"Used": [
- "urn:42d37dd6-d765-4c36-9825-248bdd6eb840"
+ "bids::maskunique_overlay"
]
},
{
- "@id": "urn:aa6d4ca9-bdd4-4043-bb1a-1c493d201709",
+ "@id": "urn:cp-ncFsCIyB",
"Label": "cp",
- "AssociatedWith": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
+ "AssociatedWith": "urn:fsl-AZ1kWvHX",
"Command": "/bin/cp /usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif .ramp.gif",
"Used": [
- "urn:55f46847-0304-40b3-aab6-776cde3785ce"
+ "bids::/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif"
]
},
{
- "@id": "urn:ca48fbe3-fd32-4b98-a794-b2d50cfc94ae",
+ "@id": "urn:fslmaths-gHoNgo4e",
"Label": "fslmaths",
- "AssociatedWith": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
+ "AssociatedWith": "urn:fsl-AZ1kWvHX",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -Tmin mask",
"Used": [
- "urn:d46d2a2a-9044-4bd6-8e4a-b3be2527ed78"
+ "bids::mask"
]
},
{
- "@id": "urn:aa77bc70-a849-4684-88f7-3f21d591ba84",
+ "@id": "urn:fslmerge-bsJhhObl",
"Label": "fslmerge",
- "AssociatedWith": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmerge -t mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/mean_func",
+ "AssociatedWith": "urn:fsl-AZ1kWvHX",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmerge -t mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/mean_func",
"Used": []
},
{
- "@id": "urn:63b76a0e-b4f2-4599-95b6-fb194a899ec3",
+ "@id": "urn:fslmaths-hDOBFMeB",
"Label": "fslmaths",
- "AssociatedWith": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
+ "AssociatedWith": "urn:fsl-AZ1kWvHX",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mean_func -Tmean mean_func",
"Used": [
- "urn:e5e87b5f-4e21-4b1b-86b8-747ce7b162c0"
+ "bids::mean_func"
]
},
{
- "@id": "urn:00dbf366-54b8-44e2-a25b-f34d7db1afbf",
+ "@id": "urn:fslmerge-MN6jqooj",
"Label": "fslmerge",
- "AssociatedWith": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmerge -t cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/stats/cope1",
+ "AssociatedWith": "urn:fsl-AZ1kWvHX",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmerge -t cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/stats/cope1",
"Used": []
},
{
- "@id": "urn:7ba4801a-9b3b-4646-8ce8-77214178f7c3",
+ "@id": "urn:fslmaths-htbOK1TX",
"Label": "fslmaths",
- "AssociatedWith": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
+ "AssociatedWith": "urn:fsl-AZ1kWvHX",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths cope1 -mas mask cope1",
"Used": [
- "urn:4734b4e5-933f-4fdc-9dc7-555961628229",
- "urn:d46d2a2a-9044-4bd6-8e4a-b3be2527ed78"
+ "bids::cope1",
+ "bids::mask"
]
},
{
- "@id": "urn:c9aa26ff-a1f8-4824-8a96-f91a726f789c",
+ "@id": "urn:printf-D4bWARwN",
"Label": "printf",
- "AssociatedWith": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
+ "AssociatedWith": "urn:fsl-AZ1kWvHX",
"Command": "printf '1.01544485714 ' >> design.lcon",
"Used": []
},
{
- "@id": "urn:663637f2-5620-4759-a680-1c5ddfc99c25",
+ "@id": "urn:fslmerge-gRKzzuEF",
"Label": "fslmerge",
- "AssociatedWith": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmerge -t varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/stats/varcope1",
+ "AssociatedWith": "urn:fsl-AZ1kWvHX",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmerge -t varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/stats/varcope1",
"Used": []
},
{
- "@id": "urn:b29799d5-56c0-4a40-9dc9-735513a0d696",
+ "@id": "urn:fslmaths-FBNBf98S",
"Label": "fslmaths",
- "AssociatedWith": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
+ "AssociatedWith": "urn:fsl-AZ1kWvHX",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths varcope1 -mas mask varcope1",
"Used": [
- "urn:5814af41-7a9c-4e1e-8470-11c709be9c25",
- "urn:d46d2a2a-9044-4bd6-8e4a-b3be2527ed78"
+ "bids::mask",
+ "bids::varcope1"
]
},
{
- "@id": "urn:537f0fb7-be91-447d-b3dd-c7e95ce9c200",
+ "@id": "urn:printf-Q7ZYIaMG",
"Label": "printf",
- "AssociatedWith": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
+ "AssociatedWith": "urn:fsl-AZ1kWvHX",
"Command": "printf '1 ' >> design.lcon",
"Used": []
}
],
"Entities": [
{
- "@id": "urn:b2625755-9228-4f29-9cdc-9e2e311271b4",
+ "@id": "bids::bg_image",
"Label": "bg_image",
"AtLocation": "bg_image",
"digest": {
@@ -442,25 +442,25 @@
}
},
{
- "@id": "urn:85d5d55e-0277-41ff-9bbb-1dd2833ef461",
+ "@id": "bids::bg_image",
"Label": "bg_image",
"AtLocation": "bg_image",
- "GeneratedBy": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
+ "GeneratedBy": "urn:fslmaths-xAVI0ILB",
"digest": {
"sha256": "ee2ea46067dbf68f9438c2eca02baa42dc59c8f171830150d0621ae3e061d7d0"
}
},
{
- "@id": "urn:3ba59dc8-2c31-4e27-bcf1-e0e497fdc1e1",
+ "@id": "bids::inputreg",
"Label": "inputreg",
"AtLocation": "inputreg",
- "GeneratedBy": "urn:b6285a9f-3c3b-4835-8421-b287dd391f8a",
+ "GeneratedBy": "urn:makedire-74G7oRAv",
"digest": {
"sha256": "d820f84544e66c638eb5c8e71e84a56b0a45e35a1b508ff270c8e01746985c3f"
}
},
{
- "@id": "urn:98687417-079d-459f-ab4a-89047b25a9ea",
+ "@id": "bids::mask",
"Label": "mask",
"AtLocation": "../mask",
"digest": {
@@ -468,52 +468,52 @@
}
},
{
- "@id": "urn:26845403-e157-4c37-9a6e-c1eeaeae3b18",
+ "@id": "bids::masksum",
"Label": "masksum",
"AtLocation": "masksum",
- "GeneratedBy": "urn:57e2f46d-dd77-4e80-91e3-0ca1293cc9eb",
+ "GeneratedBy": "urn:fslmaths-GzWzykG0",
"digest": {
"sha256": "11b44d8f49c65d763a7e80d2a07bc61d6269bc71dc9ea9f77bfe5f7795d4a58c"
}
},
{
- "@id": "urn:0a236937-57ed-4fa9-8a42-42c9f451dcab",
+ "@id": "bids::masksum",
"Label": "masksum",
"AtLocation": "masksum",
- "GeneratedBy": "urn:7d63f25f-d6b3-4cdc-8adb-96dd6839ae99",
+ "GeneratedBy": "urn:fslmaths-8xYEeypD",
"digest": {
"sha256": "11b44d8f49c65d763a7e80d2a07bc61d6269bc71dc9ea9f77bfe5f7795d4a58c"
}
},
{
- "@id": "urn:7fc2e81a-11c5-4b76-920d-9f1edce0cf30",
+ "@id": "bids::masksum_overlay",
"Label": "masksum_overlay",
"AtLocation": "masksum_overlay",
- "GeneratedBy": "urn:4c12c01c-24cf-4949-ba38-a94c7331e0ec",
+ "GeneratedBy": "urn:overlay-ncDkuQ1G",
"digest": {
"sha256": "9f347d6ec7a789bf400954fc9f6576becdbfaae343b6e778e729bb02400c3e18"
}
},
{
- "@id": "urn:d12ea473-b377-4973-9a8e-a4370097b02e",
+ "@id": "bids::masksum_overlay.png",
"Label": "masksum_overlay.png",
"AtLocation": "masksum_overlay.png",
- "GeneratedBy": "urn:a8fe7655-9fee-499e-892a-e6bdb67b388b",
+ "GeneratedBy": "urn:slicer-uWTpbMIs",
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@@ -854,10 +854,10 @@
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diff --git a/examples/from_parsers/fsl/fsl_group_btw_report_log.png b/examples/from_parsers/fsl/fsl_group_btw_report_log.png
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Binary files a/examples/from_parsers/fsl/fsl_group_btw_report_log.png and b/examples/from_parsers/fsl/fsl_group_btw_report_log.png differ
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index 39dfc4fbf..052373630 100644
--- a/examples/from_parsers/fsl/fsl_group_ols_report_log.jsonld
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"Used": []
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"Used": []
},
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"Used": []
},
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"Used": []
},
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"Used": []
},
{
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"Used": []
},
{
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"Used": []
},
{
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"Used": []
},
{
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"Used": []
},
{
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"Label": "featregapply",
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"Used": []
},
{
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"Used": []
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{
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"Used": []
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"Used": []
},
{
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"Used": []
},
{
- "@id": "urn:7a64a1ff-5591-417c-9726-2f0976688302",
+ "@id": "urn:fslmaths-VWKPlcrS",
"Label": "fslmaths",
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"Used": [
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+ "bids::bg_image"
]
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- "@id": "urn:d0d8a484-c593-4880-8c29-76a9fbc0145c",
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+ "AssociatedWith": "urn:fsl-pruTgA5U",
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"Used": []
},
{
- "@id": "urn:f2c5b2f0-2b16-4aed-b7b1-c4c79b48829c",
+ "@id": "urn:makedire-k9baSZKA",
"Label": "Make directory",
- "AssociatedWith": "urn:7184b261-fe51-4185-9016-c53543847ab3",
+ "AssociatedWith": "urn:fsl-pruTgA5U",
"Command": "mkdir -p inputreg",
"Used": []
},
{
- "@id": "urn:353d9903-e1d3-4b01-b439-a134967689da",
+ "@id": "urn:fslmaths-JgSWxigJ",
"Label": "fslmaths",
- "AssociatedWith": "urn:7184b261-fe51-4185-9016-c53543847ab3",
+ "AssociatedWith": "urn:fsl-pruTgA5U",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ../mask -mul 14 -Tmean masksum -odt short",
"Used": [
- "urn:85da9c16-cb15-4fa2-a44b-202952ce4f61"
+ "bids::mask"
]
},
{
- "@id": "urn:4e820c15-dc72-4417-9dad-09b740df92af",
+ "@id": "urn:fslmaths-7T5AFccE",
"Label": "fslmaths",
- "AssociatedWith": "urn:7184b261-fe51-4185-9016-c53543847ab3",
+ "AssociatedWith": "urn:fsl-pruTgA5U",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths masksum -thr 14 -add masksum masksum",
"Used": [
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+ "bids::masksum"
]
},
{
- "@id": "urn:554d2707-50ff-497f-8fcc-30ad2cd2c556",
+ "@id": "urn:overlay-tYpJlwJl",
"Label": "overlay",
- "AssociatedWith": "urn:7184b261-fe51-4185-9016-c53543847ab3",
+ "AssociatedWith": "urn:fsl-pruTgA5U",
"Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 0 0 -c ../bg_image -a masksum 0.9 28 masksum_overlay",
"Used": []
},
{
- "@id": "urn:27593d35-ad2c-40ff-ba78-f0f3e8dc375d",
+ "@id": "urn:slicer-tJz5uoAI",
"Label": "slicer",
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+ "AssociatedWith": "urn:fsl-pruTgA5U",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer masksum_overlay -S 2 750 masksum_overlay.png",
"Used": [
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+ "bids::masksum_overlay"
]
},
{
- "@id": "urn:e92556b3-2f40-47a8-8e64-c9c27593b5b2",
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"Label": "fslmaths",
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"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths masksum -mul 0 maskunique",
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+ "bids::masksum"
]
},
{
- "@id": "urn:26378a56-bbda-457f-b322-26a81a09886a",
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"Label": "fslmaths",
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"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/mask -mul -1 -add 1 -mul 1 -add maskunique maskunique",
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- "urn:ccb6b906-4afd-44bf-91d6-26a2970c514d"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:4b5dd777-e83d-487e-8c2e-a160089f4f05",
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"Label": "fslmaths",
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- "urn:3effd06a-cfb8-4908-a21c-776496f50fb1"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:39cc62c0-9656-46b8-b8b2-5f3566e0ee64",
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"Label": "fslmaths",
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"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/mask -mul -1 -add 1 -mul 3 -add maskunique maskunique",
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- "urn:431bd2f0-e1e0-4381-8f3b-6cc8cc8e6d72"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:8ba6d070-e993-435a-9616-3122bdecc838",
+ "@id": "urn:fslmaths-d498SwbU",
"Label": "fslmaths",
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+ "AssociatedWith": "urn:fsl-pruTgA5U",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/mask -mul -1 -add 1 -mul 4 -add maskunique maskunique",
"Used": [
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- "urn:aa0f5d9f-ef8f-40c7-ad6a-6674a7f9a4ff"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:06b6427c-ec76-4642-8bc1-2571247e248a",
+ "@id": "urn:fslmaths-4fXwGyda",
"Label": "fslmaths",
- "AssociatedWith": "urn:7184b261-fe51-4185-9016-c53543847ab3",
+ "AssociatedWith": "urn:fsl-pruTgA5U",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/mask -mul -1 -add 1 -mul 5 -add maskunique maskunique",
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- "urn:1a52d737-915e-4d9b-8a1d-38631ed6d379",
- "urn:3effd06a-cfb8-4908-a21c-776496f50fb1"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:6e5cc1ab-1c41-4b1a-9829-4deaca8b0167",
+ "@id": "urn:fslmaths-1UZofUSb",
"Label": "fslmaths",
- "AssociatedWith": "urn:7184b261-fe51-4185-9016-c53543847ab3",
+ "AssociatedWith": "urn:fsl-pruTgA5U",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/mask -mul -1 -add 1 -mul 6 -add maskunique maskunique",
"Used": [
- "urn:3effd06a-cfb8-4908-a21c-776496f50fb1",
- "urn:661acb24-0d0e-4204-ac2c-8c254641df82"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:3c47d177-cff0-479e-a57d-37eb9ab1a4c4",
+ "@id": "urn:fslmaths-BIKlZwNp",
"Label": "fslmaths",
- "AssociatedWith": "urn:7184b261-fe51-4185-9016-c53543847ab3",
+ "AssociatedWith": "urn:fsl-pruTgA5U",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/mask -mul -1 -add 1 -mul 7 -add maskunique maskunique",
"Used": [
- "urn:3effd06a-cfb8-4908-a21c-776496f50fb1",
- "urn:8676198f-410b-4255-8171-7673e732fe7f"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:ed3b68a3-f636-46e4-a09a-34a5efd2930e",
+ "@id": "urn:fslmaths-hiKmAIJI",
"Label": "fslmaths",
- "AssociatedWith": "urn:7184b261-fe51-4185-9016-c53543847ab3",
+ "AssociatedWith": "urn:fsl-pruTgA5U",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/mask -mul -1 -add 1 -mul 8 -add maskunique maskunique",
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- "urn:3effd06a-cfb8-4908-a21c-776496f50fb1",
- "urn:3f4a68bc-b2d6-4695-92e4-1eaf496365cf"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:bda90502-0355-42f7-b366-d17f5e34a690",
+ "@id": "urn:fslmaths-eywe19Yu",
"Label": "fslmaths",
- "AssociatedWith": "urn:7184b261-fe51-4185-9016-c53543847ab3",
+ "AssociatedWith": "urn:fsl-pruTgA5U",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/mask -mul -1 -add 1 -mul 9 -add maskunique maskunique",
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- "urn:3effd06a-cfb8-4908-a21c-776496f50fb1",
- "urn:5892f4d5-ff68-4975-b9c4-b358835454b7"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:09f8f839-8937-4170-8d1c-c5beab63d0b2",
+ "@id": "urn:fslmaths-OlQZMlYG",
"Label": "fslmaths",
- "AssociatedWith": "urn:7184b261-fe51-4185-9016-c53543847ab3",
+ "AssociatedWith": "urn:fsl-pruTgA5U",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/mask -mul -1 -add 1 -mul 10 -add maskunique maskunique",
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- "urn:ff4e038e-aca9-4dd5-8e66-e4b5cbb2e507"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:4d5b1a26-5ca1-4151-8aa9-8bb8be7e49aa",
+ "@id": "urn:fslmaths-YRZxT8UX",
"Label": "fslmaths",
- "AssociatedWith": "urn:7184b261-fe51-4185-9016-c53543847ab3",
+ "AssociatedWith": "urn:fsl-pruTgA5U",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/mask -mul -1 -add 1 -mul 11 -add maskunique maskunique",
"Used": [
- "urn:3effd06a-cfb8-4908-a21c-776496f50fb1",
- "urn:3f6ffef3-5208-4159-ae62-ec1f56f34b35"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:b2f73718-a51b-4452-9e31-8fc9b4017970",
+ "@id": "urn:fslmaths-7JPxpAVs",
"Label": "fslmaths",
- "AssociatedWith": "urn:7184b261-fe51-4185-9016-c53543847ab3",
+ "AssociatedWith": "urn:fsl-pruTgA5U",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/mask -mul -1 -add 1 -mul 12 -add maskunique maskunique",
"Used": [
- "urn:3effd06a-cfb8-4908-a21c-776496f50fb1",
- "urn:dbf4cddc-cc53-45dd-bdb8-ceefca12fb5d"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:816004d4-9b13-493f-998d-3f296343dadc",
+ "@id": "urn:fslmaths-w8m3u8MZ",
"Label": "fslmaths",
- "AssociatedWith": "urn:7184b261-fe51-4185-9016-c53543847ab3",
+ "AssociatedWith": "urn:fsl-pruTgA5U",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/mask -mul -1 -add 1 -mul 13 -add maskunique maskunique",
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- "urn:3effd06a-cfb8-4908-a21c-776496f50fb1"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:611642a2-088a-4b7e-b2e8-65eab6f3b9a3",
+ "@id": "urn:fslmaths-tMxDAUl5",
"Label": "fslmaths",
- "AssociatedWith": "urn:7184b261-fe51-4185-9016-c53543847ab3",
+ "AssociatedWith": "urn:fsl-pruTgA5U",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/mask -mul -1 -add 1 -mul 14 -add maskunique maskunique",
"Used": [
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- "urn:3effd06a-cfb8-4908-a21c-776496f50fb1"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:2e84766b-f6b6-4e5a-8853-b27071e11e03",
+ "@id": "urn:fslmaths-QmSHD91y",
"Label": "fslmaths",
- "AssociatedWith": "urn:7184b261-fe51-4185-9016-c53543847ab3",
+ "AssociatedWith": "urn:fsl-pruTgA5U",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths masksum -thr 13 -uthr 13 -bin -mul maskunique maskunique",
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- "urn:550f32b9-212a-4fd4-a609-6adc63225027"
+ "bids::masksum",
+ "bids::maskunique"
]
},
{
- "@id": "urn:23dee5cc-e5e2-4b05-bb2e-499cb3caf1c4",
+ "@id": "urn:overlay-4KfLztQ2",
"Label": "overlay",
- "AssociatedWith": "urn:7184b261-fe51-4185-9016-c53543847ab3",
+ "AssociatedWith": "urn:fsl-pruTgA5U",
"Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 0 0 ../bg_image -a maskunique 0.9 14 maskunique_overlay",
"Used": []
},
{
- "@id": "urn:560a7372-548e-42fa-921d-24259ff5eb0c",
+ "@id": "urn:slicer-kx0rowJX",
"Label": "slicer",
- "AssociatedWith": "urn:7184b261-fe51-4185-9016-c53543847ab3",
+ "AssociatedWith": "urn:fsl-pruTgA5U",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer maskunique_overlay -S 2 750 maskunique_overlay.png",
"Used": [
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+ "bids::maskunique_overlay"
]
},
{
- "@id": "urn:f94e103c-66d5-4680-b4e6-f5f7c734c9fd",
+ "@id": "urn:cp-YYsBl9eP",
"Label": "cp",
- "AssociatedWith": "urn:7184b261-fe51-4185-9016-c53543847ab3",
+ "AssociatedWith": "urn:fsl-pruTgA5U",
"Command": "/bin/cp /usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif .ramp.gif",
"Used": [
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+ "bids::/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif"
]
},
{
- "@id": "urn:4a5dea9f-6bdf-4711-9173-e4b12cde29a0",
+ "@id": "urn:fslmaths-3nby5gEF",
"Label": "fslmaths",
- "AssociatedWith": "urn:7184b261-fe51-4185-9016-c53543847ab3",
+ "AssociatedWith": "urn:fsl-pruTgA5U",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -Tmin mask",
"Used": [
- "urn:0eb0f6b1-0ccb-4560-ac74-fe45af46a58e"
+ "bids::mask"
]
},
{
- "@id": "urn:835bafaa-c616-48e8-b40d-7fb9d3c2d3a3",
+ "@id": "urn:fslmerge-w5YB5TQG",
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+ "AssociatedWith": "urn:fsl-pruTgA5U",
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"Used": []
},
{
- "@id": "urn:a18588f4-df77-4829-8460-3556c295d412",
+ "@id": "urn:fslmaths-OflGMfQe",
"Label": "fslmaths",
- "AssociatedWith": "urn:7184b261-fe51-4185-9016-c53543847ab3",
+ "AssociatedWith": "urn:fsl-pruTgA5U",
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"Used": [
- "urn:c75f3793-ca85-4574-8a96-672272ecca70"
+ "bids::mean_func"
]
},
{
- "@id": "urn:ebca06a5-6084-4d81-90c4-3a4f6991a90d",
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"Used": []
},
{
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"Label": "fslmaths",
- "AssociatedWith": "urn:7184b261-fe51-4185-9016-c53543847ab3",
+ "AssociatedWith": "urn:fsl-pruTgA5U",
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- "urn:a2836735-4d3b-45d7-8aa6-2414149e2686"
+ "bids::mask",
+ "bids::varcope1"
]
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{
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+ "@id": "urn:printf-eE9dcaBI",
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+ "AssociatedWith": "urn:fsl-pruTgA5U",
"Command": "printf '1 ' >> design.lcon",
"Used": []
}
],
"Entities": [
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@@ -442,25 +442,25 @@
}
},
{
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"Label": "bg_image",
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@@ -468,52 +468,52 @@
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@@ -521,16 +521,16 @@
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@@ -538,16 +538,16 @@
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{
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- "GeneratedBy": "urn:4b5dd777-e83d-487e-8c2e-a160089f4f05",
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@@ -555,16 +555,16 @@
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@@ -572,16 +572,16 @@
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{
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+ "GeneratedBy": "urn:fslmaths-d498SwbU",
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{
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@@ -589,16 +589,16 @@
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{
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{
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@@ -606,16 +606,16 @@
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@@ -623,16 +623,16 @@
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{
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@@ -725,16 +725,16 @@
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@@ -742,43 +742,43 @@
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@@ -786,16 +786,16 @@
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@@ -803,16 +803,16 @@
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@@ -820,16 +820,16 @@
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@@ -837,16 +837,16 @@
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@@ -854,10 +854,10 @@
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},
{
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diff --git a/examples/from_parsers/fsl/fsl_group_ols_report_log.png b/examples/from_parsers/fsl/fsl_group_ols_report_log.png
index e35643c2a..9925d3fe8 100644
Binary files a/examples/from_parsers/fsl/fsl_group_ols_report_log.png and b/examples/from_parsers/fsl/fsl_group_ols_report_log.png differ
diff --git a/examples/from_parsers/fsl/fsl_group_wls_report_log.jsonld b/examples/from_parsers/fsl/fsl_group_wls_report_log.jsonld
index 0e38ffa3c..eac776c10 100644
--- a/examples/from_parsers/fsl/fsl_group_wls_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_group_wls_report_log.jsonld
@@ -4,437 +4,437 @@
"Records": {
"Software": [
{
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- "RRID": "RRID:SCR_007037",
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"Label": "FSL",
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{
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},
{
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},
{
- "@id": "urn:084c8aad-390c-4fff-80c9-7ccc864e86c2",
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},
{
- "@id": "urn:0ebd0fc1-2b07-46fe-a567-1b4fd6b693e8",
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},
{
- "@id": "urn:b084ad3a-cf4b-47a4-83e6-06f3eae198c9",
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{
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},
{
- "@id": "urn:d1b9bc98-a253-4e9f-b88e-3c5199b9250d",
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},
{
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{
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{
- "@id": "urn:d29f9314-7a2c-4522-b097-5402aba8a5b4",
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{
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{
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{
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{
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+ "AssociatedWith": "urn:fsl-Qv0D3pNB",
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"Used": []
},
{
- "@id": "urn:9d1c9415-3cd9-4368-bd8f-7728c4442b1e",
+ "@id": "urn:fslmaths-EfydSzFo",
"Label": "fslmaths",
- "AssociatedWith": "urn:f921fdf0-acde-4ee9-bd00-c633b56c947a",
+ "AssociatedWith": "urn:fsl-Qv0D3pNB",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths bg_image -inm 1000 -Tmean bg_image -odt float",
"Used": [
- "urn:de17c456-a14f-44bc-9ce1-63dc7817d3c6"
+ "bids::bg_image"
]
},
{
- "@id": "urn:4d9e2482-55d7-4b91-bbc7-09a94bcb01e2",
+ "@id": "urn:fslmerge-h4I2cGx2",
"Label": "fslmerge",
- "AssociatedWith": "urn:f921fdf0-acde-4ee9-bd00-c633b56c947a",
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+ "AssociatedWith": "urn:fsl-Qv0D3pNB",
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"Used": []
},
{
- "@id": "urn:9476c583-64c7-4981-835b-573862b1757d",
+ "@id": "urn:makedire-VqwgIjpp",
"Label": "Make directory",
- "AssociatedWith": "urn:f921fdf0-acde-4ee9-bd00-c633b56c947a",
+ "AssociatedWith": "urn:fsl-Qv0D3pNB",
"Command": "mkdir -p inputreg",
"Used": []
},
{
- "@id": "urn:af40c8ba-fdd5-4c38-8e39-bbd8e2c54ca5",
+ "@id": "urn:fslmaths-o6nIOt9I",
"Label": "fslmaths",
- "AssociatedWith": "urn:f921fdf0-acde-4ee9-bd00-c633b56c947a",
+ "AssociatedWith": "urn:fsl-Qv0D3pNB",
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"Used": [
- "urn:ae890394-01bf-44f5-a3b2-d08ca303ddc6"
+ "bids::mask"
]
},
{
- "@id": "urn:3b428c80-be2a-4b11-8ee6-93612aaa80e6",
+ "@id": "urn:fslmaths-25TZgJ2Z",
"Label": "fslmaths",
- "AssociatedWith": "urn:f921fdf0-acde-4ee9-bd00-c633b56c947a",
+ "AssociatedWith": "urn:fsl-Qv0D3pNB",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths masksum -thr 14 -add masksum masksum",
"Used": [
- "urn:717c4883-95a6-438b-a1e4-8cb4424a168c"
+ "bids::masksum"
]
},
{
- "@id": "urn:0588524e-1b30-4bda-89ea-90359ecc11e4",
+ "@id": "urn:overlay-5da3Upvh",
"Label": "overlay",
- "AssociatedWith": "urn:f921fdf0-acde-4ee9-bd00-c633b56c947a",
+ "AssociatedWith": "urn:fsl-Qv0D3pNB",
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"Used": []
},
{
- "@id": "urn:d2fe0cae-b7d0-4df9-9cb1-c6858fbada4a",
+ "@id": "urn:slicer-KcGy37CS",
"Label": "slicer",
- "AssociatedWith": "urn:f921fdf0-acde-4ee9-bd00-c633b56c947a",
+ "AssociatedWith": "urn:fsl-Qv0D3pNB",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer masksum_overlay -S 2 750 masksum_overlay.png",
"Used": [
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+ "bids::masksum_overlay"
]
},
{
- "@id": "urn:374840d1-759f-4a7e-babe-e91ec845f206",
+ "@id": "urn:fslmaths-WYRQH8E1",
"Label": "fslmaths",
- "AssociatedWith": "urn:f921fdf0-acde-4ee9-bd00-c633b56c947a",
+ "AssociatedWith": "urn:fsl-Qv0D3pNB",
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"Used": [
- "urn:717c4883-95a6-438b-a1e4-8cb4424a168c"
+ "bids::masksum"
]
},
{
- "@id": "urn:7f284a13-dda9-4a1a-9fb1-c574b309533a",
+ "@id": "urn:fslmaths-PshObKmH",
"Label": "fslmaths",
- "AssociatedWith": "urn:f921fdf0-acde-4ee9-bd00-c633b56c947a",
+ "AssociatedWith": "urn:fsl-Qv0D3pNB",
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- "urn:d3666d78-32c0-424a-b170-f25ad8f10722"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:33c4a27f-28cd-4072-95b4-dc99b04d706c",
+ "@id": "urn:fslmaths-JtVZ3Vhe",
"Label": "fslmaths",
- "AssociatedWith": "urn:f921fdf0-acde-4ee9-bd00-c633b56c947a",
+ "AssociatedWith": "urn:fsl-Qv0D3pNB",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/mask -mul -1 -add 1 -mul 2 -add maskunique maskunique",
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- "urn:8a7d6591-f208-4564-b14f-dbda25796f47"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:e3b85ea8-9b53-480c-9b9b-5a44880d791e",
+ "@id": "urn:fslmaths-P5Zg83HH",
"Label": "fslmaths",
- "AssociatedWith": "urn:f921fdf0-acde-4ee9-bd00-c633b56c947a",
+ "AssociatedWith": "urn:fsl-Qv0D3pNB",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/mask -mul -1 -add 1 -mul 3 -add maskunique maskunique",
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- "urn:f880fb5b-b64a-469c-8f5e-b7f51e0f3448"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:1a77145c-9382-44e6-a248-643dc21229ae",
+ "@id": "urn:fslmaths-6PpzikfW",
"Label": "fslmaths",
- "AssociatedWith": "urn:f921fdf0-acde-4ee9-bd00-c633b56c947a",
+ "AssociatedWith": "urn:fsl-Qv0D3pNB",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/mask -mul -1 -add 1 -mul 4 -add maskunique maskunique",
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- "urn:8a7d6591-f208-4564-b14f-dbda25796f47"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:b1c9bd79-dd7f-49ee-ba68-d2adaec2898a",
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"Label": "fslmaths",
- "AssociatedWith": "urn:f921fdf0-acde-4ee9-bd00-c633b56c947a",
+ "AssociatedWith": "urn:fsl-Qv0D3pNB",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/mask -mul -1 -add 1 -mul 5 -add maskunique maskunique",
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- "urn:8a7d6591-f208-4564-b14f-dbda25796f47"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:0e211d48-5750-41bf-a72f-ad50eee970a7",
+ "@id": "urn:fslmaths-Rd0FlVhM",
"Label": "fslmaths",
- "AssociatedWith": "urn:f921fdf0-acde-4ee9-bd00-c633b56c947a",
+ "AssociatedWith": "urn:fsl-Qv0D3pNB",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/mask -mul -1 -add 1 -mul 6 -add maskunique maskunique",
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- "urn:8a7d6591-f208-4564-b14f-dbda25796f47"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:b11b4f41-0f70-4201-a5f1-0660cffdd667",
+ "@id": "urn:fslmaths-3QP8o8aF",
"Label": "fslmaths",
- "AssociatedWith": "urn:f921fdf0-acde-4ee9-bd00-c633b56c947a",
+ "AssociatedWith": "urn:fsl-Qv0D3pNB",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/mask -mul -1 -add 1 -mul 7 -add maskunique maskunique",
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- "urn:dd8e493d-1bd7-4016-a9e2-7ed48c6e8e2e"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:905a59ca-ff49-4ab5-bb91-c5d11710b0e3",
+ "@id": "urn:fslmaths-7UM4M7c6",
"Label": "fslmaths",
- "AssociatedWith": "urn:f921fdf0-acde-4ee9-bd00-c633b56c947a",
+ "AssociatedWith": "urn:fsl-Qv0D3pNB",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/mask -mul -1 -add 1 -mul 8 -add maskunique maskunique",
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- "urn:bdd1342c-4003-4852-a6a3-58c36d7d0b03"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:3938fd72-243c-41ae-bf51-1884da78d24f",
+ "@id": "urn:fslmaths-eDg3oFMF",
"Label": "fslmaths",
- "AssociatedWith": "urn:f921fdf0-acde-4ee9-bd00-c633b56c947a",
+ "AssociatedWith": "urn:fsl-Qv0D3pNB",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/mask -mul -1 -add 1 -mul 9 -add maskunique maskunique",
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- "urn:e5e12d31-550d-40e0-9a89-2ddf0ad30061"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:909264d7-89ba-4bec-af7c-d7b041f7d48a",
+ "@id": "urn:fslmaths-YvJZwpMz",
"Label": "fslmaths",
- "AssociatedWith": "urn:f921fdf0-acde-4ee9-bd00-c633b56c947a",
+ "AssociatedWith": "urn:fsl-Qv0D3pNB",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/mask -mul -1 -add 1 -mul 10 -add maskunique maskunique",
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- "urn:8a7d6591-f208-4564-b14f-dbda25796f47"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:fd8a936e-12e6-4ebe-977d-d5b97619dbed",
+ "@id": "urn:fslmaths-JTvgDKAY",
"Label": "fslmaths",
- "AssociatedWith": "urn:f921fdf0-acde-4ee9-bd00-c633b56c947a",
+ "AssociatedWith": "urn:fsl-Qv0D3pNB",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/mask -mul -1 -add 1 -mul 11 -add maskunique maskunique",
"Used": [
- "urn:8a7d6591-f208-4564-b14f-dbda25796f47",
- "urn:bb16365e-1838-49ff-ad23-11b940e8bb26"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:0e2cb7ba-383b-47de-a90f-98f7dd0e981d",
+ "@id": "urn:fslmaths-5B96iEFY",
"Label": "fslmaths",
- "AssociatedWith": "urn:f921fdf0-acde-4ee9-bd00-c633b56c947a",
+ "AssociatedWith": "urn:fsl-Qv0D3pNB",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/mask -mul -1 -add 1 -mul 12 -add maskunique maskunique",
"Used": [
- "urn:8a7d6591-f208-4564-b14f-dbda25796f47",
- "urn:ca299055-a662-4998-b793-5b0a8ffc6237"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:228f2206-5248-49de-9298-3e4562c227d9",
+ "@id": "urn:fslmaths-NfGTyrav",
"Label": "fslmaths",
- "AssociatedWith": "urn:f921fdf0-acde-4ee9-bd00-c633b56c947a",
+ "AssociatedWith": "urn:fsl-Qv0D3pNB",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/mask -mul -1 -add 1 -mul 13 -add maskunique maskunique",
"Used": [
- "urn:7805b51e-d4d1-4701-9394-a93419312766",
- "urn:8a7d6591-f208-4564-b14f-dbda25796f47"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:61c4bfe5-74e0-4a0b-9e2f-35b78911266c",
+ "@id": "urn:fslmaths-RnWwY7GC",
"Label": "fslmaths",
- "AssociatedWith": "urn:f921fdf0-acde-4ee9-bd00-c633b56c947a",
+ "AssociatedWith": "urn:fsl-Qv0D3pNB",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/mask -mul -1 -add 1 -mul 14 -add maskunique maskunique",
"Used": [
- "urn:752887fb-b81a-479d-ac56-e02666c9fc14",
- "urn:8a7d6591-f208-4564-b14f-dbda25796f47"
+ "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/mask",
+ "bids::maskunique"
]
},
{
- "@id": "urn:95324e29-58ad-4796-a13f-2e51595196ce",
+ "@id": "urn:fslmaths-o40Hcz8k",
"Label": "fslmaths",
- "AssociatedWith": "urn:f921fdf0-acde-4ee9-bd00-c633b56c947a",
+ "AssociatedWith": "urn:fsl-Qv0D3pNB",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths masksum -thr 13 -uthr 13 -bin -mul maskunique maskunique",
"Used": [
- "urn:717c4883-95a6-438b-a1e4-8cb4424a168c",
- "urn:8a7d6591-f208-4564-b14f-dbda25796f47"
+ "bids::masksum",
+ "bids::maskunique"
]
},
{
- "@id": "urn:0c7a2191-32e9-426b-8217-610f6a30b173",
+ "@id": "urn:overlay-f62oQ1Jq",
"Label": "overlay",
- "AssociatedWith": "urn:f921fdf0-acde-4ee9-bd00-c633b56c947a",
+ "AssociatedWith": "urn:fsl-Qv0D3pNB",
"Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 0 0 ../bg_image -a maskunique 0.9 14 maskunique_overlay",
"Used": []
},
{
- "@id": "urn:882d78ff-a57f-4922-b1b6-f92337927d99",
+ "@id": "urn:slicer-E5l7qDA8",
"Label": "slicer",
- "AssociatedWith": "urn:f921fdf0-acde-4ee9-bd00-c633b56c947a",
+ "AssociatedWith": "urn:fsl-Qv0D3pNB",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer maskunique_overlay -S 2 750 maskunique_overlay.png",
"Used": [
- "urn:a10c794e-57a7-4a6f-8458-b2314ac9eeb7"
+ "bids::maskunique_overlay"
]
},
{
- "@id": "urn:0093b16e-1b64-4198-89fe-50166b80ab3c",
+ "@id": "urn:cp-tcMlGCoq",
"Label": "cp",
- "AssociatedWith": "urn:f921fdf0-acde-4ee9-bd00-c633b56c947a",
+ "AssociatedWith": "urn:fsl-Qv0D3pNB",
"Command": "/bin/cp /usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif .ramp.gif",
"Used": [
- "urn:53169fdb-f990-4ee6-a17d-f6a53e7f67d9"
+ "bids::/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif"
]
},
{
- "@id": "urn:7a87bf8b-70b8-48ec-8085-804c62300433",
+ "@id": "urn:fslmaths-x0pisi83",
"Label": "fslmaths",
- "AssociatedWith": "urn:f921fdf0-acde-4ee9-bd00-c633b56c947a",
+ "AssociatedWith": "urn:fsl-Qv0D3pNB",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -Tmin mask",
"Used": [
- "urn:baa47e1c-4dc8-4f43-a3e0-8197e323d309"
+ "bids::mask"
]
},
{
- "@id": "urn:ec5c8b09-20b5-49bc-bedf-50e101ed332f",
+ "@id": "urn:fslmerge-HWC7MrJw",
"Label": "fslmerge",
- "AssociatedWith": "urn:f921fdf0-acde-4ee9-bd00-c633b56c947a",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmerge -t mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/mean_func",
+ "AssociatedWith": "urn:fsl-Qv0D3pNB",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmerge -t mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/mean_func",
"Used": []
},
{
- "@id": "urn:a0ec00b1-b359-4e9e-b8db-0bdafe8871ab",
+ "@id": "urn:fslmaths-HK0LP66D",
"Label": "fslmaths",
- "AssociatedWith": "urn:f921fdf0-acde-4ee9-bd00-c633b56c947a",
+ "AssociatedWith": "urn:fsl-Qv0D3pNB",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mean_func -Tmean mean_func",
"Used": [
- "urn:fb88b08f-d332-441d-a8a3-021f387930fb"
+ "bids::mean_func"
]
},
{
- "@id": "urn:2ad87dc8-4891-40b4-819e-83798d26f542",
+ "@id": "urn:fslmerge-nVaqQIOY",
"Label": "fslmerge",
- "AssociatedWith": "urn:f921fdf0-acde-4ee9-bd00-c633b56c947a",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmerge -t cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/stats/cope1",
+ "AssociatedWith": "urn:fsl-Qv0D3pNB",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmerge -t cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/stats/cope1",
"Used": []
},
{
- "@id": "urn:96172092-ec47-43ee-ac02-50f2e3d7a303",
+ "@id": "urn:fslmaths-IXvSjYAX",
"Label": "fslmaths",
- "AssociatedWith": "urn:f921fdf0-acde-4ee9-bd00-c633b56c947a",
+ "AssociatedWith": "urn:fsl-Qv0D3pNB",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths cope1 -mas mask cope1",
"Used": [
- "urn:2662f46d-c87c-436f-8db5-59f78d0cf41c",
- "urn:baa47e1c-4dc8-4f43-a3e0-8197e323d309"
+ "bids::cope1",
+ "bids::mask"
]
},
{
- "@id": "urn:dd08793b-9254-4f33-ade0-5f07b6d3b0d0",
+ "@id": "urn:printf-lMEA45Fd",
"Label": "printf",
- "AssociatedWith": "urn:f921fdf0-acde-4ee9-bd00-c633b56c947a",
+ "AssociatedWith": "urn:fsl-Qv0D3pNB",
"Command": "printf '1.01544485714 ' >> design.lcon",
"Used": []
},
{
- "@id": "urn:5d86a607-3005-48b0-bdf1-f80f1ffd0e59",
+ "@id": "urn:fslmerge-LaUwdWrw",
"Label": "fslmerge",
- "AssociatedWith": "urn:f921fdf0-acde-4ee9-bd00-c633b56c947a",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmerge -t varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/stats/varcope1",
+ "AssociatedWith": "urn:fsl-Qv0D3pNB",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmerge -t varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/stats/varcope1",
"Used": []
},
{
- "@id": "urn:6ad2c26d-6aab-4e86-bdf9-c83ad1cfe41b",
+ "@id": "urn:fslmaths-OPfMFJsc",
"Label": "fslmaths",
- "AssociatedWith": "urn:f921fdf0-acde-4ee9-bd00-c633b56c947a",
+ "AssociatedWith": "urn:fsl-Qv0D3pNB",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths varcope1 -mas mask varcope1",
"Used": [
- "urn:0338e284-7f9c-4721-a7e4-40da815e05e6",
- "urn:baa47e1c-4dc8-4f43-a3e0-8197e323d309"
+ "bids::mask",
+ "bids::varcope1"
]
},
{
- "@id": "urn:c5c6f22b-12bf-4fd2-b2e7-7e61038eb5c2",
+ "@id": "urn:printf-eQIlmExq",
"Label": "printf",
- "AssociatedWith": "urn:f921fdf0-acde-4ee9-bd00-c633b56c947a",
+ "AssociatedWith": "urn:fsl-Qv0D3pNB",
"Command": "printf '1 ' >> design.lcon",
"Used": []
}
],
"Entities": [
{
- "@id": "urn:de17c456-a14f-44bc-9ce1-63dc7817d3c6",
+ "@id": "bids::bg_image",
"Label": "bg_image",
"AtLocation": "bg_image",
"digest": {
@@ -442,25 +442,25 @@
}
},
{
- "@id": "urn:aa6e479e-739d-4039-8bea-d0c16c229162",
+ "@id": "bids::bg_image",
"Label": "bg_image",
"AtLocation": "bg_image",
- "GeneratedBy": "urn:9d1c9415-3cd9-4368-bd8f-7728c4442b1e",
+ "GeneratedBy": "urn:fslmaths-EfydSzFo",
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}
},
{
- "@id": "urn:b286b508-ccb9-409b-aa7d-5629f06e613e",
+ "@id": "bids::inputreg",
"Label": "inputreg",
"AtLocation": "inputreg",
- "GeneratedBy": "urn:9476c583-64c7-4981-835b-573862b1757d",
+ "GeneratedBy": "urn:makedire-VqwgIjpp",
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{
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+ "@id": "bids::mask",
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"AtLocation": "../mask",
"digest": {
@@ -468,52 +468,52 @@
}
},
{
- "@id": "urn:717c4883-95a6-438b-a1e4-8cb4424a168c",
+ "@id": "bids::masksum",
"Label": "masksum",
"AtLocation": "masksum",
- "GeneratedBy": "urn:af40c8ba-fdd5-4c38-8e39-bbd8e2c54ca5",
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},
{
- "@id": "urn:3eaf774f-7bfb-4a3b-b595-04c5e178c302",
+ "@id": "bids::masksum",
"Label": "masksum",
"AtLocation": "masksum",
- "GeneratedBy": "urn:3b428c80-be2a-4b11-8ee6-93612aaa80e6",
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{
- "@id": "urn:17b70280-d407-407f-820c-85dbabbdcd62",
+ "@id": "bids::masksum_overlay",
"Label": "masksum_overlay",
"AtLocation": "masksum_overlay",
- "GeneratedBy": "urn:0588524e-1b30-4bda-89ea-90359ecc11e4",
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{
- "@id": "urn:1170b37b-767e-4327-8f76-f61b204c411c",
+ "@id": "bids::masksum_overlay.png",
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"AtLocation": "masksum_overlay.png",
- "GeneratedBy": "urn:d2fe0cae-b7d0-4df9-9cb1-c6858fbada4a",
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{
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+ "@id": "bids::maskunique",
"Label": "maskunique",
"AtLocation": "maskunique",
- "GeneratedBy": "urn:374840d1-759f-4a7e-babe-e91ec845f206",
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{
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"digest": {
@@ -521,16 +521,16 @@
}
},
{
- "@id": "urn:2fcd8594-4286-4cdf-9100-4477f5bdce8f",
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"AtLocation": "maskunique",
- "GeneratedBy": "urn:7f284a13-dda9-4a1a-9fb1-c574b309533a",
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{
- "@id": "urn:33567cc3-fd0f-48c3-80b5-1b24fa27e605",
+ "@id": "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/mask",
"Label": "mask",
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"digest": {
@@ -538,16 +538,16 @@
}
},
{
- "@id": "urn:1963527f-b047-4c93-9fc0-eb5652e982e6",
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"AtLocation": "maskunique",
- "GeneratedBy": "urn:33c4a27f-28cd-4072-95b4-dc99b04d706c",
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- "@id": "urn:f880fb5b-b64a-469c-8f5e-b7f51e0f3448",
+ "@id": "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/mask",
"Label": "mask",
"AtLocation": "/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/mask",
"digest": {
@@ -555,16 +555,16 @@
}
},
{
- "@id": "urn:0fb09e84-8624-4873-8ca2-48abc714cb32",
+ "@id": "bids::maskunique",
"Label": "maskunique",
"AtLocation": "maskunique",
- "GeneratedBy": "urn:e3b85ea8-9b53-480c-9b9b-5a44880d791e",
+ "GeneratedBy": "urn:fslmaths-P5Zg83HH",
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{
- "@id": "urn:7b12e10c-168c-431b-8858-04df3b97fead",
+ "@id": "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/mask",
"Label": "mask",
"AtLocation": "/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/mask",
"digest": {
@@ -572,16 +572,16 @@
}
},
{
- "@id": "urn:6e7ad16e-eb28-4d13-8225-23c0fcee917f",
+ "@id": "bids::maskunique",
"Label": "maskunique",
"AtLocation": "maskunique",
- "GeneratedBy": "urn:1a77145c-9382-44e6-a248-643dc21229ae",
+ "GeneratedBy": "urn:fslmaths-6PpzikfW",
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"sha256": "b42669f6ae81e72b18aa1d23957a1f32022844786d867c099c24f0796227762a"
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{
- "@id": "urn:088af78f-6282-40f8-a566-d2d4391419f2",
+ "@id": "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/mask",
"Label": "mask",
"AtLocation": "/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/mask",
"digest": {
@@ -589,16 +589,16 @@
}
},
{
- "@id": "urn:519f480a-ebb7-4fdc-a9fc-54ebeeccfaf5",
+ "@id": "bids::maskunique",
"Label": "maskunique",
"AtLocation": "maskunique",
- "GeneratedBy": "urn:b1c9bd79-dd7f-49ee-ba68-d2adaec2898a",
+ "GeneratedBy": "urn:fslmaths-EbbCciPS",
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{
- "@id": "urn:07fd3a1c-9973-414b-bc6a-d952590585a5",
+ "@id": "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/mask",
"Label": "mask",
"AtLocation": "/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/mask",
"digest": {
@@ -606,16 +606,16 @@
}
},
{
- "@id": "urn:dbddee17-2238-4285-8fc0-8ff8e9841d64",
+ "@id": "bids::maskunique",
"Label": "maskunique",
"AtLocation": "maskunique",
- "GeneratedBy": "urn:0e211d48-5750-41bf-a72f-ad50eee970a7",
+ "GeneratedBy": "urn:fslmaths-Rd0FlVhM",
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{
- "@id": "urn:dd8e493d-1bd7-4016-a9e2-7ed48c6e8e2e",
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"Label": "mask",
"AtLocation": "/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/mask",
"digest": {
@@ -623,16 +623,16 @@
}
},
{
- "@id": "urn:bd73c660-aba1-4f2c-9734-58d416895f83",
+ "@id": "bids::maskunique",
"Label": "maskunique",
"AtLocation": "maskunique",
- "GeneratedBy": "urn:b11b4f41-0f70-4201-a5f1-0660cffdd667",
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{
- "@id": "urn:bdd1342c-4003-4852-a6a3-58c36d7d0b03",
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"Label": "mask",
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"digest": {
@@ -640,16 +640,16 @@
}
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{
- "@id": "urn:11d35b30-b777-40c4-80a3-2772b17cc600",
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"Label": "maskunique",
"AtLocation": "maskunique",
- "GeneratedBy": "urn:905a59ca-ff49-4ab5-bb91-c5d11710b0e3",
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{
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@@ -657,16 +657,16 @@
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@@ -674,16 +674,16 @@
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{
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"Label": "maskunique",
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{
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+ "@id": "bids::/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/mask",
"Label": "mask",
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"digest": {
@@ -691,16 +691,16 @@
}
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{
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- "GeneratedBy": "urn:fd8a936e-12e6-4ebe-977d-d5b97619dbed",
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{
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"digest": {
@@ -708,16 +708,16 @@
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{
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- "GeneratedBy": "urn:0e2cb7ba-383b-47de-a90f-98f7dd0e981d",
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{
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@@ -725,16 +725,16 @@
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@@ -742,43 +742,43 @@
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@@ -786,16 +786,16 @@
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{
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- "GeneratedBy": "urn:0093b16e-1b64-4198-89fe-50166b80ab3c",
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@@ -803,16 +803,16 @@
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{
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@@ -820,16 +820,16 @@
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{
- "@id": "urn:9c29ef12-a4eb-487a-b06c-8e85de3822a7",
+ "@id": "bids::mean_func",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:a0ec00b1-b359-4e9e-b8db-0bdafe8871ab",
+ "GeneratedBy": "urn:fslmaths-HK0LP66D",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:2662f46d-c87c-436f-8db5-59f78d0cf41c",
+ "@id": "bids::cope1",
"Label": "cope1",
"AtLocation": "cope1",
"digest": {
@@ -837,16 +837,16 @@
}
},
{
- "@id": "urn:a7033b8a-6e10-4b48-a89c-7502b5a51730",
+ "@id": "bids::cope1",
"Label": "cope1",
"AtLocation": "cope1",
- "GeneratedBy": "urn:96172092-ec47-43ee-ac02-50f2e3d7a303",
+ "GeneratedBy": "urn:fslmaths-IXvSjYAX",
"digest": {
"sha256": "5e9fbbe343c55dc4117cd7d8ea564719e6607f0bf66cf8833cb082a4aa9cf824"
}
},
{
- "@id": "urn:0338e284-7f9c-4721-a7e4-40da815e05e6",
+ "@id": "bids::varcope1",
"Label": "varcope1",
"AtLocation": "varcope1",
"digest": {
@@ -854,10 +854,10 @@
}
},
{
- "@id": "urn:93f188fc-1f90-49f6-b2a8-79198007a610",
+ "@id": "bids::varcope1",
"Label": "varcope1",
"AtLocation": "varcope1",
- "GeneratedBy": "urn:6ad2c26d-6aab-4e86-bdf9-c83ad1cfe41b",
+ "GeneratedBy": "urn:fslmaths-OPfMFJsc",
"digest": {
"sha256": "06459b075612b55044b7e494206fcec5dbe73b1f5f8a13439d720705495ae2ee"
}
diff --git a/examples/from_parsers/fsl/fsl_group_wls_report_log.png b/examples/from_parsers/fsl/fsl_group_wls_report_log.png
index 48d064f0e..906d630b2 100644
Binary files a/examples/from_parsers/fsl/fsl_group_wls_report_log.png and b/examples/from_parsers/fsl/fsl_group_wls_report_log.png differ
diff --git a/examples/from_parsers/fsl/fsl_hrf_fir_report_log.html b/examples/from_parsers/fsl/fsl_hrf_fir_report_log.html
index 94be2093d..cdf382b19 100644
--- a/examples/from_parsers/fsl/fsl_hrf_fir_report_log.html
+++ b/examples/from_parsers/fsl/fsl_hrf_fir_report_log.html
@@ -35,20 +35,20 @@ Progress Report / Log
326941
Initialisation
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
Total original volumes = 104
/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1
Preprocessing:Stage 1
-/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90
+/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/example_func.nii.gz -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90
Option -F ( FEAT version parameter ) selected with argument "6.00"
Option -d ( output directory ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat"
Option -l ( logfile )input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/logs/feat2_pre"
Option -R ( html unwarping report ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/report_unwarp.html"
Option -r ( html registration report ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/report_reg.html"
Option -i ( main input ) input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/example_func.nii.gz"
-Option -h ( high-res structural image ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
+Option -h ( high-res structural image ) selected with argument "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
Option -w ( highres dof ) selected with argument "BBR"
Option -x ( highres search ) selected with argument "90"
Option -s ( standard image ) selected with argument "/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain"
@@ -59,10 +59,10 @@ Progress Report / Log
/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/reg
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head
did not find file: example_func2highres.mat. Generating transform.
@@ -128,9 +128,9 @@ Progress Report / Log
/bin/rm -rf prefiltered_func_data*
Stats
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
/usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con --fcon=design.fts
Log directory is: stats
diff --git a/examples/from_parsers/fsl/fsl_hrf_fir_report_log.jsonld b/examples/from_parsers/fsl/fsl_hrf_fir_report_log.jsonld
index c197c1223..a724a8353 100644
--- a/examples/from_parsers/fsl/fsl_hrf_fir_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_hrf_fir_report_log.jsonld
@@ -4,778 +4,788 @@
"Records": {
"Software": [
{
- "@id": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:fsl-ZtRHP0hk",
"@type": "prov:SoftwareAgent",
"Label": "FSL",
- "Version": "xxx"
+ "Version": "xxx",
+ "AltIdentifier": "RRID:SCR_002823"
}
],
"Activities": [
{
- "@id": "urn:ef63cb18-25fb-485f-b5c1-5c528cb4080c",
+ "@id": "urn:fslmaths-nq5UWEBB",
"Label": "fslmaths",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
"Used": [
- "urn:caf2279a-3820-496f-be73-ce7f46be7671"
+ "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold"
]
},
{
- "@id": "urn:cfec80c8-b4bb-46d9-a53b-5f045b4743fc",
+ "@id": "urn:fslroi-N7dzlV3p",
"Label": "fslroi",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1",
"Used": [
- "urn:766de64a-5420-4b86-ad90-769f84993459"
+ "bids::prefiltered_func_data"
]
},
{
- "@id": "urn:87cf0f33-5bbd-4175-a409-80425fd78b0c",
+ "@id": "urn:mainfeat-aWd37ogx",
"Label": "mainfeatreg",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/example_func.nii.gz -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
"Used": [
- "urn:3984dd19-ea61-4d2a-b91c-d3d36c5263dc",
- "urn:71227f72-e774-4e17-ae09-07980d0ce996",
- "urn:a34697f5-7ad9-481b-bbfe-69d17ec623ff"
+ "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/example_func.nii.gz",
+ "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain",
+ "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
]
},
{
- "@id": "urn:ed266509-aff9-46ad-a6e7-91929a3fc494",
+ "@id": "urn:makedire-o9d1hW2G",
"Label": "Make directory",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/reg",
"Used": []
},
{
- "@id": "urn:cbfd75e0-0ece-4d05-8015-6b354b9673b4",
+ "@id": "urn:fslmaths-pWofaAJa",
"Label": "fslmaths",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
"Used": [
- "urn:71227f72-e774-4e17-ae09-07980d0ce996"
+ "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
]
},
{
- "@id": "urn:b97bbfdb-d42f-48d7-8905-cfb9c31056c7",
+ "@id": "urn:fslmaths-STPjLbgH",
"Label": "fslmaths",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
"Used": [
- "urn:ca8682cd-a436-44c3-9c3f-dce9182257e8"
+ "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w"
]
},
{
- "@id": "urn:d092b5ef-a0a8-4d97-b324-496566b1aec2",
+ "@id": "urn:epireg-vYrJyf18",
"Label": "epi_reg",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres",
- "Used": []
+ "Used": [
+ "bids::example_func",
+ "bids::highres",
+ "bids::highres_head"
+ ]
},
{
- "@id": "urn:93ba5941-eb9b-4d62-8502-5f902957b70d",
+ "@id": "urn:convertx-Ol04i8gE",
"Label": "convert_xfm",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat",
"Used": [
- "urn:c8dc470f-18f9-448e-a409-340bd4578f04"
+ "bids::example_func2highres.mat"
]
},
{
- "@id": "urn:19661992-cf39-4c57-8889-9f750299ca19",
+ "@id": "urn:slicer-9sLi9qYh",
"Label": "slicer",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:8fc9963c-f12b-442b-a8fa-3fc8d36e22a1",
- "urn:9b25a4c9-acc3-486d-b147-bfc7fcb1c086"
+ "bids::example_func2highres",
+ "bids::highres"
]
},
{
- "@id": "urn:ef52ae7f-9d76-4245-bd24-56a59d5a6dc3",
+ "@id": "urn:pngappen-y4HSKVDo",
"Label": "pngappend",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres1.png",
"Used": [
- "urn:2b668af4-fe26-4fa7-b147-7a6123214e69",
- "urn:4b37db3b-55f0-48c6-8364-f27cf3a480ee",
- "urn:5b455206-6b26-48a8-87d5-36e77858fb21",
- "urn:7c351dec-b47c-4488-a1be-ca1a55fdeb1e",
- "urn:7f7c9933-2af8-4d36-bd84-1774cfe99bb6",
- "urn:8774d01a-a6dd-4c0b-8182-170c0948c565",
- "urn:88ec6d95-8360-4138-8165-6d28f9b84980",
- "urn:8a37f1a8-c429-41b8-ad49-d67c9cc94329",
- "urn:8f3a6781-ee2f-445d-99bd-29309e221c13",
- "urn:a501b619-9b7f-4a9e-b7dd-99a28cff7cd5",
- "urn:a981bb84-c8a5-40af-b3fd-2879d40050d3",
- "urn:e14e4ef7-15c9-407d-88f4-a7b841746cb0"
+ "bids::sla.png",
+ "bids::slb.png",
+ "bids::slc.png",
+ "bids::sld.png",
+ "bids::sle.png",
+ "bids::slf.png",
+ "bids::slg.png",
+ "bids::slh.png",
+ "bids::sli.png",
+ "bids::slj.png",
+ "bids::slk.png",
+ "bids::sll.png"
]
},
{
- "@id": "urn:83be6f1d-ca5b-46a5-910c-502c7c9c7f4b",
+ "@id": "urn:slicer-nCd4Ud2V",
"Label": "slicer",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:8fc9963c-f12b-442b-a8fa-3fc8d36e22a1",
- "urn:9b25a4c9-acc3-486d-b147-bfc7fcb1c086"
+ "bids::example_func2highres",
+ "bids::highres"
]
},
{
- "@id": "urn:e7951802-97c3-4674-9d26-69aa78d96a32",
+ "@id": "urn:pngappen-laujh6mc",
"Label": "pngappend",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres2.png",
"Used": [
- "urn:2b668af4-fe26-4fa7-b147-7a6123214e69",
- "urn:4b37db3b-55f0-48c6-8364-f27cf3a480ee",
- "urn:5b455206-6b26-48a8-87d5-36e77858fb21",
- "urn:7c351dec-b47c-4488-a1be-ca1a55fdeb1e",
- "urn:7f7c9933-2af8-4d36-bd84-1774cfe99bb6",
- "urn:8774d01a-a6dd-4c0b-8182-170c0948c565",
- "urn:88ec6d95-8360-4138-8165-6d28f9b84980",
- "urn:8a37f1a8-c429-41b8-ad49-d67c9cc94329",
- "urn:8f3a6781-ee2f-445d-99bd-29309e221c13",
- "urn:a501b619-9b7f-4a9e-b7dd-99a28cff7cd5",
- "urn:a981bb84-c8a5-40af-b3fd-2879d40050d3",
- "urn:e14e4ef7-15c9-407d-88f4-a7b841746cb0"
+ "bids::sla.png",
+ "bids::slb.png",
+ "bids::slc.png",
+ "bids::sld.png",
+ "bids::sle.png",
+ "bids::slf.png",
+ "bids::slg.png",
+ "bids::slh.png",
+ "bids::sli.png",
+ "bids::slj.png",
+ "bids::slk.png",
+ "bids::sll.png"
]
},
{
- "@id": "urn:1e2964dc-2c07-4f9d-9101-885636e34941",
+ "@id": "urn:pngappen-JPkZrHqL",
"Label": "pngappend",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend example_func2highres1.png example_func2highres2.png example_func2highres.png",
"Used": [
- "urn:b450d637-a562-4afa-9c01-d11aafde9137",
- "urn:c753575e-7e2c-429d-9954-ee2103b515de"
+ "bids::example_func2highres1.png",
+ "bids::example_func2highres2.png"
]
},
{
- "@id": "urn:b32e0ecb-8082-4086-9d2a-384403f51379",
+ "@id": "urn:rm-N4UzNrDt",
"Label": "rm",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/bin/rm -f sl?.png example_func2highres2.png",
"Used": [
- "urn:36808c19-65e3-49cb-9369-990da661f030",
- "urn:b450d637-a562-4afa-9c01-d11aafde9137"
+ "bids::example_func2highres2.png",
+ "bids::sl?.png"
]
},
{
- "@id": "urn:9e0c1369-436f-4b6c-8dce-13e7c886d3be",
+ "@id": "urn:rm-BbCHnJGZ",
"Label": "rm",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/bin/rm example_func2highres1.png",
"Used": [
- "urn:c753575e-7e2c-429d-9954-ee2103b515de"
+ "bids::example_func2highres1.png"
]
},
{
- "@id": "urn:5efcc7da-6ea6-4ad7-865b-000b7cafae19",
+ "@id": "urn:mcflirt-mBlw9T2X",
"Label": "mcflirt",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs -spline_final",
"Used": [
- "urn:766de64a-5420-4b86-ad90-769f84993459"
+ "bids::prefiltered_func_data"
]
},
{
- "@id": "urn:253ea17d-16a9-4b4f-b9db-437c1d760ede",
+ "@id": "urn:makedire-tvzu7YZ9",
"Label": "Make directory",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/bin/mkdir -p mc",
"Used": []
},
{
- "@id": "urn:658211ea-995c-4a62-9030-1fbf43b013cc",
+ "@id": "urn:mv-tbG1qvio",
"Label": "mv",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc",
"Used": [
- "urn:0a8ced20-51bf-4c17-9698-3877f708ece6",
- "urn:391cd034-fd83-462d-bba5-f6c952efe934",
- "urn:66f27953-4be4-4fc2-9e73-7c52bce16dba",
- "urn:6bb66fa0-b3ba-478f-9b36-be86363bfe1c",
- "urn:a565191b-1db3-4743-bd31-6b8b2cbf88c2",
- "urn:f7951e4e-be9b-4d7c-b9b1-209db014bb24"
+ "bids::prefiltered_func_data_mcf.mat",
+ "bids::prefiltered_func_data_mcf.par",
+ "bids::prefiltered_func_data_mcf_abs.rms",
+ "bids::prefiltered_func_data_mcf_abs_mean.rms",
+ "bids::prefiltered_func_data_mcf_rel.rms",
+ "bids::prefiltered_func_data_mcf_rel_mean.rms"
]
},
{
- "@id": "urn:8101dccd-721c-473d-bce4-f9d73ef4f7c2",
+ "@id": "urn:fsltsplo-3Ygm84p1",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png",
"Used": [
- "urn:391cd034-fd83-462d-bba5-f6c952efe934"
+ "bids::prefiltered_func_data_mcf.par"
]
},
{
- "@id": "urn:cfef7577-e215-4909-9add-3d091919ebc5",
+ "@id": "urn:fsltsplo-PqpsKom3",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png",
"Used": [
- "urn:391cd034-fd83-462d-bba5-f6c952efe934"
+ "bids::prefiltered_func_data_mcf.par"
]
},
{
- "@id": "urn:095b5719-a730-49c9-bc74-ec5226812e96",
+ "@id": "urn:fsltsplo-ZNjGlTsw",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png",
"Used": [
- "urn:b3975f6e-1985-46b7-80da-90f1e8cf8e62"
+ "bids::prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms"
]
},
{
- "@id": "urn:34acc4e6-eeea-4eeb-8ef6-2f617abe7a79",
+ "@id": "urn:fslmaths-iQkoj0fa",
"Label": "fslmaths",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func",
"Used": [
- "urn:b57a9b24-e3af-4b0d-aac2-e5df9973dcc7"
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:94043e97-e422-407b-ac11-e740fdb6bf72",
+ "@id": "urn:bet2-sApm487o",
"Label": "bet2",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/bet2 mean_func mask -f 0.3 -n -m",
"Used": [
- "urn:b6a19b32-701a-42d0-9469-8b1da169301f"
+ "bids::mean_func"
]
},
{
- "@id": "urn:b649b7d7-7b32-4f2b-8ee0-dfbf074dff4e",
+ "@id": "urn:immv-WadYRMrM",
"Label": "immv",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/immv mask_mask mask",
"Used": [
- "urn:748557d0-dbf8-439f-9638-1d4963f93d52"
+ "bids::mask_mask"
]
},
{
- "@id": "urn:31e7bca8-5b2c-48d3-bb73-49fad30c957b",
+ "@id": "urn:fslmaths-yGAwZhHM",
"Label": "fslmaths",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet",
"Used": [
- "urn:8d3c0903-9944-4080-896f-b7cea95307e2",
- "urn:b57a9b24-e3af-4b0d-aac2-e5df9973dcc7"
+ "bids::mask",
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:94daf206-c9e2-45d9-95d0-6be1bbff9cc5",
+ "@id": "urn:fslstats-wY1o42Vq",
"Label": "fslstats",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_bet -p 2 -p 98",
"Used": [
- "urn:7b15c0f3-de8f-4ab6-8390-16fee37cc8b3"
+ "bids::prefiltered_func_data_bet"
]
},
{
- "@id": "urn:e242c59b-d93e-41c9-8735-d0be6238883a",
+ "@id": "urn:fslmaths-U5aSpbjx",
"Label": "fslmaths",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_bet -thr 74.4585571 -Tmin -bin mask -odt char",
"Used": [
- "urn:7b15c0f3-de8f-4ab6-8390-16fee37cc8b3"
+ "bids::prefiltered_func_data_bet"
]
},
{
- "@id": "urn:5efb5d23-6a8b-467e-8bed-0141cc4c6d0e",
+ "@id": "urn:fslstats-lSDl1VcC",
"Label": "fslstats",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_mcf -k mask -p 50",
"Used": [
- "urn:b57a9b24-e3af-4b0d-aac2-e5df9973dcc7"
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:e9492988-1bcb-4a89-b6e6-3c1925e1b1fc",
+ "@id": "urn:fslmaths-DdyB8Wig",
"Label": "fslmaths",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -dilF mask",
"Used": [
- "urn:8d3c0903-9944-4080-896f-b7cea95307e2"
+ "bids::mask"
]
},
{
- "@id": "urn:725ce964-546e-4bc3-b142-d8c544ff20fb",
+ "@id": "urn:fslmaths-IlGuzwXE",
"Label": "fslmaths",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh",
"Used": [
- "urn:8d3c0903-9944-4080-896f-b7cea95307e2",
- "urn:b57a9b24-e3af-4b0d-aac2-e5df9973dcc7"
+ "bids::mask",
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:eb06b57d-72f7-4db3-a83f-0b5375aaa208",
+ "@id": "urn:fslmaths-LGHPc31P",
"Label": "fslmaths",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func",
"Used": [
- "urn:dab0a08b-dacf-4844-a891-6ef77087c0aa"
+ "bids::prefiltered_func_data_thresh"
]
},
{
- "@id": "urn:4c855405-5793-42a1-9ec8-52fdcd417891",
+ "@id": "urn:susan-8xf1ZGqg",
"Label": "susan",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/susan prefiltered_func_data_thresh 445.8289035 2.54777070064 3 1 1 mean_func 445.8289035 prefiltered_func_data_smooth",
"Used": [
- "urn:dab0a08b-dacf-4844-a891-6ef77087c0aa"
+ "bids::prefiltered_func_data_thresh"
]
},
{
- "@id": "urn:9236d668-8f3d-447a-998e-8640df11727d",
+ "@id": "urn:fslmaths-ua6SnjTz",
"Label": "fslmaths",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth",
"Used": [
- "urn:582ba438-47f5-434f-a321-cfe55992160a",
- "urn:8d3c0903-9944-4080-896f-b7cea95307e2"
+ "bids::mask",
+ "bids::prefiltered_func_data_smooth"
]
},
{
- "@id": "urn:41be3c91-fe50-48dd-bc99-3ad852564c83",
+ "@id": "urn:fslmaths-Nr58QEDF",
"Label": "fslmaths",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mul 16.8225970571 prefiltered_func_data_intnorm",
"Used": [
- "urn:582ba438-47f5-434f-a321-cfe55992160a"
+ "bids::prefiltered_func_data_smooth"
]
},
{
- "@id": "urn:8b1be355-f766-44f6-b8e9-27ecdb17846e",
+ "@id": "urn:fslmaths-xGtZmbWb",
"Label": "fslmaths",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean",
"Used": [
- "urn:962cad7a-81dc-498c-9658-a367fc47be71"
+ "bids::prefiltered_func_data_intnorm"
]
},
{
- "@id": "urn:9854cce4-396d-4d48-90a3-f8269d90aea1",
+ "@id": "urn:fslmaths-tqFMMwBS",
"Label": "fslmaths",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -bptf 15.0 -1 -add tempMean prefiltered_func_data_tempfilt",
"Used": [
- "urn:962cad7a-81dc-498c-9658-a367fc47be71",
- "urn:d9762aae-4f9c-4df0-8f73-a26f14726850"
+ "bids::prefiltered_func_data_intnorm",
+ "bids::tempMean"
]
},
{
- "@id": "urn:e41da089-c6ef-43e2-aad8-f66b342a8d5b",
+ "@id": "urn:imrm-zBTUmmH3",
"Label": "imrm",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/imrm tempMean",
"Used": [
- "urn:d9762aae-4f9c-4df0-8f73-a26f14726850"
+ "bids::tempMean"
]
},
{
- "@id": "urn:3e30763b-7c05-4a4a-92e0-ad2333589ebd",
+ "@id": "urn:fslmaths-YMNePTWJ",
"Label": "fslmaths",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data",
"Used": [
- "urn:71b9fe4a-ab29-4764-8986-66a1ff95bb19"
+ "bids::prefiltered_func_data_tempfilt"
]
},
{
- "@id": "urn:711029e7-1a0b-4010-b6df-ed04fa5e35c1",
+ "@id": "urn:fslmaths-pP7eBc42",
"Label": "fslmaths",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths filtered_func_data -Tmean mean_func",
"Used": [
- "urn:7d0a4ae9-a2e7-48a7-b4df-e3e4596cb2bb"
+ "bids::filtered_func_data"
]
},
{
- "@id": "urn:7aa13188-2509-40a0-9f80-8816b8cc8f68",
+ "@id": "urn:rm-yBce1Xtf",
"Label": "rm",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/bin/rm -rf prefiltered_func_data*",
"Used": [
- "urn:926ed1ec-af3b-452a-9b53-ca78b6f581bb"
+ "bids::prefiltered_func_data*"
]
},
{
- "@id": "urn:b04e3534-b117-43c7-8bf5-b03ee2753090",
+ "@id": "urn:makedire-GybSm7me",
"Label": "Make directory",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
- "@id": "urn:3ee9492d-501c-49fa-8f15-d96306e9c0c6",
+ "@id": "urn:fslfixte-8D0gqBwQ",
"Label": "fslFixText",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
"Used": [
- "urn:cb548f71-12a7-43f4-a992-58f94d9d45df"
+ "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt"
]
},
{
- "@id": "urn:917c58f5-3975-4e53-a51e-95ab439f33d7",
+ "@id": "urn:makedire-LaEdoKMK",
"Label": "Make directory",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
- "@id": "urn:9298f076-ad34-43e2-aa3b-7864511f07e8",
+ "@id": "urn:fslfixte-Agxavi0H",
"Label": "fslFixText",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
"Used": [
- "urn:5d1a543b-6df9-4541-ae83-2c723b8c6368"
+ "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt"
]
},
{
- "@id": "urn:dfac6fe0-1044-4cdf-a45d-fe1a9c249114",
+ "@id": "urn:filmgls-P4ifUteV",
"Label": "film_gls",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con --fcon=design.fts",
- "Used": []
+ "Used": [
+ "bids::design.con",
+ "bids::design.fts",
+ "bids::design.mat",
+ "bids::filtered_func_data",
+ "bids::stats"
+ ]
},
{
- "@id": "urn:703bf55b-db97-472c-99ec-2a3a2e30d4c3",
+ "@id": "urn:smoothes-J4xR0VAI",
"Label": "smoothest",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 98 -m mask -r stats/res4d > stats/smoothness",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 98 -m mask -r stats/res4d > stats/smoothness",
"Used": [
- "urn:3c57f050-6e6c-4747-a278-14167f03b63f",
- "urn:8d3c0903-9944-4080-896f-b7cea95307e2"
+ "bids::mask",
+ "bids::stats/res4d"
]
},
{
- "@id": "urn:73f3d293-8378-44e5-b97f-f0d210d07474",
+ "@id": "urn:fslmaths-QEY7hfH5",
"Label": "fslmaths",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1",
"Used": [
- "urn:8d3c0903-9944-4080-896f-b7cea95307e2",
- "urn:da0577c7-5820-4e87-9613-c32c52586f56"
+ "bids::mask",
+ "bids::stats/zstat1"
]
},
{
- "@id": "urn:e8810ee0-cdb1-4e99-b6da-3277ccc23dd2",
+ "@id": "urn:echo-acNmJmPz",
"Label": "echo",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "echo 38352 > thresh_zstat1.vol",
"Used": []
},
{
- "@id": "urn:c065adcb-4f8a-4696-861b-6796936fc714",
+ "@id": "urn:fslmaths-IQ18U7E5",
"Label": "fslmaths",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat2 -mas mask thresh_zstat2",
"Used": [
- "urn:263e3610-fc97-46a1-a70f-f475bc13917d",
- "urn:8d3c0903-9944-4080-896f-b7cea95307e2"
+ "bids::mask",
+ "bids::stats/zstat2"
]
},
{
- "@id": "urn:b807382f-c648-42ed-85a4-e308b783d419",
+ "@id": "urn:echo-o4K0SINT",
"Label": "echo",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "echo 38352 > thresh_zstat2.vol",
"Used": []
},
{
- "@id": "urn:6a684010-69f3-41d0-b687-785d7f9eaea2",
+ "@id": "urn:fslmaths-NGxIT52n",
"Label": "fslmaths",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat3 -mas mask thresh_zstat3",
"Used": [
- "urn:8d3c0903-9944-4080-896f-b7cea95307e2",
- "urn:f9a25879-924c-40ca-beed-fd6bdae25812"
+ "bids::mask",
+ "bids::stats/zstat3"
]
},
{
- "@id": "urn:961fc3ea-0194-4640-a8b7-8774f193fee2",
+ "@id": "urn:echo-pkNaI7Dl",
"Label": "echo",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "echo 38352 > thresh_zstat3.vol",
"Used": []
},
{
- "@id": "urn:9a46fc84-5d80-45d6-beb8-5860b5ed50c5",
+ "@id": "urn:fslmaths-1y2B6YqW",
"Label": "fslmaths",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zfstat1 -mas mask thresh_zfstat1",
"Used": [
- "urn:8d3c0903-9944-4080-896f-b7cea95307e2",
- "urn:e057248b-dd5d-4c40-bd31-8505d330fb13"
+ "bids::mask",
+ "bids::stats/zfstat1"
]
},
{
- "@id": "urn:551995e2-978b-482d-afd6-fe48b36f14c7",
+ "@id": "urn:echo-VBNs5nvy",
"Label": "echo",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "echo 38352 > thresh_zfstat1.vol",
"Used": []
},
{
- "@id": "urn:158a8fa0-2415-4647-98be-add728d66819",
+ "@id": "urn:ptoz-2V4cSwE4",
"Label": "ptoz",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:d68c27b7-672e-4f70-8746-fed40682c700",
+ "@id": "urn:cluster-MgJEe6d4",
"Label": "cluster",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -t 3.090232 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z --voxuncthresh -c stats/cope1 > cluster_zstat1.txt",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -t 3.090232 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z --voxuncthresh -c stats/cope1 > cluster_zstat1.txt",
"Used": [
- "urn:1610add2-fdc2-479b-a927-1c15cee8cf73",
- "urn:367458e3-16bb-4dd1-ae1f-db628fdc3a0d"
+ "bids::stats/cope1",
+ "bids::thresh_zstat1"
]
},
{
- "@id": "urn:b2e2b66f-ee15-4e69-909e-63834dcb44d1",
+ "@id": "urn:cluster2-aRueCeCD",
"Label": "cluster2html",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat1",
"Used": [
- "urn:31c406c9-e772-4346-bc0d-e20ecfc2a8a8"
+ "bids::cluster_zstat1"
]
},
{
- "@id": "urn:d4ce1155-8e92-41de-ad87-a61a257d6e3f",
+ "@id": "urn:ptoz-nfO1AgxR",
"Label": "ptoz",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:b68b9bc1-27cc-4c62-9d49-e1f70f7aa3a0",
+ "@id": "urn:cluster-Xfz11U8L",
"Label": "cluster",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat2 -t 3.090232 --othresh=thresh_zstat2 -o cluster_mask_zstat2 --connectivity=26 --olmax=lmax_zstat2.txt --scalarname=Z --voxuncthresh -c stats/cope2 > cluster_zstat2.txt",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat2 -t 3.090232 --othresh=thresh_zstat2 -o cluster_mask_zstat2 --connectivity=26 --olmax=lmax_zstat2.txt --scalarname=Z --voxuncthresh -c stats/cope2 > cluster_zstat2.txt",
"Used": [
- "urn:0d0dc84d-f553-4433-a38d-2c1056077f45",
- "urn:5daf1c03-fc28-4693-b72d-04cd580ab021"
+ "bids::stats/cope2",
+ "bids::thresh_zstat2"
]
},
{
- "@id": "urn:a906578f-aa09-42aa-aab9-8716786196b3",
+ "@id": "urn:cluster2-Vw7VdGpH",
"Label": "cluster2html",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat2",
"Used": [
- "urn:a5a99aec-f69e-4cea-b407-27243deea155"
+ "bids::cluster_zstat2"
]
},
{
- "@id": "urn:7052b74a-50e0-439c-81df-db12832c1a44",
+ "@id": "urn:ptoz-qoMZL7p1",
"Label": "ptoz",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:dd90df62-1518-4a69-b1cd-6b31c2c95e2f",
+ "@id": "urn:cluster-YJuz1prR",
"Label": "cluster",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat3 -t 3.090232 --othresh=thresh_zstat3 -o cluster_mask_zstat3 --connectivity=26 --olmax=lmax_zstat3.txt --scalarname=Z --voxuncthresh -c stats/cope3 > cluster_zstat3.txt",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat3 -t 3.090232 --othresh=thresh_zstat3 -o cluster_mask_zstat3 --connectivity=26 --olmax=lmax_zstat3.txt --scalarname=Z --voxuncthresh -c stats/cope3 > cluster_zstat3.txt",
"Used": [
- "urn:cd620add-4300-4d26-8e71-f9bd37cb0b8e",
- "urn:d75904a1-7cd3-4610-a894-e6c3c5d76011"
+ "bids::stats/cope3",
+ "bids::thresh_zstat3"
]
},
{
- "@id": "urn:5ecde4d0-c081-4835-aa9f-906b48bc746d",
+ "@id": "urn:cluster2-as1TvHvJ",
"Label": "cluster2html",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat3",
"Used": [
- "urn:8a7f70e5-e173-4ec2-944c-7b27e4f9ec29"
+ "bids::cluster_zstat3"
]
},
{
- "@id": "urn:af85eb98-f60a-48ca-85fc-72ebed7a0c95",
+ "@id": "urn:ptoz-1CLrMKJG",
"Label": "ptoz",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:6e133963-adde-4100-b5d9-8049067b311e",
+ "@id": "urn:cluster-cFqbWSOQ",
"Label": "cluster",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zfstat1 -t 3.090232 --othresh=thresh_zfstat1 -o cluster_mask_zfstat1 --connectivity=26 --olmax=lmax_zfstat1.txt --scalarname=Z --voxuncthresh > cluster_zfstat1.txt",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zfstat1 -t 3.090232 --othresh=thresh_zfstat1 -o cluster_mask_zfstat1 --connectivity=26 --olmax=lmax_zfstat1.txt --scalarname=Z --voxuncthresh > cluster_zfstat1.txt",
"Used": [
- "urn:435a68ac-72e9-4d77-8ee2-9eb12b1468c4"
+ "bids::thresh_zfstat1"
]
},
{
- "@id": "urn:71d4b62d-e181-4b29-9cef-04ef856047a4",
+ "@id": "urn:cluster2-3aP1Q5qZ",
"Label": "cluster2html",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zfstat1",
"Used": [
- "urn:dfea9359-ff55-4f9f-80a3-b053d6b53085"
+ "bids::cluster_zfstat1"
]
},
{
- "@id": "urn:51c11372-3875-49dc-afe1-0bc1cdf18235",
+ "@id": "urn:fslstats-rhTZM5Ju",
"Label": "fslstats",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat1 -l 0.0001 -R 2>/dev/null",
"Used": [
- "urn:367458e3-16bb-4dd1-ae1f-db628fdc3a0d"
+ "bids::thresh_zstat1"
]
},
{
- "@id": "urn:1662b1a2-1679-4d8d-b615-c41a992926ca",
+ "@id": "urn:fslstats-BjgxFcRA",
"Label": "fslstats",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat2 -l 0.0001 -R 2>/dev/null",
"Used": [
- "urn:5daf1c03-fc28-4693-b72d-04cd580ab021"
+ "bids::thresh_zstat2"
]
},
{
- "@id": "urn:2aaa0e60-f652-4176-af2f-3b0f09c14266",
+ "@id": "urn:fslstats-TSEDOSLQ",
"Label": "fslstats",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat3 -l 0.0001 -R 2>/dev/null",
"Used": [
- "urn:d75904a1-7cd3-4610-a894-e6c3c5d76011"
+ "bids::thresh_zstat3"
]
},
{
- "@id": "urn:36139506-2e6f-4255-bbe7-49fb09a05bde",
+ "@id": "urn:fslstats-BP3sHODs",
"Label": "fslstats",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zfstat1 -l 0.0001 -R 2>/dev/null",
"Used": [
- "urn:435a68ac-72e9-4d77-8ee2-9eb12b1468c4"
+ "bids::thresh_zfstat1"
]
},
{
- "@id": "urn:48891029-b785-4f4f-8860-7054ddcf78ca",
+ "@id": "urn:overlay-J0LVToUU",
"Label": "overlay",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat1 3.090292 7.429559 rendered_thresh_zstat1",
"Used": []
},
{
- "@id": "urn:270d4b00-919d-46a5-8bd3-ba90ab4de77c",
+ "@id": "urn:slicer-WIJeQdex",
"Label": "slicer",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat1 -A 750 rendered_thresh_zstat1.png",
"Used": [
- "urn:854a0da7-0140-4007-b23a-63c8036c2338"
+ "bids::rendered_thresh_zstat1"
]
},
{
- "@id": "urn:6c7c5ceb-8f8a-4126-931f-3e45b2fc80f0",
+ "@id": "urn:cp-ZB6SRpaR",
"Label": "cp",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/bin/cp /usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif .ramp.gif",
"Used": [
- "urn:f653dfb6-d7f8-4895-8e06-573f04121f8c"
+ "bids::/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif"
]
},
{
- "@id": "urn:bc4ed7c6-6801-4fc5-8242-4cca359734a6",
+ "@id": "urn:overlay-ezv2kA1Z",
"Label": "overlay",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat2 3.090292 7.429559 rendered_thresh_zstat2",
"Used": []
},
{
- "@id": "urn:ca4ee33e-ec88-4ec0-9662-9065d7cc4734",
+ "@id": "urn:slicer-d8V0x0iz",
"Label": "slicer",
- "AssociatedWith": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
+ "AssociatedWith": "urn:fsl-ZtRHP0hk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat2 -A 750 rendered_thresh_zstat2.png",
"Used": [
- "urn:abaf539c-8c53-4d5b-81dd-c5c8dd66cef5"
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"AtLocation": "prefiltered_func_data",
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@@ -783,15 +793,15 @@
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@@ -799,45 +809,57 @@
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@@ -845,267 +867,259 @@
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- "GeneratedBy": "urn:83be6f1d-ca5b-46a5-910c-502c7c9c7f4b",
+ "GeneratedBy": "urn:slicer-nCd4Ud2V",
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}
},
{
- "@id": "urn:7334b08d-2196-4c73-9508-798db305ec24",
+ "@id": "bids::sli.png",
"Label": "sli.png",
"AtLocation": "sli.png",
- "GeneratedBy": "urn:83be6f1d-ca5b-46a5-910c-502c7c9c7f4b",
+ "GeneratedBy": "urn:slicer-nCd4Ud2V",
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}
},
{
- "@id": "urn:aa4b058c-938f-4994-becf-af0bcf8c7fae",
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"Label": "slj.png",
"AtLocation": "slj.png",
- "GeneratedBy": "urn:83be6f1d-ca5b-46a5-910c-502c7c9c7f4b",
+ "GeneratedBy": "urn:slicer-nCd4Ud2V",
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}
},
{
- "@id": "urn:165d380e-b35b-4ce4-9ba0-23a7bac20532",
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"Label": "slk.png",
"AtLocation": "slk.png",
- "GeneratedBy": "urn:83be6f1d-ca5b-46a5-910c-502c7c9c7f4b",
+ "GeneratedBy": "urn:slicer-nCd4Ud2V",
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}
},
{
- "@id": "urn:d593231d-fe98-4ccc-91ca-b9c788b6ef1f",
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"Label": "sll.png",
"AtLocation": "sll.png",
- "GeneratedBy": "urn:83be6f1d-ca5b-46a5-910c-502c7c9c7f4b",
+ "GeneratedBy": "urn:slicer-nCd4Ud2V",
"digest": {
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}
},
{
- "@id": "urn:b450d637-a562-4afa-9c01-d11aafde9137",
+ "@id": "bids::example_func2highres2.png",
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"AtLocation": "example_func2highres2.png",
- "GeneratedBy": "urn:e7951802-97c3-4674-9d26-69aa78d96a32",
+ "GeneratedBy": "urn:pngappen-laujh6mc",
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}
},
{
- "@id": "urn:474c0746-c8da-4cd7-a3c0-eee7a2302b9b",
+ "@id": "bids::example_func2highres.png",
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"AtLocation": "example_func2highres.png",
- "GeneratedBy": "urn:1e2964dc-2c07-4f9d-9101-885636e34941",
+ "GeneratedBy": "urn:pngappen-JPkZrHqL",
"digest": {
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}
},
{
- "@id": "urn:36808c19-65e3-49cb-9369-990da661f030",
+ "@id": "bids::sl?.png",
"Label": "sl?.png",
"AtLocation": "sl?.png",
"digest": {
@@ -1113,25 +1127,25 @@
}
},
{
- "@id": "urn:b57a9b24-e3af-4b0d-aac2-e5df9973dcc7",
+ "@id": "bids::prefiltered_func_data_mcf",
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"AtLocation": "prefiltered_func_data_mcf",
- "GeneratedBy": "urn:5efcc7da-6ea6-4ad7-865b-000b7cafae19",
+ "GeneratedBy": "urn:mcflirt-mBlw9T2X",
"digest": {
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}
},
{
- "@id": "urn:0514ce80-6ce1-44f3-9482-53f6381f5b61",
+ "@id": "bids::mc",
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"AtLocation": "mc",
- "GeneratedBy": "urn:253ea17d-16a9-4b4f-b9db-437c1d760ede",
+ "GeneratedBy": "urn:makedire-tvzu7YZ9",
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}
},
{
- "@id": "urn:6bb66fa0-b3ba-478f-9b36-be86363bfe1c",
+ "@id": "bids::prefiltered_func_data_mcf.mat",
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"AtLocation": "prefiltered_func_data_mcf.mat",
"digest": {
@@ -1139,7 +1153,7 @@
}
},
{
- "@id": "urn:391cd034-fd83-462d-bba5-f6c952efe934",
+ "@id": "bids::prefiltered_func_data_mcf.par",
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"AtLocation": "prefiltered_func_data_mcf.par",
"digest": {
@@ -1147,7 +1161,7 @@
}
},
{
- "@id": "urn:a565191b-1db3-4743-bd31-6b8b2cbf88c2",
+ "@id": "bids::prefiltered_func_data_mcf_abs.rms",
"Label": "prefiltered_func_data_mcf_abs.rms",
"AtLocation": "prefiltered_func_data_mcf_abs.rms",
"digest": {
@@ -1155,7 +1169,7 @@
}
},
{
- "@id": "urn:f7951e4e-be9b-4d7c-b9b1-209db014bb24",
+ "@id": "bids::prefiltered_func_data_mcf_abs_mean.rms",
"Label": "prefiltered_func_data_mcf_abs_mean.rms",
"AtLocation": "prefiltered_func_data_mcf_abs_mean.rms",
"digest": {
@@ -1163,7 +1177,7 @@
}
},
{
- "@id": "urn:66f27953-4be4-4fc2-9e73-7c52bce16dba",
+ "@id": "bids::prefiltered_func_data_mcf_rel.rms",
"Label": "prefiltered_func_data_mcf_rel.rms",
"AtLocation": "prefiltered_func_data_mcf_rel.rms",
"digest": {
@@ -1171,7 +1185,7 @@
}
},
{
- "@id": "urn:0a8ced20-51bf-4c17-9698-3877f708ece6",
+ "@id": "bids::prefiltered_func_data_mcf_rel_mean.rms",
"Label": "prefiltered_func_data_mcf_rel_mean.rms",
"AtLocation": "prefiltered_func_data_mcf_rel_mean.rms",
"digest": {
@@ -1179,34 +1193,34 @@
}
},
{
- "@id": "urn:1c65e019-bff5-4652-9d67-24ad71333fd7",
+ "@id": "bids::mc",
"Label": "mc",
"AtLocation": "mc",
- "GeneratedBy": "urn:658211ea-995c-4a62-9030-1fbf43b013cc",
+ "GeneratedBy": "urn:mv-tbG1qvio",
"digest": {
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}
},
{
- "@id": "urn:d4e33abf-38ab-40ee-b824-cb1c9e5d8c1c",
+ "@id": "bids::rot.png",
"Label": "rot.png",
"AtLocation": "rot.png",
- "GeneratedBy": "urn:8101dccd-721c-473d-bce4-f9d73ef4f7c2",
+ "GeneratedBy": "urn:fsltsplo-3Ygm84p1",
"digest": {
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}
},
{
- "@id": "urn:46d52892-c9a2-46ad-8f23-17546b04f64f",
+ "@id": "bids::trans.png",
"Label": "trans.png",
"AtLocation": "trans.png",
- "GeneratedBy": "urn:cfef7577-e215-4909-9add-3d091919ebc5",
+ "GeneratedBy": "urn:fsltsplo-PqpsKom3",
"digest": {
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}
},
{
- "@id": "urn:b3975f6e-1985-46b7-80da-90f1e8cf8e62",
+ "@id": "bids::prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"Label": "prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"AtLocation": "prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"digest": {
@@ -1214,34 +1228,34 @@
}
},
{
- "@id": "urn:ed74188c-0a4a-4b0a-a0a1-47234ed3304f",
+ "@id": "bids::disp.png",
"Label": "disp.png",
"AtLocation": "disp.png",
- "GeneratedBy": "urn:095b5719-a730-49c9-bc74-ec5226812e96",
+ "GeneratedBy": "urn:fsltsplo-ZNjGlTsw",
"digest": {
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}
},
{
- "@id": "urn:b6a19b32-701a-42d0-9469-8b1da169301f",
+ "@id": "bids::mean_func",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:34acc4e6-eeea-4eeb-8ef6-2f617abe7a79",
+ "GeneratedBy": "urn:fslmaths-iQkoj0fa",
"digest": {
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}
},
{
- "@id": "urn:8d3c0903-9944-4080-896f-b7cea95307e2",
+ "@id": "bids::mask",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:94043e97-e422-407b-ac11-e740fdb6bf72",
+ "GeneratedBy": "urn:bet2-sApm487o",
"digest": {
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}
},
{
- "@id": "urn:748557d0-dbf8-439f-9638-1d4963f93d52",
+ "@id": "bids::mask_mask",
"Label": "mask_mask",
"AtLocation": "mask_mask",
"digest": {
@@ -1249,132 +1263,124 @@
}
},
{
- "@id": "urn:1f147a2f-28cb-40b8-a79a-a2a99e9adf77",
+ "@id": "bids::mask",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:b649b7d7-7b32-4f2b-8ee0-dfbf074dff4e",
+ "GeneratedBy": "urn:immv-WadYRMrM",
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}
},
{
- "@id": "urn:7b15c0f3-de8f-4ab6-8390-16fee37cc8b3",
+ "@id": "bids::prefiltered_func_data_bet",
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"AtLocation": "prefiltered_func_data_bet",
- "GeneratedBy": "urn:31e7bca8-5b2c-48d3-bb73-49fad30c957b",
+ "GeneratedBy": "urn:fslmaths-yGAwZhHM",
"digest": {
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}
},
{
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- "GeneratedBy": "urn:e242c59b-d93e-41c9-8735-d0be6238883a",
+ "GeneratedBy": "urn:fslmaths-U5aSpbjx",
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}
},
{
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- "GeneratedBy": "urn:e9492988-1bcb-4a89-b6e6-3c1925e1b1fc",
+ "GeneratedBy": "urn:fslmaths-DdyB8Wig",
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}
},
{
- "@id": "urn:dab0a08b-dacf-4844-a891-6ef77087c0aa",
+ "@id": "bids::prefiltered_func_data_thresh",
"Label": "prefiltered_func_data_thresh",
"AtLocation": "prefiltered_func_data_thresh",
- "GeneratedBy": "urn:725ce964-546e-4bc3-b142-d8c544ff20fb",
+ "GeneratedBy": "urn:fslmaths-IlGuzwXE",
"digest": {
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}
},
{
- "@id": "urn:f1669840-b2b3-444f-a7d7-833c7e46505d",
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"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:eb06b57d-72f7-4db3-a83f-0b5375aaa208",
+ "GeneratedBy": "urn:fslmaths-LGHPc31P",
"digest": {
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}
},
{
- "@id": "urn:582ba438-47f5-434f-a321-cfe55992160a",
+ "@id": "bids::prefiltered_func_data_smooth",
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"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:4c855405-5793-42a1-9ec8-52fdcd417891",
+ "GeneratedBy": "urn:susan-8xf1ZGqg",
"digest": {
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}
},
{
- "@id": "urn:4c69d19b-2099-4dda-8869-85976b9ba13c",
+ "@id": "bids::prefiltered_func_data_smooth",
"Label": "prefiltered_func_data_smooth",
"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:9236d668-8f3d-447a-998e-8640df11727d",
+ "GeneratedBy": "urn:fslmaths-ua6SnjTz",
"digest": {
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}
},
{
- "@id": "urn:962cad7a-81dc-498c-9658-a367fc47be71",
+ "@id": "bids::prefiltered_func_data_intnorm",
"Label": "prefiltered_func_data_intnorm",
"AtLocation": "prefiltered_func_data_intnorm",
- "GeneratedBy": "urn:41be3c91-fe50-48dd-bc99-3ad852564c83",
+ "GeneratedBy": "urn:fslmaths-Nr58QEDF",
"digest": {
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}
},
{
- "@id": "urn:d9762aae-4f9c-4df0-8f73-a26f14726850",
+ "@id": "bids::tempMean",
"Label": "tempMean",
"AtLocation": "tempMean",
- "GeneratedBy": "urn:8b1be355-f766-44f6-b8e9-27ecdb17846e",
+ "GeneratedBy": "urn:fslmaths-xGtZmbWb",
"digest": {
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}
},
{
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- "digest": {
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- }
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- {
- "@id": "urn:71b9fe4a-ab29-4764-8986-66a1ff95bb19",
+ "@id": "bids::prefiltered_func_data_tempfilt",
"Label": "prefiltered_func_data_tempfilt",
"AtLocation": "prefiltered_func_data_tempfilt",
+ "GeneratedBy": "urn:fslmaths-tqFMMwBS",
"digest": {
"sha256": "a1836f4694e7ffdb50484626724602498c7b22b4f3cdd1e7d105efd336cbc8bd"
}
},
{
- "@id": "urn:7d0a4ae9-a2e7-48a7-b4df-e3e4596cb2bb",
+ "@id": "bids::filtered_func_data",
"Label": "filtered_func_data",
"AtLocation": "filtered_func_data",
- "GeneratedBy": "urn:3e30763b-7c05-4a4a-92e0-ad2333589ebd",
+ "GeneratedBy": "urn:fslmaths-YMNePTWJ",
"digest": {
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}
},
{
- "@id": "urn:07a3b53d-6109-42a1-853d-cdcb256e5730",
+ "@id": "bids::mean_func",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:711029e7-1a0b-4010-b6df-ed04fa5e35c1",
+ "GeneratedBy": "urn:fslmaths-pP7eBc42",
"digest": {
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}
},
{
- "@id": "urn:926ed1ec-af3b-452a-9b53-ca78b6f581bb",
+ "@id": "bids::prefiltered_func_data*",
"Label": "prefiltered_func_data*",
"AtLocation": "prefiltered_func_data*",
"digest": {
@@ -1382,164 +1388,208 @@
}
},
{
- "@id": "urn:ea8de012-dce4-4e09-b850-ed1d8f0a2896",
+ "@id": "bids::custom_timing_files",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:b04e3534-b117-43c7-8bf5-b03ee2753090",
+ "GeneratedBy": "urn:makedire-GybSm7me",
"digest": {
"sha256": "1d7e19792328d5040f2f9fb3c15d59de90fc771785f81c67039a043bd5f2ed20"
}
},
{
- "@id": "urn:cb548f71-12a7-43f4-a992-58f94d9d45df",
+ "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
"Label": "sub-01_tone_counting.txt",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
+ "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
"digest": {
- "sha256": "c120d27b9d5d81a91be0e55f5cb880b2cb7de6c655554d9c15c9c04c6232ea8e"
+ "sha256": "165398224a205d2fc0b19354e15d9b085c6d81e333b69c4697b7894a2549be0b"
}
},
{
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+ "@id": "bids::custom_timing_files/ev1.txt",
"Label": "ev1.txt",
"AtLocation": "custom_timing_files/ev1.txt",
- "GeneratedBy": "urn:3ee9492d-501c-49fa-8f15-d96306e9c0c6"
+ "GeneratedBy": "urn:fslfixte-8D0gqBwQ"
},
{
- "@id": "urn:02f4afbd-27c0-4390-8a5b-d4efa5cc53eb",
+ "@id": "bids::custom_timing_files",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:917c58f5-3975-4e53-a51e-95ab439f33d7",
+ "GeneratedBy": "urn:makedire-LaEdoKMK",
"digest": {
"sha256": "1d7e19792328d5040f2f9fb3c15d59de90fc771785f81c67039a043bd5f2ed20"
}
},
{
- "@id": "urn:5d1a543b-6df9-4541-ae83-2c723b8c6368",
+ "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
"Label": "sub-01_tone_counting_probe.txt",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
+ "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
"digest": {
- "sha256": "f09eeb82fa0be8e8759a5269403f36ec2b7dbf2c5b6caba1f0f985cc6cb3f703"
+ "sha256": "8b912293767f1a5e082311f6aaf0c44fc91fe45b0f2ae7f80e368bc2f4c2918a"
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},
{
- "@id": "urn:c87eee96-f587-4647-b19b-c4e391998eff",
+ "@id": "bids::custom_timing_files/ev2.txt",
"Label": "ev2.txt",
"AtLocation": "custom_timing_files/ev2.txt",
- "GeneratedBy": "urn:9298f076-ad34-43e2-aa3b-7864511f07e8"
+ "GeneratedBy": "urn:fslfixte-Agxavi0H"
},
{
- "@id": "urn:3c57f050-6e6c-4747-a278-14167f03b63f",
- "Label": "res4d",
- "AtLocation": "stats/res4d",
+ "@id": "bids::stats",
+ "Label": "stats",
+ "AtLocation": "stats",
"digest": {
- "sha256": "8845286f36caedf891a02afddc4175ea46f18f830b59a8c5026962184a530699"
+ "sha256": "a9f3e135372514a16d11a8038262b3eff94ccd69a9b35c4724b2759cfc944a07"
}
},
{
- "@id": "urn:307b8e93-4018-4034-b02d-3b761ef5558a",
- "Label": "smoothness",
- "AtLocation": "stats/smoothness",
- "GeneratedBy": "urn:703bf55b-db97-472c-99ec-2a3a2e30d4c3",
+ "@id": "bids::design.mat",
+ "Label": "design.mat",
+ "AtLocation": "design.mat",
"digest": {
- "sha256": "67b0aaf95a257beff60d331b56265034807ca51e67e2d312d481d5835ef0b1d0"
+ "sha256": "1c1a6ef59a355e1f6f81e741e157784ccbe066ba3594a07aa9b16781e3d5bb25"
}
},
{
- "@id": "urn:da0577c7-5820-4e87-9613-c32c52586f56",
- "Label": "zstat1",
- "AtLocation": "stats/zstat1",
+ "@id": "bids::design.con",
+ "Label": "design.con",
+ "AtLocation": "design.con",
"digest": {
- "sha256": "70ae47cee1ea1d3f1f6f8aa7ac51f2641cb2fcb745dfd8cc54a389346e6fa094"
+ "sha256": "5808d1be37dd8f2a4906b710bb384fbee62faa4a46b2bc6847afc8962ed4eb54"
}
},
{
- "@id": "urn:367458e3-16bb-4dd1-ae1f-db628fdc3a0d",
+ "@id": "bids::design.fts",
+ "Label": "design.fts",
+ "AtLocation": "design.fts",
+ "digest": {
+ "sha256": "02a711eee20a847faffeeb6f54318dca6c1508e74c4de8a3016cec0a070ddb77"
+ }
+ },
+ {
+ "@id": "bids::stats",
+ "Label": "stats",
+ "AtLocation": "stats",
+ "GeneratedBy": "urn:filmgls-P4ifUteV",
+ "digest": {
+ "sha256": "a9f3e135372514a16d11a8038262b3eff94ccd69a9b35c4724b2759cfc944a07"
+ }
+ },
+ {
+ "@id": "bids::stats/res4d",
+ "Label": "res4d",
+ "AtLocation": "stats/res4d"
+ },
+ {
+ "@id": "bids::stats/smoothness",
+ "Label": "smoothness",
+ "AtLocation": "stats/smoothness",
+ "GeneratedBy": "urn:smoothes-J4xR0VAI"
+ },
+ {
+ "@id": "bids::stats/zstat1",
+ "Label": "zstat1",
+ "AtLocation": "stats/zstat1"
+ },
+ {
+ "@id": "bids::thresh_zstat1",
"Label": "thresh_zstat1",
"AtLocation": "thresh_zstat1",
- "GeneratedBy": "urn:73f3d293-8378-44e5-b97f-f0d210d07474",
+ "GeneratedBy": "urn:fslmaths-QEY7hfH5",
"digest": {
"sha256": "662e7ba670e124d15bb3cc18b818868f76604578034b524c8882f35fc5db413f"
}
},
{
- "@id": "urn:263e3610-fc97-46a1-a70f-f475bc13917d",
+ "@id": "bids::stats/zstat2",
"Label": "zstat2",
- "AtLocation": "stats/zstat2",
- "digest": {
- "sha256": "b6b265908257e91648f7007e172c3ba159d9231b0acfce7fbf48d754f8cfe52c"
- }
+ "AtLocation": "stats/zstat2"
},
{
- "@id": "urn:5daf1c03-fc28-4693-b72d-04cd580ab021",
+ "@id": "bids::thresh_zstat2",
"Label": "thresh_zstat2",
"AtLocation": "thresh_zstat2",
- "GeneratedBy": "urn:c065adcb-4f8a-4696-861b-6796936fc714",
+ "GeneratedBy": "urn:fslmaths-IQ18U7E5",
"digest": {
"sha256": "fe707ed68d72f4376668be45a2030f2d00fa81534a3e95bf92b6a499fa8595bd"
}
},
{
- "@id": "urn:f9a25879-924c-40ca-beed-fd6bdae25812",
+ "@id": "bids::stats/zstat3",
"Label": "zstat3",
- "AtLocation": "stats/zstat3",
- "digest": {
- "sha256": "2375921a9294c98b426a10611f5bf5998097ae3798c731661bd4b66b4114e300"
- }
+ "AtLocation": "stats/zstat3"
},
{
- "@id": "urn:d75904a1-7cd3-4610-a894-e6c3c5d76011",
+ "@id": "bids::thresh_zstat3",
"Label": "thresh_zstat3",
"AtLocation": "thresh_zstat3",
- "GeneratedBy": "urn:6a684010-69f3-41d0-b687-785d7f9eaea2",
+ "GeneratedBy": "urn:fslmaths-NGxIT52n",
"digest": {
"sha256": "d0f88769369dc8215d7373817e8f9a48482b508bb9deb2ca29904069bb23f484"
}
},
{
- "@id": "urn:e057248b-dd5d-4c40-bd31-8505d330fb13",
+ "@id": "bids::stats/zfstat1",
"Label": "zfstat1",
- "AtLocation": "stats/zfstat1",
- "digest": {
- "sha256": "7411c38cb93415865a53b21dc0427506ed7994230aca73062e72251f77549cb9"
- }
+ "AtLocation": "stats/zfstat1"
},
{
- "@id": "urn:435a68ac-72e9-4d77-8ee2-9eb12b1468c4",
+ "@id": "bids::thresh_zfstat1",
"Label": "thresh_zfstat1",
"AtLocation": "thresh_zfstat1",
- "GeneratedBy": "urn:9a46fc84-5d80-45d6-beb8-5860b5ed50c5",
+ "GeneratedBy": "urn:fslmaths-1y2B6YqW",
"digest": {
"sha256": "e4e927e247bdf8ff3b58b41cbb9db7643b27df1f7578c506950eb4b1ca2d0031"
}
},
{
- "@id": "urn:1610add2-fdc2-479b-a927-1c15cee8cf73",
+ "@id": "bids::stats/cope1",
"Label": "cope1",
- "AtLocation": "stats/cope1",
- "digest": {
- "sha256": "bf3b603569da6dbe3d6f0e8667d346f3ac943c9d01d2fc9743ce17abeb1547fb"
- }
+ "AtLocation": "stats/cope1"
},
{
- "@id": "urn:5ba3d6e3-7d1d-4ccf-ae35-3caf3a004ecf",
+ "@id": "bids::cluster_mask_zstat1",
"Label": "cluster_mask_zstat1",
"AtLocation": "cluster_mask_zstat1",
- "GeneratedBy": "urn:d68c27b7-672e-4f70-8746-fed40682c700",
+ "GeneratedBy": "urn:cluster-MgJEe6d4",
"digest": {
"sha256": "b28c170e33d2917cac55183786616a9e976e5e7f30dc7c8666341f12ed6d0277"
}
},
{
- "@id": "urn:9eed7245-2062-4382-a312-e3700ce4e6ff",
+ "@id": "bids::thresh_zstat1",
+ "Label": "thresh_zstat1",
+ "AtLocation": "thresh_zstat1",
+ "GeneratedBy": "urn:cluster-MgJEe6d4",
+ "digest": {
+ "sha256": "662e7ba670e124d15bb3cc18b818868f76604578034b524c8882f35fc5db413f"
+ }
+ },
+ {
+ "@id": "bids::lmax_zstat1.txt",
+ "Label": "lmax_zstat1.txt",
+ "AtLocation": "lmax_zstat1.txt",
+ "GeneratedBy": "urn:cluster-MgJEe6d4",
+ "digest": {
+ "sha256": "d44ee21719775397a1a95ede6778d25404b50e8bd259dbdf02d2fde635fc81a5"
+ }
+ },
+ {
+ "@id": "bids::stats/cope1",
"Label": "cope1",
"AtLocation": "stats/cope1",
- "GeneratedBy": "urn:d68c27b7-672e-4f70-8746-fed40682c700",
+ "GeneratedBy": "urn:cluster-MgJEe6d4"
+ },
+ {
+ "@id": "bids::cluster_zstat1.txt",
+ "Label": "cluster_zstat1.txt",
+ "AtLocation": "cluster_zstat1.txt",
+ "GeneratedBy": "urn:cluster-MgJEe6d4",
"digest": {
- "sha256": "bf3b603569da6dbe3d6f0e8667d346f3ac943c9d01d2fc9743ce17abeb1547fb"
+ "sha256": "b06695ff4f0a8158fa439b1ddf224b58d344606d400885c177390d09506e8e4c"
}
},
{
- "@id": "urn:31c406c9-e772-4346-bc0d-e20ecfc2a8a8",
+ "@id": "bids::cluster_zstat1",
"Label": "cluster_zstat1",
"AtLocation": "cluster_zstat1",
"digest": {
@@ -1547,33 +1597,54 @@
}
},
{
- "@id": "urn:0d0dc84d-f553-4433-a38d-2c1056077f45",
+ "@id": "bids::stats/cope2",
"Label": "cope2",
- "AtLocation": "stats/cope2",
- "digest": {
- "sha256": "5f073baabd78c1c473fed55b511738f0ffe30d9fc1f23352a16ec058daacd88c"
- }
+ "AtLocation": "stats/cope2"
},
{
- "@id": "urn:cdc2d3c8-eace-4a0f-99ee-54b0afbb95e0",
+ "@id": "bids::cluster_mask_zstat2",
"Label": "cluster_mask_zstat2",
"AtLocation": "cluster_mask_zstat2",
- "GeneratedBy": "urn:b68b9bc1-27cc-4c62-9d49-e1f70f7aa3a0",
+ "GeneratedBy": "urn:cluster-Xfz11U8L",
"digest": {
"sha256": "b88bb3cd4d809827a5c0a45cb4f6aac570cb25b7e056d5986d81d879548da121"
}
},
{
- "@id": "urn:b5870dff-e3fe-4ef7-a78c-3f71f29e7942",
+ "@id": "bids::thresh_zstat2",
+ "Label": "thresh_zstat2",
+ "AtLocation": "thresh_zstat2",
+ "GeneratedBy": "urn:cluster-Xfz11U8L",
+ "digest": {
+ "sha256": "fe707ed68d72f4376668be45a2030f2d00fa81534a3e95bf92b6a499fa8595bd"
+ }
+ },
+ {
+ "@id": "bids::lmax_zstat2.txt",
+ "Label": "lmax_zstat2.txt",
+ "AtLocation": "lmax_zstat2.txt",
+ "GeneratedBy": "urn:cluster-Xfz11U8L",
+ "digest": {
+ "sha256": "23ca5266a11743c7252c1758989cf555126dd598ae07080cf11f0a7c9e8a988b"
+ }
+ },
+ {
+ "@id": "bids::stats/cope2",
"Label": "cope2",
"AtLocation": "stats/cope2",
- "GeneratedBy": "urn:b68b9bc1-27cc-4c62-9d49-e1f70f7aa3a0",
+ "GeneratedBy": "urn:cluster-Xfz11U8L"
+ },
+ {
+ "@id": "bids::cluster_zstat2.txt",
+ "Label": "cluster_zstat2.txt",
+ "AtLocation": "cluster_zstat2.txt",
+ "GeneratedBy": "urn:cluster-Xfz11U8L",
"digest": {
- "sha256": "5f073baabd78c1c473fed55b511738f0ffe30d9fc1f23352a16ec058daacd88c"
+ "sha256": "05b4675c829a96e029b38d828f0160bb2299d2d76d7c1248cd45119f0c6c9c2e"
}
},
{
- "@id": "urn:a5a99aec-f69e-4cea-b407-27243deea155",
+ "@id": "bids::cluster_zstat2",
"Label": "cluster_zstat2",
"AtLocation": "cluster_zstat2",
"digest": {
@@ -1581,33 +1652,54 @@
}
},
{
- "@id": "urn:cd620add-4300-4d26-8e71-f9bd37cb0b8e",
+ "@id": "bids::stats/cope3",
"Label": "cope3",
- "AtLocation": "stats/cope3",
- "digest": {
- "sha256": "4f5e165fb3b62e5ef5397e9f93b4572ba23f3ffe3c9f118e8a2a9cba52e2fe0e"
- }
+ "AtLocation": "stats/cope3"
},
{
- "@id": "urn:6318eb1f-583c-409c-91e4-51a47494e702",
+ "@id": "bids::cluster_mask_zstat3",
"Label": "cluster_mask_zstat3",
"AtLocation": "cluster_mask_zstat3",
- "GeneratedBy": "urn:dd90df62-1518-4a69-b1cd-6b31c2c95e2f",
+ "GeneratedBy": "urn:cluster-YJuz1prR",
"digest": {
"sha256": "fac31b7cc91c4dbb519375fa9238cfde00689381b0783d7e3b623a937b9f51d0"
}
},
{
- "@id": "urn:96707788-783b-4a32-88cc-425b7e5cc0a2",
+ "@id": "bids::thresh_zstat3",
+ "Label": "thresh_zstat3",
+ "AtLocation": "thresh_zstat3",
+ "GeneratedBy": "urn:cluster-YJuz1prR",
+ "digest": {
+ "sha256": "d0f88769369dc8215d7373817e8f9a48482b508bb9deb2ca29904069bb23f484"
+ }
+ },
+ {
+ "@id": "bids::lmax_zstat3.txt",
+ "Label": "lmax_zstat3.txt",
+ "AtLocation": "lmax_zstat3.txt",
+ "GeneratedBy": "urn:cluster-YJuz1prR",
+ "digest": {
+ "sha256": "9786cf311d8427bc717d3d91faa64a67cb151e8e40043e6cc30e896b724f55f2"
+ }
+ },
+ {
+ "@id": "bids::stats/cope3",
"Label": "cope3",
"AtLocation": "stats/cope3",
- "GeneratedBy": "urn:dd90df62-1518-4a69-b1cd-6b31c2c95e2f",
+ "GeneratedBy": "urn:cluster-YJuz1prR"
+ },
+ {
+ "@id": "bids::cluster_zstat3.txt",
+ "Label": "cluster_zstat3.txt",
+ "AtLocation": "cluster_zstat3.txt",
+ "GeneratedBy": "urn:cluster-YJuz1prR",
"digest": {
- "sha256": "4f5e165fb3b62e5ef5397e9f93b4572ba23f3ffe3c9f118e8a2a9cba52e2fe0e"
+ "sha256": "edeacd33c60c6b43daae0c296f32ca021cca90824ee868b061f1ac10758f807f"
}
},
{
- "@id": "urn:8a7f70e5-e173-4ec2-944c-7b27e4f9ec29",
+ "@id": "bids::cluster_zstat3",
"Label": "cluster_zstat3",
"AtLocation": "cluster_zstat3",
"digest": {
@@ -1615,16 +1707,43 @@
}
},
{
- "@id": "urn:18e2f45e-748e-4659-9dd3-fd58912f36ba",
+ "@id": "bids::cluster_mask_zfstat1",
"Label": "cluster_mask_zfstat1",
"AtLocation": "cluster_mask_zfstat1",
- "GeneratedBy": "urn:6e133963-adde-4100-b5d9-8049067b311e",
+ "GeneratedBy": "urn:cluster-cFqbWSOQ",
"digest": {
"sha256": "3523a5abe83ae8c76dd74f74632bc34163aac475152d48a6b79f37eca7dfe022"
}
},
{
- "@id": "urn:dfea9359-ff55-4f9f-80a3-b053d6b53085",
+ "@id": "bids::thresh_zfstat1",
+ "Label": "thresh_zfstat1",
+ "AtLocation": "thresh_zfstat1",
+ "GeneratedBy": "urn:cluster-cFqbWSOQ",
+ "digest": {
+ "sha256": "e4e927e247bdf8ff3b58b41cbb9db7643b27df1f7578c506950eb4b1ca2d0031"
+ }
+ },
+ {
+ "@id": "bids::lmax_zfstat1.txt",
+ "Label": "lmax_zfstat1.txt",
+ "AtLocation": "lmax_zfstat1.txt",
+ "GeneratedBy": "urn:cluster-cFqbWSOQ",
+ "digest": {
+ "sha256": "f6140171309069ed9586f94b07f187a4bbea683c429dc6a5558047a484c5e8a1"
+ }
+ },
+ {
+ "@id": "bids::cluster_zfstat1.txt",
+ "Label": "cluster_zfstat1.txt",
+ "AtLocation": "cluster_zfstat1.txt",
+ "GeneratedBy": "urn:cluster-cFqbWSOQ",
+ "digest": {
+ "sha256": "0b5d4fcb253267ddae2859bc1226696992a2f6db2dba10d35c80399bd51477d4"
+ }
+ },
+ {
+ "@id": "bids::cluster_zfstat1",
"Label": "cluster_zfstat1",
"AtLocation": "cluster_zfstat1",
"digest": {
@@ -1632,25 +1751,25 @@
}
},
{
- "@id": "urn:854a0da7-0140-4007-b23a-63c8036c2338",
+ "@id": "bids::rendered_thresh_zstat1",
"Label": "rendered_thresh_zstat1",
"AtLocation": "rendered_thresh_zstat1",
- "GeneratedBy": "urn:48891029-b785-4f4f-8860-7054ddcf78ca",
+ "GeneratedBy": "urn:overlay-J0LVToUU",
"digest": {
"sha256": "de5b9d44d95f4252f491eb45c76a0ae2b4d2c75b58664fc0df7d9153810c0bf6"
}
},
{
- "@id": "urn:dee38932-e432-45ac-9034-ec463c0c71d4",
+ "@id": "bids::rendered_thresh_zstat1.png",
"Label": "rendered_thresh_zstat1.png",
"AtLocation": "rendered_thresh_zstat1.png",
- "GeneratedBy": "urn:270d4b00-919d-46a5-8bd3-ba90ab4de77c",
+ "GeneratedBy": "urn:slicer-WIJeQdex",
"digest": {
"sha256": "15d6a8bf7a902df8c5feeb7468a3d0caacf9eb3067c0840c2f4763f5e2301527"
}
},
{
- "@id": "urn:f653dfb6-d7f8-4895-8e06-573f04121f8c",
+ "@id": "bids::/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif",
"Label": "ramp.gif",
"AtLocation": "/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif",
"digest": {
@@ -1658,82 +1777,82 @@
}
},
{
- "@id": "urn:50551edf-7b41-4868-96c8-6f50ef1afcc5",
+ "@id": "bids::.ramp.gif",
"Label": ".ramp.gif",
"AtLocation": ".ramp.gif",
- "GeneratedBy": "urn:6c7c5ceb-8f8a-4126-931f-3e45b2fc80f0",
+ "GeneratedBy": "urn:cp-ZB6SRpaR",
"digest": {
"sha256": "93f4284ccb854d5a41401d9360a13223017b67479cb289a33d83836922e028a4"
}
},
{
- "@id": "urn:abaf539c-8c53-4d5b-81dd-c5c8dd66cef5",
+ "@id": "bids::rendered_thresh_zstat2",
"Label": "rendered_thresh_zstat2",
"AtLocation": "rendered_thresh_zstat2",
- "GeneratedBy": "urn:bc4ed7c6-6801-4fc5-8242-4cca359734a6",
+ "GeneratedBy": "urn:overlay-ezv2kA1Z",
"digest": {
"sha256": "b988cb8ba2b862b6fa88f223fcd3279c70e2ea217477bd1ec664c023be079cad"
}
},
{
- "@id": "urn:f6360992-6c3c-4790-874c-7469907d535a",
+ "@id": "bids::rendered_thresh_zstat2.png",
"Label": "rendered_thresh_zstat2.png",
"AtLocation": "rendered_thresh_zstat2.png",
- "GeneratedBy": "urn:ca4ee33e-ec88-4ec0-9662-9065d7cc4734",
+ "GeneratedBy": "urn:slicer-d8V0x0iz",
"digest": {
"sha256": "0d60298d9eb509148075cbac8a22e6a95de919f17a069624fb42f86c29e1e199"
}
},
{
- "@id": "urn:11801d7e-8459-47fd-bfb3-024e9bf5501d",
+ "@id": "bids::rendered_thresh_zstat3",
"Label": "rendered_thresh_zstat3",
"AtLocation": "rendered_thresh_zstat3",
- "GeneratedBy": "urn:fff5c382-53bd-4b97-a58a-1fe3dbded5df",
+ "GeneratedBy": "urn:overlay-N8TFYaTb",
"digest": {
"sha256": "baac012afec8f9407f78df00034058a245d984bb1b1f86843d46a04a7eaa5b3d"
}
},
{
- "@id": "urn:68638674-b35e-4ee2-ac81-93b0eed1dc4a",
+ "@id": "bids::rendered_thresh_zstat3.png",
"Label": "rendered_thresh_zstat3.png",
"AtLocation": "rendered_thresh_zstat3.png",
- "GeneratedBy": "urn:544d0fc1-89f3-4a63-b15c-b845ef1a2a66",
+ "GeneratedBy": "urn:slicer-ziPQUrhv",
"digest": {
"sha256": "39c4457a05e454cfbb59862f8e62681c66ad6ce780ba01c4b55dd12e59c43637"
}
},
{
- "@id": "urn:5bcbb31a-da10-4a45-b7eb-04dac91e5b3c",
+ "@id": "bids::rendered_thresh_zfstat1",
"Label": "rendered_thresh_zfstat1",
"AtLocation": "rendered_thresh_zfstat1",
- "GeneratedBy": "urn:8cb2d405-f78e-461f-a680-56abf991cd9e",
+ "GeneratedBy": "urn:overlay-SHScIMUN",
"digest": {
"sha256": "91b064bdcf6f2eec9fb87c161e52152f3343ed4de0cf5e5ba6153f970250aa5f"
}
},
{
- "@id": "urn:c105ae15-b7b6-45a1-998a-edabc1944c3e",
+ "@id": "bids::rendered_thresh_zfstat1.png",
"Label": "rendered_thresh_zfstat1.png",
"AtLocation": "rendered_thresh_zfstat1.png",
- "GeneratedBy": "urn:8915d9d3-e7d2-49a6-96a2-bf9c91c8ee61",
+ "GeneratedBy": "urn:slicer-fXpdJStv",
"digest": {
"sha256": "c4c15c63489169ecb9747342259541d6b999ff25baaedfa066ecd1c00b761067"
}
},
{
- "@id": "urn:b1d963a1-adde-478c-9572-0e6491214316",
+ "@id": "bids::tsplot",
"Label": "tsplot",
"AtLocation": "tsplot",
- "GeneratedBy": "urn:6f371063-f2c7-47dd-8a3b-6d0d986e115e",
+ "GeneratedBy": "urn:makedire-vSBvvW3S",
"digest": {
"sha256": "2a74042f4edf02288edf16961307f741651efb4346e102a04b7603e781d1625e"
}
},
{
- "@id": "urn:1b27e140-7a1e-44d0-b08b-6050245e2a3d",
+ "@id": "bids::tsplot",
"Label": "tsplot",
"AtLocation": "tsplot",
- "GeneratedBy": "urn:49ef5b81-19e3-4c4e-b711-c5adb8849ec0",
+ "GeneratedBy": "urn:tsplot-C8ocrLYQ",
"digest": {
"sha256": "2a74042f4edf02288edf16961307f741651efb4346e102a04b7603e781d1625e"
}
diff --git a/examples/from_parsers/fsl/fsl_hrf_fir_report_log.png b/examples/from_parsers/fsl/fsl_hrf_fir_report_log.png
index c9e74c2e8..83862052c 100644
Binary files a/examples/from_parsers/fsl/fsl_hrf_fir_report_log.png and b/examples/from_parsers/fsl/fsl_hrf_fir_report_log.png differ
diff --git a/examples/from_parsers/fsl/fsl_hrf_gammadiff_report_log.html b/examples/from_parsers/fsl/fsl_hrf_gammadiff_report_log.html
index 842258e0c..a722a6f3c 100644
--- a/examples/from_parsers/fsl/fsl_hrf_gammadiff_report_log.html
+++ b/examples/from_parsers/fsl/fsl_hrf_gammadiff_report_log.html
@@ -35,20 +35,20 @@ Progress Report / Log
326946
Initialisation
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
Total original volumes = 104
/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1
Preprocessing:Stage 1
-/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90
+/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/example_func.nii.gz -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90
Option -F ( FEAT version parameter ) selected with argument "6.00"
Option -d ( output directory ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat"
Option -l ( logfile )input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/logs/feat2_pre"
Option -R ( html unwarping report ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/report_unwarp.html"
Option -r ( html registration report ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/report_reg.html"
Option -i ( main input ) input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/example_func.nii.gz"
-Option -h ( high-res structural image ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
+Option -h ( high-res structural image ) selected with argument "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
Option -w ( highres dof ) selected with argument "BBR"
Option -x ( highres search ) selected with argument "90"
Option -s ( standard image ) selected with argument "/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain"
@@ -59,10 +59,10 @@ Progress Report / Log
/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/reg
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head
did not find file: example_func2highres.mat. Generating transform.
@@ -128,9 +128,9 @@ Progress Report / Log
/bin/rm -rf prefiltered_func_data*
Stats
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
/usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con
Log directory is: stats
diff --git a/examples/from_parsers/fsl/fsl_hrf_gammadiff_report_log.jsonld b/examples/from_parsers/fsl/fsl_hrf_gammadiff_report_log.jsonld
index 06ef7c190..9b94b027f 100644
--- a/examples/from_parsers/fsl/fsl_hrf_gammadiff_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_hrf_gammadiff_report_log.jsonld
@@ -4,575 +4,584 @@
"Records": {
"Software": [
{
- "@id": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:fsl-rMiU3aNs",
"@type": "prov:SoftwareAgent",
"Label": "FSL",
- "Version": "xxx"
+ "Version": "xxx",
+ "AltIdentifier": "RRID:SCR_002823"
}
],
"Activities": [
{
- "@id": "urn:8c6a8fad-4a10-4e63-902e-cb713291e98b",
+ "@id": "urn:fslmaths-rEBajozz",
"Label": "fslmaths",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
"Used": [
- "urn:debeb16c-5b95-4d17-bf55-7b5f67d88815"
+ "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold"
]
},
{
- "@id": "urn:2a27b562-f2c8-4d65-87e7-8324ee4b0b9a",
+ "@id": "urn:fslroi-UkZikbZ1",
"Label": "fslroi",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1",
"Used": [
- "urn:ac72bb00-f067-43c0-93f1-c19535495c63"
+ "bids::prefiltered_func_data"
]
},
{
- "@id": "urn:ae29f890-cf49-4621-9cbe-6eeeab313c8e",
+ "@id": "urn:mainfeat-xtuN7r3U",
"Label": "mainfeatreg",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/example_func.nii.gz -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
"Used": [
- "urn:0a2bd5ea-a64e-42a0-ae31-150e7a1257b4",
- "urn:b9dd4585-53b2-46d3-86ef-605a4028c435",
- "urn:fad38cb7-5e1a-4f82-ac2d-4f0cc81b0b2a"
+ "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/example_func.nii.gz",
+ "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain",
+ "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
]
},
{
- "@id": "urn:4ece4936-b75e-4cdf-a4fa-c1748c3364db",
+ "@id": "urn:makedire-f8e3PQFv",
"Label": "Make directory",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/reg",
"Used": []
},
{
- "@id": "urn:d3e9b075-7f99-4789-a358-bfc920fed3c3",
+ "@id": "urn:fslmaths-XsmDlg5h",
"Label": "fslmaths",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
"Used": [
- "urn:0a2bd5ea-a64e-42a0-ae31-150e7a1257b4"
+ "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
]
},
{
- "@id": "urn:51a344a6-d5d1-479d-802c-4912345b4574",
+ "@id": "urn:fslmaths-UULvGrJ8",
"Label": "fslmaths",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
"Used": [
- "urn:b25b166c-87b5-473b-a60f-ad6c25f3622e"
+ "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w"
]
},
{
- "@id": "urn:1435c1bd-2e36-477a-b417-5f57093bedde",
+ "@id": "urn:epireg-SVZAbVXX",
"Label": "epi_reg",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "/usr/local/packages/fsl-5.0.10/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres",
- "Used": []
+ "Used": [
+ "bids::example_func",
+ "bids::highres",
+ "bids::highres_head"
+ ]
},
{
- "@id": "urn:8a3f7a24-c685-4532-be83-851ae63ca6ad",
+ "@id": "urn:convertx-9dX90OeD",
"Label": "convert_xfm",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "/usr/local/packages/fsl-5.0.10/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat",
"Used": [
- "urn:aa250c9a-a324-4cbb-bd5b-2eb21542af2a"
+ "bids::example_func2highres.mat"
]
},
{
- "@id": "urn:0f920aab-f8e2-487a-b2c8-77fdd14ff21c",
+ "@id": "urn:slicer-Rxdnb6PS",
"Label": "slicer",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:aa69b8f4-4148-47a4-a8fa-9dfb4d9aae01",
- "urn:d9c5d9f6-d211-47e7-993d-ca16b373b789"
+ "bids::example_func2highres",
+ "bids::highres"
]
},
{
- "@id": "urn:84a2fd0f-cef6-4ec3-a2b4-defce849f38f",
+ "@id": "urn:pngappen-Lbj7szgB",
"Label": "pngappend",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres1.png",
"Used": [
- "urn:20c82882-8ba2-4c91-9eb1-ab785bfec6fb",
- "urn:246c334f-7c51-4acd-9d77-7d54242fd2d7",
- "urn:346f2f07-2990-484f-9e23-d74ce972f99a",
- "urn:3a2c9ee8-541c-4bc9-8e5b-13a00b8688c7",
- "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
- "urn:549cda09-ef87-4910-a306-2c99b47b18e2",
- "urn:a1f10b4f-25b3-4000-b3f6-31730c142bdc",
- "urn:adee1c78-e6cf-4a0e-9264-2ceaceb54ee0",
- "urn:b1b7f674-9292-490a-9b80-8d2a29faf9d4",
- "urn:b1e7295b-8203-48e0-ad4e-03135f3e8d6c",
- "urn:b96fb921-457b-4883-9be8-b07579a040e0",
- "urn:ec251330-d3c1-4154-8da1-e690bdf5e956"
+ "bids::sla.png",
+ "bids::slb.png",
+ "bids::slc.png",
+ "bids::sld.png",
+ "bids::sle.png",
+ "bids::slf.png",
+ "bids::slg.png",
+ "bids::slh.png",
+ "bids::sli.png",
+ "bids::slj.png",
+ "bids::slk.png",
+ "bids::sll.png"
]
},
{
- "@id": "urn:b9336d7f-7863-4a9c-bda6-7cfde4a6b9e8",
+ "@id": "urn:slicer-Z3jvXsRD",
"Label": "slicer",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:aa69b8f4-4148-47a4-a8fa-9dfb4d9aae01",
- "urn:d9c5d9f6-d211-47e7-993d-ca16b373b789"
+ "bids::example_func2highres",
+ "bids::highres"
]
},
{
- "@id": "urn:b9ea35db-d498-431f-88a6-0669481d8bd2",
+ "@id": "urn:pngappen-51oaKZzY",
"Label": "pngappend",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres2.png",
"Used": [
- "urn:20c82882-8ba2-4c91-9eb1-ab785bfec6fb",
- "urn:246c334f-7c51-4acd-9d77-7d54242fd2d7",
- "urn:346f2f07-2990-484f-9e23-d74ce972f99a",
- "urn:3a2c9ee8-541c-4bc9-8e5b-13a00b8688c7",
- "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
- "urn:549cda09-ef87-4910-a306-2c99b47b18e2",
- "urn:a1f10b4f-25b3-4000-b3f6-31730c142bdc",
- "urn:adee1c78-e6cf-4a0e-9264-2ceaceb54ee0",
- "urn:b1b7f674-9292-490a-9b80-8d2a29faf9d4",
- "urn:b1e7295b-8203-48e0-ad4e-03135f3e8d6c",
- "urn:b96fb921-457b-4883-9be8-b07579a040e0",
- "urn:ec251330-d3c1-4154-8da1-e690bdf5e956"
+ "bids::sla.png",
+ "bids::slb.png",
+ "bids::slc.png",
+ "bids::sld.png",
+ "bids::sle.png",
+ "bids::slf.png",
+ "bids::slg.png",
+ "bids::slh.png",
+ "bids::sli.png",
+ "bids::slj.png",
+ "bids::slk.png",
+ "bids::sll.png"
]
},
{
- "@id": "urn:1ab1395a-bd77-4c9c-97e0-6e01726808ce",
+ "@id": "urn:pngappen-lbmNy7oN",
"Label": "pngappend",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend example_func2highres1.png example_func2highres2.png example_func2highres.png",
"Used": [
- "urn:7f84ea18-06fe-4c30-89d2-ddfcf648b295",
- "urn:efbf63f3-1453-44d7-943f-5ad271b15594"
+ "bids::example_func2highres1.png",
+ "bids::example_func2highres2.png"
]
},
{
- "@id": "urn:f10a5ad8-0374-4fc2-ad92-70ddf88959c8",
+ "@id": "urn:rm-5vefOeJG",
"Label": "rm",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "/bin/rm -f sl?.png example_func2highres2.png",
"Used": [
- "urn:714cd3ec-0190-4792-93f3-8c566734b8a4",
- "urn:efbf63f3-1453-44d7-943f-5ad271b15594"
+ "bids::example_func2highres2.png",
+ "bids::sl?.png"
]
},
{
- "@id": "urn:9dce6e79-71ef-43e8-997d-4841605ad7c3",
+ "@id": "urn:rm-vE1cgYfE",
"Label": "rm",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "/bin/rm example_func2highres1.png",
"Used": [
- "urn:7f84ea18-06fe-4c30-89d2-ddfcf648b295"
+ "bids::example_func2highres1.png"
]
},
{
- "@id": "urn:f1ebdf2e-24f8-49fd-8cf4-c135b087159d",
+ "@id": "urn:mcflirt-mpdbH7Bm",
"Label": "mcflirt",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "/usr/local/packages/fsl-5.0.10/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs -spline_final",
"Used": [
- "urn:ac72bb00-f067-43c0-93f1-c19535495c63"
+ "bids::prefiltered_func_data"
]
},
{
- "@id": "urn:0723034d-fc73-4fc4-9deb-605b9add0ee7",
+ "@id": "urn:makedire-J2lSormN",
"Label": "Make directory",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "/bin/mkdir -p mc",
"Used": []
},
{
- "@id": "urn:0134c831-73b9-47b6-80a6-41535abaf825",
+ "@id": "urn:mv-xhrmBOA4",
"Label": "mv",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "/bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc",
"Used": [
- "urn:086568a2-e38c-44a5-ac87-7bbb46fb1215",
- "urn:64b3106f-d986-42e5-bea5-ad79de7eed00",
- "urn:76f8224d-55bf-46a5-bc7f-2973c300c08f",
- "urn:8ae4d11f-5d8d-474d-b00b-f7e5c882df15",
- "urn:9f26b129-9763-4b04-860e-3f44465c99ad",
- "urn:e648781f-7a62-4523-8c8c-24cc9bfea61a"
+ "bids::prefiltered_func_data_mcf.mat",
+ "bids::prefiltered_func_data_mcf.par",
+ "bids::prefiltered_func_data_mcf_abs.rms",
+ "bids::prefiltered_func_data_mcf_abs_mean.rms",
+ "bids::prefiltered_func_data_mcf_rel.rms",
+ "bids::prefiltered_func_data_mcf_rel_mean.rms"
]
},
{
- "@id": "urn:91ccbfe0-c5ec-43f2-92a1-79ae778813a9",
+ "@id": "urn:fsltsplo-BXivmu30",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png",
"Used": [
- "urn:e648781f-7a62-4523-8c8c-24cc9bfea61a"
+ "bids::prefiltered_func_data_mcf.par"
]
},
{
- "@id": "urn:1d1b3389-23b1-48cb-9e01-94d17230ada3",
+ "@id": "urn:fsltsplo-Wjiiv0E3",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png",
"Used": [
- "urn:e648781f-7a62-4523-8c8c-24cc9bfea61a"
+ "bids::prefiltered_func_data_mcf.par"
]
},
{
- "@id": "urn:4dc466e1-b429-43bb-b880-add7232b7347",
+ "@id": "urn:fsltsplo-Fzexq6k9",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png",
"Used": [
- "urn:f33a292b-a905-408f-ba76-441a2058a27b"
+ "bids::prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms"
]
},
{
- "@id": "urn:95b6a627-a7cb-4607-b603-d359f8b3c75c",
+ "@id": "urn:fslmaths-a5rzZke7",
"Label": "fslmaths",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func",
"Used": [
- "urn:3fd6b10a-ad16-41ce-987c-d9b67e25d95e"
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:19cea046-4b73-4065-8d07-f2ab4cd05577",
+ "@id": "urn:bet2-udXsp4cv",
"Label": "bet2",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "/usr/local/packages/fsl-5.0.10/bin/bet2 mean_func mask -f 0.3 -n -m",
"Used": [
- "urn:c3acf82f-0adc-4874-bd69-b28b507542c7"
+ "bids::mean_func"
]
},
{
- "@id": "urn:7cd59bc5-33fb-4897-b2bb-5cfee20798ee",
+ "@id": "urn:immv-ZYFWZ1Gn",
"Label": "immv",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "/usr/local/packages/fsl-5.0.10/bin/immv mask_mask mask",
"Used": [
- "urn:d254e790-3eb0-457a-a728-94483f898737"
+ "bids::mask_mask"
]
},
{
- "@id": "urn:920dddce-28c6-421c-882c-9a68550b6b34",
+ "@id": "urn:fslmaths-I1OS1SJP",
"Label": "fslmaths",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet",
"Used": [
- "urn:3fd6b10a-ad16-41ce-987c-d9b67e25d95e",
- "urn:b5bab357-1440-40f7-a07a-e81de6dee8b8"
+ "bids::mask",
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:aca48b64-0f58-44c1-bf54-eb7e9089f5b9",
+ "@id": "urn:fslstats-wezyh368",
"Label": "fslstats",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_bet -p 2 -p 98",
"Used": [
- "urn:a4f12a49-cdd0-4f79-8ec4-1e30561765ee"
+ "bids::prefiltered_func_data_bet"
]
},
{
- "@id": "urn:3f64e75a-698c-4349-9f6a-7bd538d135df",
+ "@id": "urn:fslmaths-7snwdwRw",
"Label": "fslmaths",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_bet -thr 74.4585571 -Tmin -bin mask -odt char",
"Used": [
- "urn:a4f12a49-cdd0-4f79-8ec4-1e30561765ee"
+ "bids::prefiltered_func_data_bet"
]
},
{
- "@id": "urn:5c0e3a05-6e09-4bc9-bb52-e8c4c019ce22",
+ "@id": "urn:fslstats-4Qi1I0em",
"Label": "fslstats",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_mcf -k mask -p 50",
"Used": [
- "urn:3fd6b10a-ad16-41ce-987c-d9b67e25d95e"
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:71f1ade3-2b62-4c18-a187-26d24d3a7f1a",
+ "@id": "urn:fslmaths-8b8qCEmy",
"Label": "fslmaths",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -dilF mask",
"Used": [
- "urn:b5bab357-1440-40f7-a07a-e81de6dee8b8"
+ "bids::mask"
]
},
{
- "@id": "urn:9fc79763-50ca-44d0-af53-ea663f18a6c9",
+ "@id": "urn:fslmaths-exNmgmHg",
"Label": "fslmaths",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh",
"Used": [
- "urn:3fd6b10a-ad16-41ce-987c-d9b67e25d95e",
- "urn:b5bab357-1440-40f7-a07a-e81de6dee8b8"
+ "bids::mask",
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:8abe0474-66d5-4e8d-b799-4ca935562832",
+ "@id": "urn:fslmaths-9zvUeSVt",
"Label": "fslmaths",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func",
"Used": [
- "urn:a6e50cb0-3790-46cd-97c4-6108afc39afe"
+ "bids::prefiltered_func_data_thresh"
]
},
{
- "@id": "urn:9c9633d5-e312-4218-beaf-ee48cdb1b684",
+ "@id": "urn:susan-hUivqJAf",
"Label": "susan",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "/usr/local/packages/fsl-5.0.10/bin/susan prefiltered_func_data_thresh 445.8289035 2.54777070064 3 1 1 mean_func 445.8289035 prefiltered_func_data_smooth",
"Used": [
- "urn:a6e50cb0-3790-46cd-97c4-6108afc39afe"
+ "bids::prefiltered_func_data_thresh"
]
},
{
- "@id": "urn:8a4b04a5-355c-436b-a9cd-d1ba1623a3de",
+ "@id": "urn:fslmaths-GuMPegWU",
"Label": "fslmaths",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth",
"Used": [
- "urn:b5bab357-1440-40f7-a07a-e81de6dee8b8",
- "urn:e6777837-2f7c-4cb1-ab0f-9ad45c985501"
+ "bids::mask",
+ "bids::prefiltered_func_data_smooth"
]
},
{
- "@id": "urn:6f513969-f03e-43be-a09b-5dd6b976de3c",
+ "@id": "urn:fslmaths-Uywrv3qZ",
"Label": "fslmaths",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mul 16.8225970571 prefiltered_func_data_intnorm",
"Used": [
- "urn:e6777837-2f7c-4cb1-ab0f-9ad45c985501"
+ "bids::prefiltered_func_data_smooth"
]
},
{
- "@id": "urn:9734bf62-20af-427c-a298-49437e993740",
+ "@id": "urn:fslmaths-UCRih4mS",
"Label": "fslmaths",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean",
"Used": [
- "urn:617710f9-1f1a-416f-ae6b-d2994da8000b"
+ "bids::prefiltered_func_data_intnorm"
]
},
{
- "@id": "urn:dbb688bc-e370-4644-9913-9ae6f2e86ecb",
+ "@id": "urn:fslmaths-S1K6eyBe",
"Label": "fslmaths",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -bptf 15.0 -1 -add tempMean prefiltered_func_data_tempfilt",
"Used": [
- "urn:617710f9-1f1a-416f-ae6b-d2994da8000b",
- "urn:8683b331-474b-43db-938a-3fb2df8077ff"
+ "bids::prefiltered_func_data_intnorm",
+ "bids::tempMean"
]
},
{
- "@id": "urn:49b19b62-af92-47fa-8c77-2337c2f05775",
+ "@id": "urn:imrm-P5LbywF2",
"Label": "imrm",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "/usr/local/packages/fsl-5.0.10/bin/imrm tempMean",
"Used": [
- "urn:8683b331-474b-43db-938a-3fb2df8077ff"
+ "bids::tempMean"
]
},
{
- "@id": "urn:2aafb6ce-d198-41d6-ab3e-16b28401a64a",
+ "@id": "urn:fslmaths-iqrY5SnA",
"Label": "fslmaths",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data",
"Used": [
- "urn:f9d61dcc-d611-48da-8113-8e5d940d45bf"
+ "bids::prefiltered_func_data_tempfilt"
]
},
{
- "@id": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "@id": "urn:fslmaths-dabqvNXy",
"Label": "fslmaths",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths filtered_func_data -Tmean mean_func",
"Used": [
- "urn:678f852c-890c-4abc-bf0a-1e737c5189bc"
+ "bids::filtered_func_data"
]
},
{
- "@id": "urn:8c858fbe-04ee-48dc-bab5-c1ae2ef9159c",
+ "@id": "urn:rm-Q738Srjt",
"Label": "rm",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "/bin/rm -rf prefiltered_func_data*",
"Used": [
- "urn:2fd43732-f606-4c9b-a9f0-74885d47be97"
+ "bids::prefiltered_func_data*"
]
},
{
- "@id": "urn:249dda2c-c59c-44e3-9a54-ec97b2d2c422",
+ "@id": "urn:makedire-np0NfI2n",
"Label": "Make directory",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
- "@id": "urn:df27cd3b-d715-4b02-b53b-a3b58ad15509",
+ "@id": "urn:fslfixte-9tAyRn9N",
"Label": "fslFixText",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
"Used": [
- "urn:1d06d47e-8469-4b81-9404-fbc57017ad23"
+ "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt"
]
},
{
- "@id": "urn:cb1c0160-0e2f-4a93-b70f-8f61530cdb27",
+ "@id": "urn:makedire-mO0uYErJ",
"Label": "Make directory",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
- "@id": "urn:5fee107f-6a26-4850-849e-b57806b77df2",
+ "@id": "urn:fslfixte-xwMlvwHA",
"Label": "fslFixText",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
"Used": [
- "urn:03b235ce-bedb-404b-8ea4-83225a07fb37"
+ "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt"
]
},
{
- "@id": "urn:46e28345-fd6e-4493-8d14-61325dd2787f",
+ "@id": "urn:filmgls-bPmqxXVL",
"Label": "film_gls",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
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- "Used": []
+ "Used": [
+ "bids::design.con",
+ "bids::design.mat",
+ "bids::filtered_func_data",
+ "bids::stats"
+ ]
},
{
- "@id": "urn:0bb5d0b3-84fd-4dd6-86ca-6e39ee7c9ca2",
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- "Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 102 -m mask -r stats/res4d > stats/smoothness",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 102 -m mask -r stats/res4d > stats/smoothness",
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- "urn:b5bab357-1440-40f7-a07a-e81de6dee8b8"
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+ "bids::stats/res4d"
]
},
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- "urn:b5bab357-1440-40f7-a07a-e81de6dee8b8"
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+ "bids::stats/zstat1"
]
},
{
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"Used": []
},
{
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+ "AssociatedWith": "urn:fsl-rMiU3aNs",
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"Used": []
},
{
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+ "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -t 3.090232 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z --voxuncthresh -c stats/cope1 > cluster_zstat1.txt",
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- "urn:54de5eb3-f9ac-4833-886e-bf68285dca2b"
+ "bids::stats/cope1",
+ "bids::thresh_zstat1"
]
},
{
- "@id": "urn:fa5adf0f-a40a-43dc-b563-398664d6a64e",
+ "@id": "urn:cluster2-4aUMZyUO",
"Label": "cluster2html",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat1",
"Used": [
- "urn:701df0dc-45e0-40bd-9782-a2e4d6b55efa"
+ "bids::cluster_zstat1"
]
},
{
- "@id": "urn:b552aaae-f3a6-43f9-a28e-2adaa38edc2c",
+ "@id": "urn:fslstats-pInnygxp",
"Label": "fslstats",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat1 -l 0.0001 -R 2>/dev/null",
"Used": [
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+ "bids::thresh_zstat1"
]
},
{
- "@id": "urn:652558c1-a31d-4c8a-a9c3-822ea694f3d3",
+ "@id": "urn:overlay-iRpUE43m",
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- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
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"Used": []
},
{
- "@id": "urn:f4ad58dc-3808-48a2-ab28-b91512eceeb8",
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"Label": "slicer",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
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"Used": [
- "urn:98af3652-a864-476a-b2d5-059404150cbd"
+ "bids::rendered_thresh_zstat1"
]
},
{
- "@id": "urn:b1cc91c7-f921-41c1-8be7-392416eeeb13",
+ "@id": "urn:cp-yLQL77nx",
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- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "/bin/cp /usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif .ramp.gif",
"Used": [
- "urn:99cd507b-7b91-48e6-a47e-1d09955693bf"
+ "bids::/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif"
]
},
{
- "@id": "urn:a2736bdd-b58b-4fd5-b985-64805c68ad20",
+ "@id": "urn:makedire-mY11e8bD",
"Label": "Make directory",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "mkdir -p tsplot",
"Used": []
},
{
- "@id": "urn:0b2038d7-d9aa-47f4-9a7c-4fcf52ee799b",
+ "@id": "urn:tsplot-ms47hBRT",
"Label": "tsplot",
- "AssociatedWith": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "AssociatedWith": "urn:fsl-rMiU3aNs",
"Command": "/usr/local/packages/fsl-5.0.10/bin/tsplot . -f filtered_func_data -o tsplot",
"Used": []
}
],
"Entities": [
{
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+ "@id": "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold",
"Label": "sub-01_task-tonecounting_bold",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold",
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"digest": {
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}
},
{
- "@id": "urn:ac72bb00-f067-43c0-93f1-c19535495c63",
+ "@id": "bids::prefiltered_func_data",
"Label": "prefiltered_func_data",
"AtLocation": "prefiltered_func_data",
- "GeneratedBy": "urn:8c6a8fad-4a10-4e63-902e-cb713291e98b",
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{
- "@id": "urn:cfaa20a5-21e5-49c6-bfed-2d23065164c6",
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"Label": "example_func",
"AtLocation": "example_func",
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"Label": "example_func.nii.gz",
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"digest": {
@@ -580,15 +589,15 @@
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"Label": "sub-01_T1w_brain",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
+ "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
"digest": {
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"AtLocation": "/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain",
"digest": {
@@ -596,45 +605,57 @@
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"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat",
- "GeneratedBy": "urn:ae29f890-cf49-4621-9cbe-6eeeab313c8e"
+ "GeneratedBy": "urn:mainfeat-xtuN7r3U"
},
{
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"Label": "reg",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/reg",
- "GeneratedBy": "urn:4ece4936-b75e-4cdf-a4fa-c1748c3364db",
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"Label": "highres",
"AtLocation": "highres",
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- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
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- "GeneratedBy": "urn:51a344a6-d5d1-479d-802c-4912345b4574"
+ "@id": "bids::highres_head",
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+ "GeneratedBy": "urn:fslmaths-UULvGrJ8",
+ "digest": {
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"digest": {
@@ -642,267 +663,259 @@
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}
},
{
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+ "@id": "bids::example_func2highres1.png",
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"AtLocation": "example_func2highres1.png",
- "GeneratedBy": "urn:84a2fd0f-cef6-4ec3-a2b4-defce849f38f",
+ "GeneratedBy": "urn:pngappen-Lbj7szgB",
"digest": {
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}
},
{
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+ "@id": "bids::sla.png",
"Label": "sla.png",
"AtLocation": "sla.png",
- "GeneratedBy": "urn:b9336d7f-7863-4a9c-bda6-7cfde4a6b9e8",
+ "GeneratedBy": "urn:slicer-Z3jvXsRD",
"digest": {
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}
},
{
- "@id": "urn:e44fb4cb-778d-41e7-9cbc-5d6cc1a73c68",
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"Label": "slb.png",
"AtLocation": "slb.png",
- "GeneratedBy": "urn:b9336d7f-7863-4a9c-bda6-7cfde4a6b9e8",
+ "GeneratedBy": "urn:slicer-Z3jvXsRD",
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}
},
{
- "@id": "urn:3ba5cd1f-fdfc-400a-a1ae-227bdfe70c50",
+ "@id": "bids::slc.png",
"Label": "slc.png",
"AtLocation": "slc.png",
- "GeneratedBy": "urn:b9336d7f-7863-4a9c-bda6-7cfde4a6b9e8",
+ "GeneratedBy": "urn:slicer-Z3jvXsRD",
"digest": {
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}
},
{
- "@id": "urn:ee9b61ac-ad90-4f3c-96d4-1de0cc21438c",
+ "@id": "bids::sld.png",
"Label": "sld.png",
"AtLocation": "sld.png",
- "GeneratedBy": "urn:b9336d7f-7863-4a9c-bda6-7cfde4a6b9e8",
+ "GeneratedBy": "urn:slicer-Z3jvXsRD",
"digest": {
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}
},
{
- "@id": "urn:e400d490-8f67-46f0-a5ba-4a3262ea3bae",
+ "@id": "bids::sle.png",
"Label": "sle.png",
"AtLocation": "sle.png",
- "GeneratedBy": "urn:b9336d7f-7863-4a9c-bda6-7cfde4a6b9e8",
+ "GeneratedBy": "urn:slicer-Z3jvXsRD",
"digest": {
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}
},
{
- "@id": "urn:e6575988-076c-4dac-868c-1cba20f3c597",
+ "@id": "bids::slf.png",
"Label": "slf.png",
"AtLocation": "slf.png",
- "GeneratedBy": "urn:b9336d7f-7863-4a9c-bda6-7cfde4a6b9e8",
+ "GeneratedBy": "urn:slicer-Z3jvXsRD",
"digest": {
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}
},
{
- "@id": "urn:183fa34a-9df4-4380-85c5-75f4e62fa9cc",
+ "@id": "bids::slg.png",
"Label": "slg.png",
"AtLocation": "slg.png",
- "GeneratedBy": "urn:b9336d7f-7863-4a9c-bda6-7cfde4a6b9e8",
+ "GeneratedBy": "urn:slicer-Z3jvXsRD",
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}
},
{
- "@id": "urn:231abdc8-7275-44f3-86b3-b8cd318f4207",
+ "@id": "bids::slh.png",
"Label": "slh.png",
"AtLocation": "slh.png",
- "GeneratedBy": "urn:b9336d7f-7863-4a9c-bda6-7cfde4a6b9e8",
+ "GeneratedBy": "urn:slicer-Z3jvXsRD",
"digest": {
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}
},
{
- "@id": "urn:ee7debe5-41b6-4ac0-874d-e3b6c7944a04",
+ "@id": "bids::sli.png",
"Label": "sli.png",
"AtLocation": "sli.png",
- "GeneratedBy": "urn:b9336d7f-7863-4a9c-bda6-7cfde4a6b9e8",
+ "GeneratedBy": "urn:slicer-Z3jvXsRD",
"digest": {
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}
},
{
- "@id": "urn:86a2c39f-8c70-46ea-a91d-e12263267963",
+ "@id": "bids::slj.png",
"Label": "slj.png",
"AtLocation": "slj.png",
- "GeneratedBy": "urn:b9336d7f-7863-4a9c-bda6-7cfde4a6b9e8",
+ "GeneratedBy": "urn:slicer-Z3jvXsRD",
"digest": {
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}
},
{
- "@id": "urn:65603e13-f0b7-4788-91a0-dff5363681c9",
+ "@id": "bids::slk.png",
"Label": "slk.png",
"AtLocation": "slk.png",
- "GeneratedBy": "urn:b9336d7f-7863-4a9c-bda6-7cfde4a6b9e8",
+ "GeneratedBy": "urn:slicer-Z3jvXsRD",
"digest": {
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}
},
{
- "@id": "urn:4d5696da-b769-4e33-9d69-07fac85ea539",
+ "@id": "bids::sll.png",
"Label": "sll.png",
"AtLocation": "sll.png",
- "GeneratedBy": "urn:b9336d7f-7863-4a9c-bda6-7cfde4a6b9e8",
+ "GeneratedBy": "urn:slicer-Z3jvXsRD",
"digest": {
"sha256": "0b9c965bbea7bb7d1f251ea0f2973f485727fbbc91357e30aee25ff9869f5009"
}
},
{
- "@id": "urn:efbf63f3-1453-44d7-943f-5ad271b15594",
+ "@id": "bids::example_func2highres2.png",
"Label": "example_func2highres2.png",
"AtLocation": "example_func2highres2.png",
- "GeneratedBy": "urn:b9ea35db-d498-431f-88a6-0669481d8bd2",
+ "GeneratedBy": "urn:pngappen-51oaKZzY",
"digest": {
"sha256": "4e622cf27c5f4d28786e7ccdc4e88253f4e5a855818d597ceec90fa78f0d437c"
}
},
{
- "@id": "urn:3474c8cd-db1d-499b-a758-30039fb6ad37",
+ "@id": "bids::example_func2highres.png",
"Label": "example_func2highres.png",
"AtLocation": "example_func2highres.png",
- "GeneratedBy": "urn:1ab1395a-bd77-4c9c-97e0-6e01726808ce",
+ "GeneratedBy": "urn:pngappen-lbmNy7oN",
"digest": {
"sha256": "31960f4162da045cb9b73a0eb3cac33f09d5a2ec1f146f1e457c4a59f478f3e8"
}
},
{
- "@id": "urn:714cd3ec-0190-4792-93f3-8c566734b8a4",
+ "@id": "bids::sl?.png",
"Label": "sl?.png",
"AtLocation": "sl?.png",
"digest": {
@@ -910,25 +923,25 @@
}
},
{
- "@id": "urn:3fd6b10a-ad16-41ce-987c-d9b67e25d95e",
+ "@id": "bids::prefiltered_func_data_mcf",
"Label": "prefiltered_func_data_mcf",
"AtLocation": "prefiltered_func_data_mcf",
- "GeneratedBy": "urn:f1ebdf2e-24f8-49fd-8cf4-c135b087159d",
+ "GeneratedBy": "urn:mcflirt-mpdbH7Bm",
"digest": {
"sha256": "83371e264d408de4f678b8182097b39c86bd0a618ca76af6d1dfee5db0903b78"
}
},
{
- "@id": "urn:9f72ed22-2e83-4615-b7d0-34dd51fb3a97",
+ "@id": "bids::mc",
"Label": "mc",
"AtLocation": "mc",
- "GeneratedBy": "urn:0723034d-fc73-4fc4-9deb-605b9add0ee7",
+ "GeneratedBy": "urn:makedire-J2lSormN",
"digest": {
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}
},
{
- "@id": "urn:64b3106f-d986-42e5-bea5-ad79de7eed00",
+ "@id": "bids::prefiltered_func_data_mcf.mat",
"Label": "prefiltered_func_data_mcf.mat",
"AtLocation": "prefiltered_func_data_mcf.mat",
"digest": {
@@ -936,7 +949,7 @@
}
},
{
- "@id": "urn:e648781f-7a62-4523-8c8c-24cc9bfea61a",
+ "@id": "bids::prefiltered_func_data_mcf.par",
"Label": "prefiltered_func_data_mcf.par",
"AtLocation": "prefiltered_func_data_mcf.par",
"digest": {
@@ -944,7 +957,7 @@
}
},
{
- "@id": "urn:086568a2-e38c-44a5-ac87-7bbb46fb1215",
+ "@id": "bids::prefiltered_func_data_mcf_abs.rms",
"Label": "prefiltered_func_data_mcf_abs.rms",
"AtLocation": "prefiltered_func_data_mcf_abs.rms",
"digest": {
@@ -952,7 +965,7 @@
}
},
{
- "@id": "urn:76f8224d-55bf-46a5-bc7f-2973c300c08f",
+ "@id": "bids::prefiltered_func_data_mcf_abs_mean.rms",
"Label": "prefiltered_func_data_mcf_abs_mean.rms",
"AtLocation": "prefiltered_func_data_mcf_abs_mean.rms",
"digest": {
@@ -960,7 +973,7 @@
}
},
{
- "@id": "urn:8ae4d11f-5d8d-474d-b00b-f7e5c882df15",
+ "@id": "bids::prefiltered_func_data_mcf_rel.rms",
"Label": "prefiltered_func_data_mcf_rel.rms",
"AtLocation": "prefiltered_func_data_mcf_rel.rms",
"digest": {
@@ -968,7 +981,7 @@
}
},
{
- "@id": "urn:9f26b129-9763-4b04-860e-3f44465c99ad",
+ "@id": "bids::prefiltered_func_data_mcf_rel_mean.rms",
"Label": "prefiltered_func_data_mcf_rel_mean.rms",
"AtLocation": "prefiltered_func_data_mcf_rel_mean.rms",
"digest": {
@@ -976,34 +989,34 @@
}
},
{
- "@id": "urn:b5d49317-69e9-4232-b911-58eab6897675",
+ "@id": "bids::mc",
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"AtLocation": "mc",
- "GeneratedBy": "urn:0134c831-73b9-47b6-80a6-41535abaf825",
+ "GeneratedBy": "urn:mv-xhrmBOA4",
"digest": {
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}
},
{
- "@id": "urn:7271accf-6874-4774-8e77-f2c8317f2b9b",
+ "@id": "bids::rot.png",
"Label": "rot.png",
"AtLocation": "rot.png",
- "GeneratedBy": "urn:91ccbfe0-c5ec-43f2-92a1-79ae778813a9",
+ "GeneratedBy": "urn:fsltsplo-BXivmu30",
"digest": {
"sha256": "b8776603f8865a358b2273847d21e63491e7c2e10567fb640608dd47ba721f29"
}
},
{
- "@id": "urn:5a59dd20-8346-4538-8661-9396d02224d7",
+ "@id": "bids::trans.png",
"Label": "trans.png",
"AtLocation": "trans.png",
- "GeneratedBy": "urn:1d1b3389-23b1-48cb-9e01-94d17230ada3",
+ "GeneratedBy": "urn:fsltsplo-Wjiiv0E3",
"digest": {
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}
},
{
- "@id": "urn:f33a292b-a905-408f-ba76-441a2058a27b",
+ "@id": "bids::prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"Label": "prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"AtLocation": "prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"digest": {
@@ -1011,34 +1024,34 @@
}
},
{
- "@id": "urn:dda87c51-4f5a-49b0-928d-a53c9b3c47f6",
+ "@id": "bids::disp.png",
"Label": "disp.png",
"AtLocation": "disp.png",
- "GeneratedBy": "urn:4dc466e1-b429-43bb-b880-add7232b7347",
+ "GeneratedBy": "urn:fsltsplo-Fzexq6k9",
"digest": {
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}
},
{
- "@id": "urn:c3acf82f-0adc-4874-bd69-b28b507542c7",
+ "@id": "bids::mean_func",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:95b6a627-a7cb-4607-b603-d359f8b3c75c",
+ "GeneratedBy": "urn:fslmaths-a5rzZke7",
"digest": {
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}
},
{
- "@id": "urn:b5bab357-1440-40f7-a07a-e81de6dee8b8",
+ "@id": "bids::mask",
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"AtLocation": "mask",
- "GeneratedBy": "urn:19cea046-4b73-4065-8d07-f2ab4cd05577",
+ "GeneratedBy": "urn:bet2-udXsp4cv",
"digest": {
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}
},
{
- "@id": "urn:d254e790-3eb0-457a-a728-94483f898737",
+ "@id": "bids::mask_mask",
"Label": "mask_mask",
"AtLocation": "mask_mask",
"digest": {
@@ -1046,132 +1059,124 @@
}
},
{
- "@id": "urn:1a0a3bff-cc42-4522-8a1b-0ec281a16e51",
+ "@id": "bids::mask",
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"AtLocation": "mask",
- "GeneratedBy": "urn:7cd59bc5-33fb-4897-b2bb-5cfee20798ee",
+ "GeneratedBy": "urn:immv-ZYFWZ1Gn",
"digest": {
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}
},
{
- "@id": "urn:a4f12a49-cdd0-4f79-8ec4-1e30561765ee",
+ "@id": "bids::prefiltered_func_data_bet",
"Label": "prefiltered_func_data_bet",
"AtLocation": "prefiltered_func_data_bet",
- "GeneratedBy": "urn:920dddce-28c6-421c-882c-9a68550b6b34",
+ "GeneratedBy": "urn:fslmaths-I1OS1SJP",
"digest": {
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}
},
{
- "@id": "urn:924f0baf-a156-4e39-835b-4b9974948de2",
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- "GeneratedBy": "urn:3f64e75a-698c-4349-9f6a-7bd538d135df",
+ "GeneratedBy": "urn:fslmaths-7snwdwRw",
"digest": {
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}
},
{
- "@id": "urn:09ebc5dc-0466-4923-bd49-13831d041c86",
+ "@id": "bids::mask",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:71f1ade3-2b62-4c18-a187-26d24d3a7f1a",
+ "GeneratedBy": "urn:fslmaths-8b8qCEmy",
"digest": {
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}
},
{
- "@id": "urn:a6e50cb0-3790-46cd-97c4-6108afc39afe",
+ "@id": "bids::prefiltered_func_data_thresh",
"Label": "prefiltered_func_data_thresh",
"AtLocation": "prefiltered_func_data_thresh",
- "GeneratedBy": "urn:9fc79763-50ca-44d0-af53-ea663f18a6c9",
+ "GeneratedBy": "urn:fslmaths-exNmgmHg",
"digest": {
"sha256": "c5c015a8df079b497bbce596808cbbdc09fb39411f490244de192dfa72d33640"
}
},
{
- "@id": "urn:a05bcc8c-767e-4ef9-ad52-82fdcf352918",
+ "@id": "bids::mean_func",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:8abe0474-66d5-4e8d-b799-4ca935562832",
+ "GeneratedBy": "urn:fslmaths-9zvUeSVt",
"digest": {
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}
},
{
- "@id": "urn:e6777837-2f7c-4cb1-ab0f-9ad45c985501",
+ "@id": "bids::prefiltered_func_data_smooth",
"Label": "prefiltered_func_data_smooth",
"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:9c9633d5-e312-4218-beaf-ee48cdb1b684",
+ "GeneratedBy": "urn:susan-hUivqJAf",
"digest": {
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}
},
{
- "@id": "urn:0b11c98b-cb04-4ad6-943f-b7e64be5838a",
+ "@id": "bids::prefiltered_func_data_smooth",
"Label": "prefiltered_func_data_smooth",
"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:8a4b04a5-355c-436b-a9cd-d1ba1623a3de",
+ "GeneratedBy": "urn:fslmaths-GuMPegWU",
"digest": {
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}
},
{
- "@id": "urn:617710f9-1f1a-416f-ae6b-d2994da8000b",
+ "@id": "bids::prefiltered_func_data_intnorm",
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"AtLocation": "prefiltered_func_data_intnorm",
- "GeneratedBy": "urn:6f513969-f03e-43be-a09b-5dd6b976de3c",
+ "GeneratedBy": "urn:fslmaths-Uywrv3qZ",
"digest": {
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}
},
{
- "@id": "urn:8683b331-474b-43db-938a-3fb2df8077ff",
+ "@id": "bids::tempMean",
"Label": "tempMean",
"AtLocation": "tempMean",
- "GeneratedBy": "urn:9734bf62-20af-427c-a298-49437e993740",
+ "GeneratedBy": "urn:fslmaths-UCRih4mS",
"digest": {
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},
{
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- "digest": {
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- }
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- {
- "@id": "urn:f9d61dcc-d611-48da-8113-8e5d940d45bf",
+ "@id": "bids::prefiltered_func_data_tempfilt",
"Label": "prefiltered_func_data_tempfilt",
"AtLocation": "prefiltered_func_data_tempfilt",
+ "GeneratedBy": "urn:fslmaths-S1K6eyBe",
"digest": {
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}
},
{
- "@id": "urn:678f852c-890c-4abc-bf0a-1e737c5189bc",
+ "@id": "bids::filtered_func_data",
"Label": "filtered_func_data",
"AtLocation": "filtered_func_data",
- "GeneratedBy": "urn:2aafb6ce-d198-41d6-ab3e-16b28401a64a",
+ "GeneratedBy": "urn:fslmaths-iqrY5SnA",
"digest": {
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}
},
{
- "@id": "urn:8cb47f6b-5181-4500-9572-0906eac7e750",
+ "@id": "bids::mean_func",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "GeneratedBy": "urn:fslmaths-dabqvNXy",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:2fd43732-f606-4c9b-a9f0-74885d47be97",
+ "@id": "bids::prefiltered_func_data*",
"Label": "prefiltered_func_data*",
"AtLocation": "prefiltered_func_data*",
"digest": {
@@ -1179,113 +1184,158 @@
}
},
{
- "@id": "urn:4eec28c2-77b1-4e2a-b5ad-a4bf544143f9",
+ "@id": "bids::custom_timing_files",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:249dda2c-c59c-44e3-9a54-ec97b2d2c422",
+ "GeneratedBy": "urn:makedire-np0NfI2n",
"digest": {
"sha256": "1d7e19792328d5040f2f9fb3c15d59de90fc771785f81c67039a043bd5f2ed20"
}
},
{
- "@id": "urn:1d06d47e-8469-4b81-9404-fbc57017ad23",
+ "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
"Label": "sub-01_tone_counting.txt",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
+ "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
"digest": {
- "sha256": "c120d27b9d5d81a91be0e55f5cb880b2cb7de6c655554d9c15c9c04c6232ea8e"
+ "sha256": "165398224a205d2fc0b19354e15d9b085c6d81e333b69c4697b7894a2549be0b"
}
},
{
- "@id": "urn:ef4d92a2-528c-4884-9e55-9b6f0f020e18",
+ "@id": "bids::custom_timing_files/ev1.txt",
"Label": "ev1.txt",
"AtLocation": "custom_timing_files/ev1.txt",
- "GeneratedBy": "urn:df27cd3b-d715-4b02-b53b-a3b58ad15509"
+ "GeneratedBy": "urn:fslfixte-9tAyRn9N"
},
{
- "@id": "urn:906a7e97-4954-4db4-90a8-66b1d76cd022",
+ "@id": "bids::custom_timing_files",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:cb1c0160-0e2f-4a93-b70f-8f61530cdb27",
+ "GeneratedBy": "urn:makedire-mO0uYErJ",
"digest": {
"sha256": "1d7e19792328d5040f2f9fb3c15d59de90fc771785f81c67039a043bd5f2ed20"
}
},
{
- "@id": "urn:03b235ce-bedb-404b-8ea4-83225a07fb37",
+ "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
"Label": "sub-01_tone_counting_probe.txt",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
+ "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
"digest": {
- "sha256": "f09eeb82fa0be8e8759a5269403f36ec2b7dbf2c5b6caba1f0f985cc6cb3f703"
+ "sha256": "8b912293767f1a5e082311f6aaf0c44fc91fe45b0f2ae7f80e368bc2f4c2918a"
}
},
{
- "@id": "urn:f92c7377-ad99-4aab-bed1-84cd8c46c153",
+ "@id": "bids::custom_timing_files/ev2.txt",
"Label": "ev2.txt",
"AtLocation": "custom_timing_files/ev2.txt",
- "GeneratedBy": "urn:5fee107f-6a26-4850-849e-b57806b77df2"
+ "GeneratedBy": "urn:fslfixte-xwMlvwHA"
},
{
- "@id": "urn:9138c461-25d9-4077-b2c2-acf0e0cef1fd",
- "Label": "res4d",
- "AtLocation": "stats/res4d",
+ "@id": "bids::stats",
+ "Label": "stats",
+ "AtLocation": "stats",
"digest": {
- "sha256": "8845286f36caedf891a02afddc4175ea46f18f830b59a8c5026962184a530699"
+ "sha256": "a9f3e135372514a16d11a8038262b3eff94ccd69a9b35c4724b2759cfc944a07"
}
},
{
- "@id": "urn:30a127a0-5da6-41e9-b18f-b0d0213d8bad",
- "Label": "smoothness",
- "AtLocation": "stats/smoothness",
- "GeneratedBy": "urn:0bb5d0b3-84fd-4dd6-86ca-6e39ee7c9ca2",
+ "@id": "bids::design.mat",
+ "Label": "design.mat",
+ "AtLocation": "design.mat",
"digest": {
- "sha256": "67b0aaf95a257beff60d331b56265034807ca51e67e2d312d481d5835ef0b1d0"
+ "sha256": "1c1a6ef59a355e1f6f81e741e157784ccbe066ba3594a07aa9b16781e3d5bb25"
}
},
{
- "@id": "urn:3f99163c-feeb-4ddf-b9a3-98fbe5c4c030",
- "Label": "zstat1",
- "AtLocation": "stats/zstat1",
+ "@id": "bids::design.con",
+ "Label": "design.con",
+ "AtLocation": "design.con",
"digest": {
- "sha256": "70ae47cee1ea1d3f1f6f8aa7ac51f2641cb2fcb745dfd8cc54a389346e6fa094"
+ "sha256": "5808d1be37dd8f2a4906b710bb384fbee62faa4a46b2bc6847afc8962ed4eb54"
}
},
{
- "@id": "urn:54de5eb3-f9ac-4833-886e-bf68285dca2b",
+ "@id": "bids::stats",
+ "Label": "stats",
+ "AtLocation": "stats",
+ "GeneratedBy": "urn:filmgls-bPmqxXVL",
+ "digest": {
+ "sha256": "a9f3e135372514a16d11a8038262b3eff94ccd69a9b35c4724b2759cfc944a07"
+ }
+ },
+ {
+ "@id": "bids::stats/res4d",
+ "Label": "res4d",
+ "AtLocation": "stats/res4d"
+ },
+ {
+ "@id": "bids::stats/smoothness",
+ "Label": "smoothness",
+ "AtLocation": "stats/smoothness",
+ "GeneratedBy": "urn:smoothes-liqoxwMg"
+ },
+ {
+ "@id": "bids::stats/zstat1",
+ "Label": "zstat1",
+ "AtLocation": "stats/zstat1"
+ },
+ {
+ "@id": "bids::thresh_zstat1",
"Label": "thresh_zstat1",
"AtLocation": "thresh_zstat1",
- "GeneratedBy": "urn:e73ff039-8349-4916-94b3-209aa86d7a3f",
+ "GeneratedBy": "urn:fslmaths-9UeSkXvv",
"digest": {
"sha256": "662e7ba670e124d15bb3cc18b818868f76604578034b524c8882f35fc5db413f"
}
},
{
- "@id": "urn:0a6241b6-2152-4e5b-8113-cc6c69d9197b",
+ "@id": "bids::stats/cope1",
"Label": "cope1",
- "AtLocation": "stats/cope1",
- "digest": {
- "sha256": "bf3b603569da6dbe3d6f0e8667d346f3ac943c9d01d2fc9743ce17abeb1547fb"
- }
+ "AtLocation": "stats/cope1"
},
{
- "@id": "urn:5420810d-a31a-49fd-acd7-8b299036cc1f",
+ "@id": "bids::cluster_mask_zstat1",
"Label": "cluster_mask_zstat1",
"AtLocation": "cluster_mask_zstat1",
- "GeneratedBy": "urn:a3f63c7e-f657-4071-82d5-23c6f12857a3",
+ "GeneratedBy": "urn:cluster-xTOqvqc1",
"digest": {
"sha256": "b28c170e33d2917cac55183786616a9e976e5e7f30dc7c8666341f12ed6d0277"
}
},
{
- "@id": "urn:3a301cd9-25da-471b-8223-bad090c7347d",
+ "@id": "bids::thresh_zstat1",
+ "Label": "thresh_zstat1",
+ "AtLocation": "thresh_zstat1",
+ "GeneratedBy": "urn:cluster-xTOqvqc1",
+ "digest": {
+ "sha256": "662e7ba670e124d15bb3cc18b818868f76604578034b524c8882f35fc5db413f"
+ }
+ },
+ {
+ "@id": "bids::lmax_zstat1.txt",
+ "Label": "lmax_zstat1.txt",
+ "AtLocation": "lmax_zstat1.txt",
+ "GeneratedBy": "urn:cluster-xTOqvqc1",
+ "digest": {
+ "sha256": "d44ee21719775397a1a95ede6778d25404b50e8bd259dbdf02d2fde635fc81a5"
+ }
+ },
+ {
+ "@id": "bids::stats/cope1",
"Label": "cope1",
"AtLocation": "stats/cope1",
- "GeneratedBy": "urn:a3f63c7e-f657-4071-82d5-23c6f12857a3",
+ "GeneratedBy": "urn:cluster-xTOqvqc1"
+ },
+ {
+ "@id": "bids::cluster_zstat1.txt",
+ "Label": "cluster_zstat1.txt",
+ "AtLocation": "cluster_zstat1.txt",
+ "GeneratedBy": "urn:cluster-xTOqvqc1",
"digest": {
- "sha256": "bf3b603569da6dbe3d6f0e8667d346f3ac943c9d01d2fc9743ce17abeb1547fb"
+ "sha256": "b06695ff4f0a8158fa439b1ddf224b58d344606d400885c177390d09506e8e4c"
}
},
{
- "@id": "urn:701df0dc-45e0-40bd-9782-a2e4d6b55efa",
+ "@id": "bids::cluster_zstat1",
"Label": "cluster_zstat1",
"AtLocation": "cluster_zstat1",
"digest": {
@@ -1293,25 +1343,25 @@
}
},
{
- "@id": "urn:98af3652-a864-476a-b2d5-059404150cbd",
+ "@id": "bids::rendered_thresh_zstat1",
"Label": "rendered_thresh_zstat1",
"AtLocation": "rendered_thresh_zstat1",
- "GeneratedBy": "urn:652558c1-a31d-4c8a-a9c3-822ea694f3d3",
+ "GeneratedBy": "urn:overlay-iRpUE43m",
"digest": {
"sha256": "de5b9d44d95f4252f491eb45c76a0ae2b4d2c75b58664fc0df7d9153810c0bf6"
}
},
{
- "@id": "urn:bdbf17fa-bfef-4bd5-90d8-f02ac4320a78",
+ "@id": "bids::rendered_thresh_zstat1.png",
"Label": "rendered_thresh_zstat1.png",
"AtLocation": "rendered_thresh_zstat1.png",
- "GeneratedBy": "urn:f4ad58dc-3808-48a2-ab28-b91512eceeb8",
+ "GeneratedBy": "urn:slicer-dPyNd78C",
"digest": {
"sha256": "15d6a8bf7a902df8c5feeb7468a3d0caacf9eb3067c0840c2f4763f5e2301527"
}
},
{
- "@id": "urn:99cd507b-7b91-48e6-a47e-1d09955693bf",
+ "@id": "bids::/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif",
"Label": "ramp.gif",
"AtLocation": "/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif",
"digest": {
@@ -1319,28 +1369,28 @@
}
},
{
- "@id": "urn:99e36abe-ae11-4401-99aa-a5ddc3092b09",
+ "@id": "bids::.ramp.gif",
"Label": ".ramp.gif",
"AtLocation": ".ramp.gif",
- "GeneratedBy": "urn:b1cc91c7-f921-41c1-8be7-392416eeeb13",
+ "GeneratedBy": "urn:cp-yLQL77nx",
"digest": {
"sha256": "93f4284ccb854d5a41401d9360a13223017b67479cb289a33d83836922e028a4"
}
},
{
- "@id": "urn:fa33f60b-37bd-4d5b-b7a2-d803058269e0",
+ "@id": "bids::tsplot",
"Label": "tsplot",
"AtLocation": "tsplot",
- "GeneratedBy": "urn:a2736bdd-b58b-4fd5-b985-64805c68ad20",
+ "GeneratedBy": "urn:makedire-mY11e8bD",
"digest": {
"sha256": "2a74042f4edf02288edf16961307f741651efb4346e102a04b7603e781d1625e"
}
},
{
- "@id": "urn:8339701c-d6f7-49d6-8d0e-657dc2e062cc",
+ "@id": "bids::tsplot",
"Label": "tsplot",
"AtLocation": "tsplot",
- "GeneratedBy": "urn:0b2038d7-d9aa-47f4-9a7c-4fcf52ee799b",
+ "GeneratedBy": "urn:tsplot-ms47hBRT",
"digest": {
"sha256": "2a74042f4edf02288edf16961307f741651efb4346e102a04b7603e781d1625e"
}
diff --git a/examples/from_parsers/fsl/fsl_hrf_gammadiff_report_log.png b/examples/from_parsers/fsl/fsl_hrf_gammadiff_report_log.png
index 07daca01f..a0c211c8e 100644
Binary files a/examples/from_parsers/fsl/fsl_hrf_gammadiff_report_log.png and b/examples/from_parsers/fsl/fsl_hrf_gammadiff_report_log.png differ
diff --git a/examples/from_parsers/fsl/fsl_motion_reg_der_report_log.html b/examples/from_parsers/fsl/fsl_motion_reg_der_report_log.html
index 4be811d25..a7d230d3f 100644
--- a/examples/from_parsers/fsl/fsl_motion_reg_der_report_log.html
+++ b/examples/from_parsers/fsl/fsl_motion_reg_der_report_log.html
@@ -35,20 +35,20 @@ Progress Report / Log
326885
Initialisation
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
Total original volumes = 104
/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1
Preprocessing:Stage 1
-/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90
+/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/example_func.nii.gz -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90
Option -F ( FEAT version parameter ) selected with argument "6.00"
Option -d ( output directory ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat"
Option -l ( logfile )input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/logs/feat2_pre"
Option -R ( html unwarping report ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/report_unwarp.html"
Option -r ( html registration report ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/report_reg.html"
Option -i ( main input ) input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/example_func.nii.gz"
-Option -h ( high-res structural image ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
+Option -h ( high-res structural image ) selected with argument "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
Option -w ( highres dof ) selected with argument "BBR"
Option -x ( highres search ) selected with argument "90"
Option -s ( standard image ) selected with argument "/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain"
@@ -59,10 +59,10 @@ Progress Report / Log
/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/reg
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head
did not find file: example_func2highres.mat. Generating transform.
@@ -128,9 +128,9 @@ Progress Report / Log
/bin/rm -rf prefiltered_func_data*
Stats
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
/usr/local/packages/fsl-5.0.10/bin/mp_diffpow.sh mc/prefiltered_func_data_mcf.par mc/prefiltered_func_data_mcf_diff
diff --git a/examples/from_parsers/fsl/fsl_motion_reg_der_report_log.jsonld b/examples/from_parsers/fsl/fsl_motion_reg_der_report_log.jsonld
index a55b01a8c..5e8e40d50 100644
--- a/examples/from_parsers/fsl/fsl_motion_reg_der_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_motion_reg_der_report_log.jsonld
@@ -4,607 +4,616 @@
"Records": {
"Software": [
{
- "@id": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:fsl-O45Gx0i4",
"@type": "prov:SoftwareAgent",
"Label": "FSL",
- "Version": "xxx"
+ "Version": "xxx",
+ "AltIdentifier": "RRID:SCR_002823"
}
],
"Activities": [
{
- "@id": "urn:3b503358-3e90-4650-ba12-fa5787079082",
+ "@id": "urn:fslmaths-dC2a0X3Y",
"Label": "fslmaths",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
"Used": [
- "urn:ab6737f0-65b9-4811-934c-b7085bad7b9a"
+ "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold"
]
},
{
- "@id": "urn:e053f1c8-fbb5-4abf-9f26-83bacb965b3b",
+ "@id": "urn:fslroi-P33frSjV",
"Label": "fslroi",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1",
"Used": [
- "urn:9fb1321c-e5fc-4d51-bbaf-b8c047d3ac80"
+ "bids::prefiltered_func_data"
]
},
{
- "@id": "urn:ad6afb1f-16c3-42d2-b5c1-ed7709d5baf8",
+ "@id": "urn:mainfeat-pePifb0g",
"Label": "mainfeatreg",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/example_func.nii.gz -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
"Used": [
- "urn:2d6bc1b8-06a4-44f4-a749-6e56f1afb928",
- "urn:9dbd3cdb-fc0b-4d4f-8dee-ef7ac394468e",
- "urn:9df834a4-e7db-4a93-b135-78a21e8af4cf"
+ "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/example_func.nii.gz",
+ "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain",
+ "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
]
},
{
- "@id": "urn:9f0418c9-37e3-442e-9c7e-546a9ca91950",
+ "@id": "urn:makedire-GvuKuCNk",
"Label": "Make directory",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/reg",
"Used": []
},
{
- "@id": "urn:9ae492e3-19fd-4cb2-9c73-520962c16993",
+ "@id": "urn:fslmaths-suuOqrDC",
"Label": "fslmaths",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
"Used": [
- "urn:2d6bc1b8-06a4-44f4-a749-6e56f1afb928"
+ "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
]
},
{
- "@id": "urn:f22d3031-ad76-4284-a165-40cc1f7e75b2",
+ "@id": "urn:fslmaths-q8MSO5Am",
"Label": "fslmaths",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
"Used": [
- "urn:570b107d-2aad-41e1-b0c0-03f7a7ee2734"
+ "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w"
]
},
{
- "@id": "urn:21490073-5880-42a1-a555-78fc1684a71b",
+ "@id": "urn:epireg-5k2Yi4nS",
"Label": "epi_reg",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/usr/local/packages/fsl-5.0.10/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres",
- "Used": []
+ "Used": [
+ "bids::example_func",
+ "bids::highres",
+ "bids::highres_head"
+ ]
},
{
- "@id": "urn:e7f88111-476b-45b1-8905-39d0075e680a",
+ "@id": "urn:convertx-n5s09vhW",
"Label": "convert_xfm",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/usr/local/packages/fsl-5.0.10/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat",
"Used": [
- "urn:e8e9e392-b899-461a-8588-64440b803a57"
+ "bids::example_func2highres.mat"
]
},
{
- "@id": "urn:4d24a4be-9740-4c9e-a23e-7000ce2ea510",
+ "@id": "urn:slicer-dKDUNHY2",
"Label": "slicer",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:03f18f63-6da0-4cef-bc7c-af56235662fa",
- "urn:f3da51a8-5835-48b7-b300-aa60d22b491a"
+ "bids::example_func2highres",
+ "bids::highres"
]
},
{
- "@id": "urn:8ddf91f7-79c9-47c1-b563-2ab053ba3d6f",
+ "@id": "urn:pngappen-wVG3Hr3e",
"Label": "pngappend",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres1.png",
"Used": [
- "urn:0251ee81-099a-4ebc-98ce-451c65834a94",
- "urn:192c4bff-3ba4-420d-b993-ae441786ddcb",
- "urn:302ebdbf-d0d6-4b88-ab41-87f4f06e3912",
- "urn:7138ee41-a1a7-4e90-8634-1fbd9e69bec4",
- "urn:8bde6cef-d597-4805-a798-f881ef0ce6da",
- "urn:ab283958-f080-464f-ae38-49bb0a5105e6",
- "urn:ac56e858-82f0-4ace-90b6-4ac45f773e93",
- "urn:ac846955-fde3-40f9-b985-4b30238f1f1f",
- "urn:b4b9ae0b-4c3c-4412-acd1-762a876097d8",
- "urn:b869493c-9952-4578-8ce7-e15a2f6e1c23",
- "urn:b8ebf28b-6cc9-4040-851b-6784925385f7",
- "urn:e1e7caef-17a4-4cc0-9292-7012723265a8"
+ "bids::sla.png",
+ "bids::slb.png",
+ "bids::slc.png",
+ "bids::sld.png",
+ "bids::sle.png",
+ "bids::slf.png",
+ "bids::slg.png",
+ "bids::slh.png",
+ "bids::sli.png",
+ "bids::slj.png",
+ "bids::slk.png",
+ "bids::sll.png"
]
},
{
- "@id": "urn:423b51c1-468f-4ff0-bc27-b2433543427f",
+ "@id": "urn:slicer-Taflf26K",
"Label": "slicer",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:03f18f63-6da0-4cef-bc7c-af56235662fa",
- "urn:f3da51a8-5835-48b7-b300-aa60d22b491a"
+ "bids::example_func2highres",
+ "bids::highres"
]
},
{
- "@id": "urn:59f57dbb-caad-42e2-b412-f3e90f2fa4aa",
+ "@id": "urn:pngappen-lfBGx27W",
"Label": "pngappend",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres2.png",
"Used": [
- "urn:0251ee81-099a-4ebc-98ce-451c65834a94",
- "urn:192c4bff-3ba4-420d-b993-ae441786ddcb",
- "urn:302ebdbf-d0d6-4b88-ab41-87f4f06e3912",
- "urn:7138ee41-a1a7-4e90-8634-1fbd9e69bec4",
- "urn:8bde6cef-d597-4805-a798-f881ef0ce6da",
- "urn:ab283958-f080-464f-ae38-49bb0a5105e6",
- "urn:ac56e858-82f0-4ace-90b6-4ac45f773e93",
- "urn:ac846955-fde3-40f9-b985-4b30238f1f1f",
- "urn:b4b9ae0b-4c3c-4412-acd1-762a876097d8",
- "urn:b869493c-9952-4578-8ce7-e15a2f6e1c23",
- "urn:b8ebf28b-6cc9-4040-851b-6784925385f7",
- "urn:e1e7caef-17a4-4cc0-9292-7012723265a8"
+ "bids::sla.png",
+ "bids::slb.png",
+ "bids::slc.png",
+ "bids::sld.png",
+ "bids::sle.png",
+ "bids::slf.png",
+ "bids::slg.png",
+ "bids::slh.png",
+ "bids::sli.png",
+ "bids::slj.png",
+ "bids::slk.png",
+ "bids::sll.png"
]
},
{
- "@id": "urn:c99b701f-4e3e-42c7-9395-6f2c2ba4e03f",
+ "@id": "urn:pngappen-CNwT0NHH",
"Label": "pngappend",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend example_func2highres1.png example_func2highres2.png example_func2highres.png",
"Used": [
- "urn:2d9cacf2-0c11-4580-8104-b75009019253",
- "urn:e1ce9fe6-0fdc-4973-bdb9-eb0e5bcbea6e"
+ "bids::example_func2highres1.png",
+ "bids::example_func2highres2.png"
]
},
{
- "@id": "urn:f50cf39d-823f-485a-bbc6-f6ebf1bbc99d",
+ "@id": "urn:rm-BtXDPS1B",
"Label": "rm",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/bin/rm -f sl?.png example_func2highres2.png",
"Used": [
- "urn:8168ad2f-138b-4b62-99c7-756dbb9cc014",
- "urn:e1ce9fe6-0fdc-4973-bdb9-eb0e5bcbea6e"
+ "bids::example_func2highres2.png",
+ "bids::sl?.png"
]
},
{
- "@id": "urn:2e7bdac9-e43c-43cc-86e4-37ee58774229",
+ "@id": "urn:rm-fyjZBW6p",
"Label": "rm",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/bin/rm example_func2highres1.png",
"Used": [
- "urn:2d9cacf2-0c11-4580-8104-b75009019253"
+ "bids::example_func2highres1.png"
]
},
{
- "@id": "urn:aa7cc227-1492-4b80-a441-76db5060599b",
+ "@id": "urn:mcflirt-odII8geb",
"Label": "mcflirt",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/usr/local/packages/fsl-5.0.10/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs -spline_final",
"Used": [
- "urn:9fb1321c-e5fc-4d51-bbaf-b8c047d3ac80"
+ "bids::prefiltered_func_data"
]
},
{
- "@id": "urn:6a60a386-74a3-475a-a222-594448a74486",
+ "@id": "urn:makedire-UK92L4x7",
"Label": "Make directory",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/bin/mkdir -p mc",
"Used": []
},
{
- "@id": "urn:9c9b4cb0-4148-4ac9-abec-285cd3234228",
+ "@id": "urn:mv-I5FDYgY1",
"Label": "mv",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc",
"Used": [
- "urn:05bf14da-84ae-4952-9681-5aeae5c4e66b",
- "urn:20adc457-4cb5-47e7-b992-ee701f634086",
- "urn:3639999c-eed2-4529-b8da-8e2e9ae92a0b",
- "urn:3a074d65-3870-4836-8b82-142937eadec0",
- "urn:757f4edc-d6f0-4c10-b93f-a62dbdff6c54",
- "urn:bfce5176-4c49-4689-a492-b874f6fb9187"
+ "bids::prefiltered_func_data_mcf.mat",
+ "bids::prefiltered_func_data_mcf.par",
+ "bids::prefiltered_func_data_mcf_abs.rms",
+ "bids::prefiltered_func_data_mcf_abs_mean.rms",
+ "bids::prefiltered_func_data_mcf_rel.rms",
+ "bids::prefiltered_func_data_mcf_rel_mean.rms"
]
},
{
- "@id": "urn:73216f9b-6c6c-4495-898c-b6e33ab2a9f4",
+ "@id": "urn:fsltsplo-OyOBbM9y",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png",
"Used": [
- "urn:05bf14da-84ae-4952-9681-5aeae5c4e66b"
+ "bids::prefiltered_func_data_mcf.par"
]
},
{
- "@id": "urn:4eedac58-1578-4f7f-a158-576db499125e",
+ "@id": "urn:fsltsplo-Oe0ij16S",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png",
"Used": [
- "urn:05bf14da-84ae-4952-9681-5aeae5c4e66b"
+ "bids::prefiltered_func_data_mcf.par"
]
},
{
- "@id": "urn:9e5668f5-2b7b-477c-883e-08a7cf7064c7",
+ "@id": "urn:fsltsplo-MM1luFDP",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png",
"Used": [
- "urn:bd82cd22-8ef8-4d4b-b705-233e1e6f43d3"
+ "bids::prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms"
]
},
{
- "@id": "urn:fa33d422-288f-482a-9654-1817f7f1f217",
+ "@id": "urn:fslmaths-EYKSK00I",
"Label": "fslmaths",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func",
"Used": [
- "urn:1a7bf0ee-20cf-41e0-9479-2831210c5957"
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:90916e20-80a6-4f45-93dc-07564c491938",
+ "@id": "urn:bet2-PQSk41oe",
"Label": "bet2",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/usr/local/packages/fsl-5.0.10/bin/bet2 mean_func mask -f 0.3 -n -m",
"Used": [
- "urn:cc3c31ab-c304-46e8-a45d-d21331ec0eba"
+ "bids::mean_func"
]
},
{
- "@id": "urn:8fa49467-d795-4959-b9a5-b348e239e62c",
+ "@id": "urn:immv-IjjkMRPp",
"Label": "immv",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/usr/local/packages/fsl-5.0.10/bin/immv mask_mask mask",
"Used": [
- "urn:a39b454f-e907-4aa9-8514-34bce78645df"
+ "bids::mask_mask"
]
},
{
- "@id": "urn:fa61b105-1d73-47fc-93f5-be09bf53c7cc",
+ "@id": "urn:fslmaths-XqLE8pkt",
"Label": "fslmaths",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet",
"Used": [
- "urn:1a7bf0ee-20cf-41e0-9479-2831210c5957",
- "urn:8da457f6-6aae-4cbb-8ed8-dd30f4cf4c30"
+ "bids::mask",
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:03064a8a-0e28-467d-bbe9-8e9cdba8bc5d",
+ "@id": "urn:fslstats-Jr6RWDPe",
"Label": "fslstats",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_bet -p 2 -p 98",
"Used": [
- "urn:de1871d8-045a-467f-9dc9-e90f0985bb89"
+ "bids::prefiltered_func_data_bet"
]
},
{
- "@id": "urn:9852ebd4-54f0-4016-8588-1be4e8b1ff1b",
+ "@id": "urn:fslmaths-VL4VqblJ",
"Label": "fslmaths",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_bet -thr 74.4585571 -Tmin -bin mask -odt char",
"Used": [
- "urn:de1871d8-045a-467f-9dc9-e90f0985bb89"
+ "bids::prefiltered_func_data_bet"
]
},
{
- "@id": "urn:bdc69aa0-c3f4-4504-b159-0a00c9e69b56",
+ "@id": "urn:fslstats-7umKtLfk",
"Label": "fslstats",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_mcf -k mask -p 50",
"Used": [
- "urn:1a7bf0ee-20cf-41e0-9479-2831210c5957"
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:acde19c7-3af9-4068-bfb4-7e467ac0017f",
+ "@id": "urn:fslmaths-ut9tGWVe",
"Label": "fslmaths",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -dilF mask",
"Used": [
- "urn:8da457f6-6aae-4cbb-8ed8-dd30f4cf4c30"
+ "bids::mask"
]
},
{
- "@id": "urn:ccd87bea-cc31-4cc3-9005-34da90ca2810",
+ "@id": "urn:fslmaths-nOE8yxx7",
"Label": "fslmaths",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh",
"Used": [
- "urn:1a7bf0ee-20cf-41e0-9479-2831210c5957",
- "urn:8da457f6-6aae-4cbb-8ed8-dd30f4cf4c30"
+ "bids::mask",
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:8b37acbd-590d-4b87-bb5a-0681c734a3d3",
+ "@id": "urn:fslmaths-OjIaOvPw",
"Label": "fslmaths",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func",
"Used": [
- "urn:ed02a601-2201-43da-b2f7-06ca4ab55d01"
+ "bids::prefiltered_func_data_thresh"
]
},
{
- "@id": "urn:0836490c-40f2-462e-a071-1558e448e0dd",
+ "@id": "urn:susan-SmymgzPJ",
"Label": "susan",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/usr/local/packages/fsl-5.0.10/bin/susan prefiltered_func_data_thresh 445.8289035 2.54777070064 3 1 1 mean_func 445.8289035 prefiltered_func_data_smooth",
"Used": [
- "urn:ed02a601-2201-43da-b2f7-06ca4ab55d01"
+ "bids::prefiltered_func_data_thresh"
]
},
{
- "@id": "urn:d7a66507-3350-42b8-9e9f-f37d0e3d31f7",
+ "@id": "urn:fslmaths-O8pCVrLL",
"Label": "fslmaths",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth",
"Used": [
- "urn:65fccdc3-0cf4-46b6-b5ae-6472af9204c6",
- "urn:8da457f6-6aae-4cbb-8ed8-dd30f4cf4c30"
+ "bids::mask",
+ "bids::prefiltered_func_data_smooth"
]
},
{
- "@id": "urn:6fd64536-641a-413b-8d77-390f0514fea8",
+ "@id": "urn:fslmaths-MZCCcDOx",
"Label": "fslmaths",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mul 16.8225970571 prefiltered_func_data_intnorm",
"Used": [
- "urn:65fccdc3-0cf4-46b6-b5ae-6472af9204c6"
+ "bids::prefiltered_func_data_smooth"
]
},
{
- "@id": "urn:b60f8029-dace-4def-b134-96c533ed2469",
+ "@id": "urn:fslmaths-As3g3UB7",
"Label": "fslmaths",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean",
"Used": [
- "urn:584874b2-dc50-4bcc-ba3f-57f724c25516"
+ "bids::prefiltered_func_data_intnorm"
]
},
{
- "@id": "urn:231336c7-5029-499e-aa70-72035c9d8213",
+ "@id": "urn:fslmaths-I24yLD9V",
"Label": "fslmaths",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -bptf 15.0 -1 -add tempMean prefiltered_func_data_tempfilt",
"Used": [
- "urn:584874b2-dc50-4bcc-ba3f-57f724c25516",
- "urn:e1bd11f2-70d0-4021-9a88-556768d353e1"
+ "bids::prefiltered_func_data_intnorm",
+ "bids::tempMean"
]
},
{
- "@id": "urn:04d7f3d7-1ab8-40a5-b6ec-16f7bb2570e3",
+ "@id": "urn:imrm-JrZFnovL",
"Label": "imrm",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/usr/local/packages/fsl-5.0.10/bin/imrm tempMean",
"Used": [
- "urn:e1bd11f2-70d0-4021-9a88-556768d353e1"
+ "bids::tempMean"
]
},
{
- "@id": "urn:fc4f2b90-f6c6-410a-a8ff-78d8206b5df0",
+ "@id": "urn:fslmaths-P4mbrSSu",
"Label": "fslmaths",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data",
"Used": [
- "urn:7b84f725-23d1-47b6-bd1a-8a066b03a9c8"
+ "bids::prefiltered_func_data_tempfilt"
]
},
{
- "@id": "urn:5d73a76e-4df1-4fd3-a040-769dac5ac08d",
+ "@id": "urn:fslmaths-ZreUCdz4",
"Label": "fslmaths",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths filtered_func_data -Tmean mean_func",
"Used": [
- "urn:5a3ed7a7-f404-4238-9a73-9992979af9d4"
+ "bids::filtered_func_data"
]
},
{
- "@id": "urn:cbc9b629-6395-406a-8661-234f76bf6faa",
+ "@id": "urn:rm-hm0Sr96f",
"Label": "rm",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/bin/rm -rf prefiltered_func_data*",
"Used": [
- "urn:2ed1140e-d2cf-45c7-9717-66283f93a8af"
+ "bids::prefiltered_func_data*"
]
},
{
- "@id": "urn:dbcf467f-1db2-4626-a77a-4ff116e8eff2",
+ "@id": "urn:makedire-GemLkPxp",
"Label": "Make directory",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
- "@id": "urn:c57f3b03-6b8b-4a49-91ad-10414a5bb1f6",
+ "@id": "urn:fslfixte-iX0H2Ui2",
"Label": "fslFixText",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
"Used": [
- "urn:715350ea-baf9-4e67-af8b-4c223751977f"
+ "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt"
]
},
{
- "@id": "urn:cbb044da-cc8b-4ef7-977c-2c3794c9027a",
+ "@id": "urn:makedire-6kNWcrAo",
"Label": "Make directory",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
- "@id": "urn:e4f1c0c1-d62c-4d95-9f6a-2dc7252f0873",
+ "@id": "urn:fslfixte-bY3ov1IQ",
"Label": "fslFixText",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
"Used": [
- "urn:fcf71ded-26d2-4518-a3e8-bb58b66bdb22"
+ "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt"
]
},
{
- "@id": "urn:5c602888-1bca-4c78-8710-3274acc87d5e",
+ "@id": "urn:mpdiffpo-ymFrapRB",
"Label": "mp_diffpow.sh",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/usr/local/packages/fsl-5.0.10/bin/mp_diffpow.sh mc/prefiltered_func_data_mcf.par mc/prefiltered_func_data_mcf_diff",
"Used": [
- "urn:a054bb26-df1e-4d57-bb67-aac6b5241eb0"
+ "bids::mc/prefiltered_func_data_mcf.par"
]
},
{
- "@id": "urn:f63fa016-1a71-44d7-bc13-a604c467686c",
+ "@id": "urn:paste-ASrDOVxs",
"Label": "paste",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
- "Command": "paste -d ' ' mc/prefiltered_func_data_mcf.par mc/prefiltered_func_data_mcf_diff.dat > mc/prefiltered_func_data_mcf_final.par",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
+ "Command": "paste -d ' ' mc/prefiltered_func_data_mcf.par mc/prefiltered_func_data_mcf_diff.dat > mc/prefiltered_func_data_mcf_final.par",
"Used": []
},
{
- "@id": "urn:a819e5fd-24db-440d-99af-4019da3551b7",
+ "@id": "urn:paste-KbppIr8M",
"Label": "paste",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
- "Command": "paste -d ' ' mc/prefiltered_func_data_mcf_final.par > confoundevs.txt",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
+ "Command": "paste -d ' ' mc/prefiltered_func_data_mcf_final.par > confoundevs.txt",
"Used": []
},
{
- "@id": "urn:04bb8948-1c2b-49c6-a426-7fda9ebaf912",
+ "@id": "urn:featmode-dY5I3r5p",
"Label": "feat_model",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/usr/local/packages/fsl-5.0.10/bin/feat_model design confoundevs.txt",
"Used": [
- "urn:ba63f369-bdcf-4064-8aef-f45a16a720c4"
+ "bids::design"
]
},
{
- "@id": "urn:b3f32508-01de-40f6-bd45-51193bbf573e",
+ "@id": "urn:filmgls-3IoqFYtu",
"Label": "film_gls",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con",
- "Used": []
+ "Used": [
+ "bids::design.con",
+ "bids::design.mat",
+ "bids::filtered_func_data",
+ "bids::stats"
+ ]
},
{
- "@id": "urn:7bd5dc94-90f0-4d26-b304-d5ecea6af65e",
+ "@id": "urn:smoothes-paAW6C17",
"Label": "smoothest",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 78 -m mask -r stats/res4d > stats/smoothness",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 78 -m mask -r stats/res4d > stats/smoothness",
"Used": [
- "urn:8da457f6-6aae-4cbb-8ed8-dd30f4cf4c30",
- "urn:b5eac9fd-9254-4683-accf-f45cc6caaa64"
+ "bids::mask",
+ "bids::stats/res4d"
]
},
{
- "@id": "urn:73cd9e98-c666-404b-ae9b-7ac11c80b23f",
+ "@id": "urn:fslmaths-H8tXahSy",
"Label": "fslmaths",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1",
"Used": [
- "urn:6f086e2c-b943-4856-a4e4-b79e5ce78fb0",
- "urn:8da457f6-6aae-4cbb-8ed8-dd30f4cf4c30"
+ "bids::mask",
+ "bids::stats/zstat1"
]
},
{
- "@id": "urn:b591798c-d607-4b73-9ffd-0e7d6e22f4bb",
+ "@id": "urn:echo-JYr0kACn",
"Label": "echo",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "echo 38352 > thresh_zstat1.vol",
"Used": []
},
{
- "@id": "urn:f82cd723-49bf-43c0-a2d9-438e84b33318",
+ "@id": "urn:ptoz-In84LLOp",
"Label": "ptoz",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:2777a5ba-b8f6-4bb8-8a26-ff00ab683a62",
+ "@id": "urn:cluster-E7oup06U",
"Label": "cluster",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -t 3.090232 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z --voxuncthresh -c stats/cope1 > cluster_zstat1.txt",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -t 3.090232 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z --voxuncthresh -c stats/cope1 > cluster_zstat1.txt",
"Used": [
- "urn:5255d402-08a6-4dd0-aefa-d239d213fce0",
- "urn:62a462c1-c20a-4255-b51a-4b0d02ff5a35"
+ "bids::stats/cope1",
+ "bids::thresh_zstat1"
]
},
{
- "@id": "urn:0df9b60d-731f-4e80-8d0b-bd8d32e8516b",
+ "@id": "urn:cluster2-ymvd5MhO",
"Label": "cluster2html",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat1",
"Used": [
- "urn:d5163407-701a-404f-9edd-ef1427791617"
+ "bids::cluster_zstat1"
]
},
{
- "@id": "urn:11f7d34b-6364-461b-af8e-ce7c7f9de369",
+ "@id": "urn:fslstats-c927620Q",
"Label": "fslstats",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat1 -l 0.0001 -R 2>/dev/null",
"Used": [
- "urn:5255d402-08a6-4dd0-aefa-d239d213fce0"
+ "bids::thresh_zstat1"
]
},
{
- "@id": "urn:08595e41-b6d0-4515-b786-e782353f3718",
+ "@id": "urn:overlay-9EILhFVq",
"Label": "overlay",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "AssociatedWith": "urn:fsl-O45Gx0i4",
"Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat1 3.093412 5.467648 rendered_thresh_zstat1",
"Used": []
},
{
- "@id": "urn:18b0a656-3c03-498e-b5c1-fa41f1592e42",
+ "@id": "urn:slicer-lKcrJvxP",
"Label": "slicer",
- "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
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@@ -612,15 +621,15 @@
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@@ -628,45 +637,57 @@
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- "@id": "urn:d9fdde3f-514e-4357-a7f3-b4be87251abc",
+ "@id": "bids::slk.png",
"Label": "slk.png",
"AtLocation": "slk.png",
- "GeneratedBy": "urn:423b51c1-468f-4ff0-bc27-b2433543427f",
+ "GeneratedBy": "urn:slicer-Taflf26K",
"digest": {
"sha256": "c540df2ed1d697609b08bd955a2ca31f3aeca3395c403edd9b036be63682eb64"
}
},
{
- "@id": "urn:4850cca1-5789-48af-9d8b-1388f2a13215",
+ "@id": "bids::sll.png",
"Label": "sll.png",
"AtLocation": "sll.png",
- "GeneratedBy": "urn:423b51c1-468f-4ff0-bc27-b2433543427f",
+ "GeneratedBy": "urn:slicer-Taflf26K",
"digest": {
"sha256": "0b9c965bbea7bb7d1f251ea0f2973f485727fbbc91357e30aee25ff9869f5009"
}
},
{
- "@id": "urn:e1ce9fe6-0fdc-4973-bdb9-eb0e5bcbea6e",
+ "@id": "bids::example_func2highres2.png",
"Label": "example_func2highres2.png",
"AtLocation": "example_func2highres2.png",
- "GeneratedBy": "urn:59f57dbb-caad-42e2-b412-f3e90f2fa4aa",
+ "GeneratedBy": "urn:pngappen-lfBGx27W",
"digest": {
"sha256": "4e622cf27c5f4d28786e7ccdc4e88253f4e5a855818d597ceec90fa78f0d437c"
}
},
{
- "@id": "urn:2e269bf3-ecc6-4bfd-b04c-ddb690e70fdb",
+ "@id": "bids::example_func2highres.png",
"Label": "example_func2highres.png",
"AtLocation": "example_func2highres.png",
- "GeneratedBy": "urn:c99b701f-4e3e-42c7-9395-6f2c2ba4e03f",
+ "GeneratedBy": "urn:pngappen-CNwT0NHH",
"digest": {
"sha256": "31960f4162da045cb9b73a0eb3cac33f09d5a2ec1f146f1e457c4a59f478f3e8"
}
},
{
- "@id": "urn:8168ad2f-138b-4b62-99c7-756dbb9cc014",
+ "@id": "bids::sl?.png",
"Label": "sl?.png",
"AtLocation": "sl?.png",
"digest": {
@@ -942,25 +955,25 @@
}
},
{
- "@id": "urn:1a7bf0ee-20cf-41e0-9479-2831210c5957",
+ "@id": "bids::prefiltered_func_data_mcf",
"Label": "prefiltered_func_data_mcf",
"AtLocation": "prefiltered_func_data_mcf",
- "GeneratedBy": "urn:aa7cc227-1492-4b80-a441-76db5060599b",
+ "GeneratedBy": "urn:mcflirt-odII8geb",
"digest": {
"sha256": "83371e264d408de4f678b8182097b39c86bd0a618ca76af6d1dfee5db0903b78"
}
},
{
- "@id": "urn:a5e9a442-6e07-4e62-aead-07f42bd0f50c",
+ "@id": "bids::mc",
"Label": "mc",
"AtLocation": "mc",
- "GeneratedBy": "urn:6a60a386-74a3-475a-a222-594448a74486",
+ "GeneratedBy": "urn:makedire-UK92L4x7",
"digest": {
"sha256": "a1a8fa7b1d2bf5bc0a263e95f926d3d9b656d2572455245d46edf48e93744ffa"
}
},
{
- "@id": "urn:3a074d65-3870-4836-8b82-142937eadec0",
+ "@id": "bids::prefiltered_func_data_mcf.mat",
"Label": "prefiltered_func_data_mcf.mat",
"AtLocation": "prefiltered_func_data_mcf.mat",
"digest": {
@@ -968,7 +981,7 @@
}
},
{
- "@id": "urn:05bf14da-84ae-4952-9681-5aeae5c4e66b",
+ "@id": "bids::prefiltered_func_data_mcf.par",
"Label": "prefiltered_func_data_mcf.par",
"AtLocation": "prefiltered_func_data_mcf.par",
"digest": {
@@ -976,7 +989,7 @@
}
},
{
- "@id": "urn:bfce5176-4c49-4689-a492-b874f6fb9187",
+ "@id": "bids::prefiltered_func_data_mcf_abs.rms",
"Label": "prefiltered_func_data_mcf_abs.rms",
"AtLocation": "prefiltered_func_data_mcf_abs.rms",
"digest": {
@@ -984,7 +997,7 @@
}
},
{
- "@id": "urn:757f4edc-d6f0-4c10-b93f-a62dbdff6c54",
+ "@id": "bids::prefiltered_func_data_mcf_abs_mean.rms",
"Label": "prefiltered_func_data_mcf_abs_mean.rms",
"AtLocation": "prefiltered_func_data_mcf_abs_mean.rms",
"digest": {
@@ -992,7 +1005,7 @@
}
},
{
- "@id": "urn:20adc457-4cb5-47e7-b992-ee701f634086",
+ "@id": "bids::prefiltered_func_data_mcf_rel.rms",
"Label": "prefiltered_func_data_mcf_rel.rms",
"AtLocation": "prefiltered_func_data_mcf_rel.rms",
"digest": {
@@ -1000,7 +1013,7 @@
}
},
{
- "@id": "urn:3639999c-eed2-4529-b8da-8e2e9ae92a0b",
+ "@id": "bids::prefiltered_func_data_mcf_rel_mean.rms",
"Label": "prefiltered_func_data_mcf_rel_mean.rms",
"AtLocation": "prefiltered_func_data_mcf_rel_mean.rms",
"digest": {
@@ -1008,34 +1021,34 @@
}
},
{
- "@id": "urn:ea89480e-c072-4df9-a9d5-d7ef51adb5ce",
+ "@id": "bids::mc",
"Label": "mc",
"AtLocation": "mc",
- "GeneratedBy": "urn:9c9b4cb0-4148-4ac9-abec-285cd3234228",
+ "GeneratedBy": "urn:mv-I5FDYgY1",
"digest": {
"sha256": "a1a8fa7b1d2bf5bc0a263e95f926d3d9b656d2572455245d46edf48e93744ffa"
}
},
{
- "@id": "urn:79cdd853-fa0c-45bb-b58a-4fa937a6c46c",
+ "@id": "bids::rot.png",
"Label": "rot.png",
"AtLocation": "rot.png",
- "GeneratedBy": "urn:73216f9b-6c6c-4495-898c-b6e33ab2a9f4",
+ "GeneratedBy": "urn:fsltsplo-OyOBbM9y",
"digest": {
"sha256": "b8776603f8865a358b2273847d21e63491e7c2e10567fb640608dd47ba721f29"
}
},
{
- "@id": "urn:b30575e5-b909-41d7-81b2-1c3b1f00624d",
+ "@id": "bids::trans.png",
"Label": "trans.png",
"AtLocation": "trans.png",
- "GeneratedBy": "urn:4eedac58-1578-4f7f-a158-576db499125e",
+ "GeneratedBy": "urn:fsltsplo-Oe0ij16S",
"digest": {
"sha256": "496eac1d0ac15e80928780c73766c7791a1707291b2b9a6d1781c2f6a38de3cd"
}
},
{
- "@id": "urn:bd82cd22-8ef8-4d4b-b705-233e1e6f43d3",
+ "@id": "bids::prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"Label": "prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"AtLocation": "prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"digest": {
@@ -1043,34 +1056,34 @@
}
},
{
- "@id": "urn:e6e2b2a3-2877-473a-ac88-37bc4f7b79e6",
+ "@id": "bids::disp.png",
"Label": "disp.png",
"AtLocation": "disp.png",
- "GeneratedBy": "urn:9e5668f5-2b7b-477c-883e-08a7cf7064c7",
+ "GeneratedBy": "urn:fsltsplo-MM1luFDP",
"digest": {
"sha256": "c4615e07e04f0c390d969482634cb62e81d47c818d2866ee866ec9c64a5350fd"
}
},
{
- "@id": "urn:cc3c31ab-c304-46e8-a45d-d21331ec0eba",
+ "@id": "bids::mean_func",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:fa33d422-288f-482a-9654-1817f7f1f217",
+ "GeneratedBy": "urn:fslmaths-EYKSK00I",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:8da457f6-6aae-4cbb-8ed8-dd30f4cf4c30",
+ "@id": "bids::mask",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:90916e20-80a6-4f45-93dc-07564c491938",
+ "GeneratedBy": "urn:bet2-PQSk41oe",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:a39b454f-e907-4aa9-8514-34bce78645df",
+ "@id": "bids::mask_mask",
"Label": "mask_mask",
"AtLocation": "mask_mask",
"digest": {
@@ -1078,132 +1091,124 @@
}
},
{
- "@id": "urn:de3b0abf-5f0c-4836-84f6-bc9644c12c1f",
+ "@id": "bids::mask",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:8fa49467-d795-4959-b9a5-b348e239e62c",
+ "GeneratedBy": "urn:immv-IjjkMRPp",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:de1871d8-045a-467f-9dc9-e90f0985bb89",
+ "@id": "bids::prefiltered_func_data_bet",
"Label": "prefiltered_func_data_bet",
"AtLocation": "prefiltered_func_data_bet",
- "GeneratedBy": "urn:fa61b105-1d73-47fc-93f5-be09bf53c7cc",
+ "GeneratedBy": "urn:fslmaths-XqLE8pkt",
"digest": {
"sha256": "c01f21947b38d9886528dec14edf23dfb55304b7da67569fe93902472b286cf4"
}
},
{
- "@id": "urn:dac3b6a2-ac99-4ff0-9d34-e10ef4cc8206",
+ "@id": "bids::mask",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:9852ebd4-54f0-4016-8588-1be4e8b1ff1b",
+ "GeneratedBy": "urn:fslmaths-VL4VqblJ",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:ecd7913d-2d7a-454b-a4e9-4c3500333405",
+ "@id": "bids::mask",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:acde19c7-3af9-4068-bfb4-7e467ac0017f",
+ "GeneratedBy": "urn:fslmaths-ut9tGWVe",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:ed02a601-2201-43da-b2f7-06ca4ab55d01",
+ "@id": "bids::prefiltered_func_data_thresh",
"Label": "prefiltered_func_data_thresh",
"AtLocation": "prefiltered_func_data_thresh",
- "GeneratedBy": "urn:ccd87bea-cc31-4cc3-9005-34da90ca2810",
+ "GeneratedBy": "urn:fslmaths-nOE8yxx7",
"digest": {
"sha256": "c5c015a8df079b497bbce596808cbbdc09fb39411f490244de192dfa72d33640"
}
},
{
- "@id": "urn:0a9c58e1-195b-4951-9914-70483b001f50",
+ "@id": "bids::mean_func",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:8b37acbd-590d-4b87-bb5a-0681c734a3d3",
+ "GeneratedBy": "urn:fslmaths-OjIaOvPw",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:65fccdc3-0cf4-46b6-b5ae-6472af9204c6",
+ "@id": "bids::prefiltered_func_data_smooth",
"Label": "prefiltered_func_data_smooth",
"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:0836490c-40f2-462e-a071-1558e448e0dd",
+ "GeneratedBy": "urn:susan-SmymgzPJ",
"digest": {
"sha256": "2a4901d885fce0b083c9f99364da8dcff184635e74ab011f53a68cfc6827b429"
}
},
{
- "@id": "urn:6b77283c-0366-4a19-b108-5a6f3bafe64f",
+ "@id": "bids::prefiltered_func_data_smooth",
"Label": "prefiltered_func_data_smooth",
"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:d7a66507-3350-42b8-9e9f-f37d0e3d31f7",
+ "GeneratedBy": "urn:fslmaths-O8pCVrLL",
"digest": {
"sha256": "2a4901d885fce0b083c9f99364da8dcff184635e74ab011f53a68cfc6827b429"
}
},
{
- "@id": "urn:584874b2-dc50-4bcc-ba3f-57f724c25516",
+ "@id": "bids::prefiltered_func_data_intnorm",
"Label": "prefiltered_func_data_intnorm",
"AtLocation": "prefiltered_func_data_intnorm",
- "GeneratedBy": "urn:6fd64536-641a-413b-8d77-390f0514fea8",
+ "GeneratedBy": "urn:fslmaths-MZCCcDOx",
"digest": {
"sha256": "0698a276f6f0fdccfb06033926d333a176503a09aaa87b78384fbffbf1c54dee"
}
},
{
- "@id": "urn:e1bd11f2-70d0-4021-9a88-556768d353e1",
+ "@id": "bids::tempMean",
"Label": "tempMean",
"AtLocation": "tempMean",
- "GeneratedBy": "urn:b60f8029-dace-4def-b134-96c533ed2469",
+ "GeneratedBy": "urn:fslmaths-As3g3UB7",
"digest": {
"sha256": "1a01513c76bc17516b60df315a1922789ce79d72e66e105fbf2723df9cb1b038"
}
},
{
- "@id": "urn:9381c42a-f942-49f3-bcf2-577fbb62b05c",
- "Label": "15.0",
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- "GeneratedBy": "urn:231336c7-5029-499e-aa70-72035c9d8213",
- "digest": {
- "sha256": "552db91328a881034f16ec50203ba34d4af448f52c616eb28db6c07aa575a286"
- }
- },
- {
- "@id": "urn:7b84f725-23d1-47b6-bd1a-8a066b03a9c8",
+ "@id": "bids::prefiltered_func_data_tempfilt",
"Label": "prefiltered_func_data_tempfilt",
"AtLocation": "prefiltered_func_data_tempfilt",
+ "GeneratedBy": "urn:fslmaths-I24yLD9V",
"digest": {
"sha256": "a1836f4694e7ffdb50484626724602498c7b22b4f3cdd1e7d105efd336cbc8bd"
}
},
{
- "@id": "urn:5a3ed7a7-f404-4238-9a73-9992979af9d4",
+ "@id": "bids::filtered_func_data",
"Label": "filtered_func_data",
"AtLocation": "filtered_func_data",
- "GeneratedBy": "urn:fc4f2b90-f6c6-410a-a8ff-78d8206b5df0",
+ "GeneratedBy": "urn:fslmaths-P4mbrSSu",
"digest": {
"sha256": "2a1854e3b48a54f88e063191e25159015a0afbd300d18a1cfda37b4b68a1ee69"
}
},
{
- "@id": "urn:2eea1906-9589-474a-88a7-4c881e278ee4",
+ "@id": "bids::mean_func",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:5d73a76e-4df1-4fd3-a040-769dac5ac08d",
+ "GeneratedBy": "urn:fslmaths-ZreUCdz4",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:2ed1140e-d2cf-45c7-9717-66283f93a8af",
+ "@id": "bids::prefiltered_func_data*",
"Label": "prefiltered_func_data*",
"AtLocation": "prefiltered_func_data*",
"digest": {
@@ -1211,64 +1216,64 @@
}
},
{
- "@id": "urn:1513ce1b-68ad-4e5e-bc6f-67d41158cf03",
+ "@id": "bids::custom_timing_files",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:dbcf467f-1db2-4626-a77a-4ff116e8eff2",
+ "GeneratedBy": "urn:makedire-GemLkPxp",
"digest": {
"sha256": "1d7e19792328d5040f2f9fb3c15d59de90fc771785f81c67039a043bd5f2ed20"
}
},
{
- "@id": "urn:715350ea-baf9-4e67-af8b-4c223751977f",
+ "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
"Label": "sub-01_tone_counting.txt",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
+ "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
"digest": {
- "sha256": "c120d27b9d5d81a91be0e55f5cb880b2cb7de6c655554d9c15c9c04c6232ea8e"
+ "sha256": "165398224a205d2fc0b19354e15d9b085c6d81e333b69c4697b7894a2549be0b"
}
},
{
- "@id": "urn:f4175f7f-1672-46eb-aba1-2ec74d8ac766",
+ "@id": "bids::custom_timing_files/ev1.txt",
"Label": "ev1.txt",
"AtLocation": "custom_timing_files/ev1.txt",
- "GeneratedBy": "urn:c57f3b03-6b8b-4a49-91ad-10414a5bb1f6"
+ "GeneratedBy": "urn:fslfixte-iX0H2Ui2"
},
{
- "@id": "urn:519e09f7-3485-43b6-bbe5-d045cfa8a316",
+ "@id": "bids::custom_timing_files",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:cbb044da-cc8b-4ef7-977c-2c3794c9027a",
+ "GeneratedBy": "urn:makedire-6kNWcrAo",
"digest": {
"sha256": "1d7e19792328d5040f2f9fb3c15d59de90fc771785f81c67039a043bd5f2ed20"
}
},
{
- "@id": "urn:fcf71ded-26d2-4518-a3e8-bb58b66bdb22",
+ "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
"Label": "sub-01_tone_counting_probe.txt",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
+ "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
"digest": {
- "sha256": "f09eeb82fa0be8e8759a5269403f36ec2b7dbf2c5b6caba1f0f985cc6cb3f703"
+ "sha256": "8b912293767f1a5e082311f6aaf0c44fc91fe45b0f2ae7f80e368bc2f4c2918a"
}
},
{
- "@id": "urn:4fe9ad80-620c-406c-a242-7f323181a475",
+ "@id": "bids::custom_timing_files/ev2.txt",
"Label": "ev2.txt",
"AtLocation": "custom_timing_files/ev2.txt",
- "GeneratedBy": "urn:e4f1c0c1-d62c-4d95-9f6a-2dc7252f0873"
+ "GeneratedBy": "urn:fslfixte-bY3ov1IQ"
},
{
- "@id": "urn:a054bb26-df1e-4d57-bb67-aac6b5241eb0",
+ "@id": "bids::mc/prefiltered_func_data_mcf.par",
"Label": "prefiltered_func_data_mcf.par",
"AtLocation": "mc/prefiltered_func_data_mcf.par"
},
{
- "@id": "urn:5c5397d3-55c6-4311-aa95-59d746473bec",
+ "@id": "bids::mc/prefiltered_func_data_mcf_diff",
"Label": "prefiltered_func_data_mcf_diff",
"AtLocation": "mc/prefiltered_func_data_mcf_diff",
- "GeneratedBy": "urn:5c602888-1bca-4c78-8710-3274acc87d5e"
+ "GeneratedBy": "urn:mpdiffpo-ymFrapRB"
},
{
- "@id": "urn:ba63f369-bdcf-4064-8aef-f45a16a720c4",
+ "@id": "bids::design",
"Label": "design",
"AtLocation": "design",
"digest": {
@@ -1276,67 +1281,112 @@
}
},
{
- "@id": "urn:b5eac9fd-9254-4683-accf-f45cc6caaa64",
- "Label": "res4d",
- "AtLocation": "stats/res4d",
+ "@id": "bids::stats",
+ "Label": "stats",
+ "AtLocation": "stats",
"digest": {
- "sha256": "8845286f36caedf891a02afddc4175ea46f18f830b59a8c5026962184a530699"
+ "sha256": "a9f3e135372514a16d11a8038262b3eff94ccd69a9b35c4724b2759cfc944a07"
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},
{
- "@id": "urn:a49dacf2-01e0-4a32-aa85-02ab54a8d3b9",
- "Label": "smoothness",
- "AtLocation": "stats/smoothness",
- "GeneratedBy": "urn:7bd5dc94-90f0-4d26-b304-d5ecea6af65e",
+ "@id": "bids::design.mat",
+ "Label": "design.mat",
+ "AtLocation": "design.mat",
"digest": {
- "sha256": "67b0aaf95a257beff60d331b56265034807ca51e67e2d312d481d5835ef0b1d0"
+ "sha256": "1c1a6ef59a355e1f6f81e741e157784ccbe066ba3594a07aa9b16781e3d5bb25"
}
},
{
- "@id": "urn:6f086e2c-b943-4856-a4e4-b79e5ce78fb0",
- "Label": "zstat1",
- "AtLocation": "stats/zstat1",
+ "@id": "bids::design.con",
+ "Label": "design.con",
+ "AtLocation": "design.con",
"digest": {
- "sha256": "70ae47cee1ea1d3f1f6f8aa7ac51f2641cb2fcb745dfd8cc54a389346e6fa094"
+ "sha256": "5808d1be37dd8f2a4906b710bb384fbee62faa4a46b2bc6847afc8962ed4eb54"
}
},
{
- "@id": "urn:5255d402-08a6-4dd0-aefa-d239d213fce0",
+ "@id": "bids::stats",
+ "Label": "stats",
+ "AtLocation": "stats",
+ "GeneratedBy": "urn:filmgls-3IoqFYtu",
+ "digest": {
+ "sha256": "a9f3e135372514a16d11a8038262b3eff94ccd69a9b35c4724b2759cfc944a07"
+ }
+ },
+ {
+ "@id": "bids::stats/res4d",
+ "Label": "res4d",
+ "AtLocation": "stats/res4d"
+ },
+ {
+ "@id": "bids::stats/smoothness",
+ "Label": "smoothness",
+ "AtLocation": "stats/smoothness",
+ "GeneratedBy": "urn:smoothes-paAW6C17"
+ },
+ {
+ "@id": "bids::stats/zstat1",
+ "Label": "zstat1",
+ "AtLocation": "stats/zstat1"
+ },
+ {
+ "@id": "bids::thresh_zstat1",
"Label": "thresh_zstat1",
"AtLocation": "thresh_zstat1",
- "GeneratedBy": "urn:73cd9e98-c666-404b-ae9b-7ac11c80b23f",
+ "GeneratedBy": "urn:fslmaths-H8tXahSy",
"digest": {
"sha256": "662e7ba670e124d15bb3cc18b818868f76604578034b524c8882f35fc5db413f"
}
},
{
- "@id": "urn:62a462c1-c20a-4255-b51a-4b0d02ff5a35",
+ "@id": "bids::stats/cope1",
"Label": "cope1",
- "AtLocation": "stats/cope1",
- "digest": {
- "sha256": "bf3b603569da6dbe3d6f0e8667d346f3ac943c9d01d2fc9743ce17abeb1547fb"
- }
+ "AtLocation": "stats/cope1"
},
{
- "@id": "urn:e6997f21-9f7f-4f04-8936-c6985a945567",
+ "@id": "bids::cluster_mask_zstat1",
"Label": "cluster_mask_zstat1",
"AtLocation": "cluster_mask_zstat1",
- "GeneratedBy": "urn:2777a5ba-b8f6-4bb8-8a26-ff00ab683a62",
+ "GeneratedBy": "urn:cluster-E7oup06U",
"digest": {
"sha256": "b28c170e33d2917cac55183786616a9e976e5e7f30dc7c8666341f12ed6d0277"
}
},
{
- "@id": "urn:23be68f7-c7f8-4eb2-b641-133be843e323",
+ "@id": "bids::thresh_zstat1",
+ "Label": "thresh_zstat1",
+ "AtLocation": "thresh_zstat1",
+ "GeneratedBy": "urn:cluster-E7oup06U",
+ "digest": {
+ "sha256": "662e7ba670e124d15bb3cc18b818868f76604578034b524c8882f35fc5db413f"
+ }
+ },
+ {
+ "@id": "bids::lmax_zstat1.txt",
+ "Label": "lmax_zstat1.txt",
+ "AtLocation": "lmax_zstat1.txt",
+ "GeneratedBy": "urn:cluster-E7oup06U",
+ "digest": {
+ "sha256": "d44ee21719775397a1a95ede6778d25404b50e8bd259dbdf02d2fde635fc81a5"
+ }
+ },
+ {
+ "@id": "bids::stats/cope1",
"Label": "cope1",
"AtLocation": "stats/cope1",
- "GeneratedBy": "urn:2777a5ba-b8f6-4bb8-8a26-ff00ab683a62",
+ "GeneratedBy": "urn:cluster-E7oup06U"
+ },
+ {
+ "@id": "bids::cluster_zstat1.txt",
+ "Label": "cluster_zstat1.txt",
+ "AtLocation": "cluster_zstat1.txt",
+ "GeneratedBy": "urn:cluster-E7oup06U",
"digest": {
- "sha256": "bf3b603569da6dbe3d6f0e8667d346f3ac943c9d01d2fc9743ce17abeb1547fb"
+ "sha256": "b06695ff4f0a8158fa439b1ddf224b58d344606d400885c177390d09506e8e4c"
}
},
{
- "@id": "urn:d5163407-701a-404f-9edd-ef1427791617",
+ "@id": "bids::cluster_zstat1",
"Label": "cluster_zstat1",
"AtLocation": "cluster_zstat1",
"digest": {
@@ -1344,25 +1394,25 @@
}
},
{
- "@id": "urn:66375eb5-3649-457d-a56b-f5e53f3e3cf7",
+ "@id": "bids::rendered_thresh_zstat1",
"Label": "rendered_thresh_zstat1",
"AtLocation": "rendered_thresh_zstat1",
- "GeneratedBy": "urn:08595e41-b6d0-4515-b786-e782353f3718",
+ "GeneratedBy": "urn:overlay-9EILhFVq",
"digest": {
"sha256": "de5b9d44d95f4252f491eb45c76a0ae2b4d2c75b58664fc0df7d9153810c0bf6"
}
},
{
- "@id": "urn:9ffffff2-cbde-492e-826e-c36fa45269c4",
+ "@id": "bids::rendered_thresh_zstat1.png",
"Label": "rendered_thresh_zstat1.png",
"AtLocation": "rendered_thresh_zstat1.png",
- "GeneratedBy": "urn:18b0a656-3c03-498e-b5c1-fa41f1592e42",
+ "GeneratedBy": "urn:slicer-lKcrJvxP",
"digest": {
"sha256": "15d6a8bf7a902df8c5feeb7468a3d0caacf9eb3067c0840c2f4763f5e2301527"
}
},
{
- "@id": "urn:6dd32c60-529c-4e5e-b6d5-67ab04a4796f",
+ "@id": "bids::/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif",
"Label": "ramp.gif",
"AtLocation": "/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif",
"digest": {
@@ -1370,28 +1420,28 @@
}
},
{
- "@id": "urn:bd48635b-88cf-43db-8e3d-0c149fc6cbbb",
+ "@id": "bids::.ramp.gif",
"Label": ".ramp.gif",
"AtLocation": ".ramp.gif",
- "GeneratedBy": "urn:fb9c408c-80e0-4ff0-b375-4886297f18bf",
+ "GeneratedBy": "urn:cp-pEZlO6Nc",
"digest": {
"sha256": "93f4284ccb854d5a41401d9360a13223017b67479cb289a33d83836922e028a4"
}
},
{
- "@id": "urn:4cb49b45-2fc1-44d0-b942-81ef74816b9e",
+ "@id": "bids::tsplot",
"Label": "tsplot",
"AtLocation": "tsplot",
- "GeneratedBy": "urn:26abca2c-13dd-49f6-8680-caa46c170d5f",
+ "GeneratedBy": "urn:makedire-M3VVjUGh",
"digest": {
"sha256": "2a74042f4edf02288edf16961307f741651efb4346e102a04b7603e781d1625e"
}
},
{
- "@id": "urn:cc69fc0d-25e0-46fe-8712-4370967c20e5",
+ "@id": "bids::tsplot",
"Label": "tsplot",
"AtLocation": "tsplot",
- "GeneratedBy": "urn:c141d9b9-99a2-4453-ac73-a8fd148700f6",
+ "GeneratedBy": "urn:tsplot-DUfA2b5q",
"digest": {
"sha256": "2a74042f4edf02288edf16961307f741651efb4346e102a04b7603e781d1625e"
}
diff --git a/examples/from_parsers/fsl/fsl_motion_reg_der_report_log.png b/examples/from_parsers/fsl/fsl_motion_reg_der_report_log.png
index 3776ea02e..20b304b5e 100644
Binary files a/examples/from_parsers/fsl/fsl_motion_reg_der_report_log.png and b/examples/from_parsers/fsl/fsl_motion_reg_der_report_log.png differ
diff --git a/examples/from_parsers/fsl/fsl_motion_reg_report_log.html b/examples/from_parsers/fsl/fsl_motion_reg_report_log.html
index 0fce4c357..bf9a31113 100644
--- a/examples/from_parsers/fsl/fsl_motion_reg_report_log.html
+++ b/examples/from_parsers/fsl/fsl_motion_reg_report_log.html
@@ -35,20 +35,20 @@ Progress Report / Log
326890
Initialisation
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
Total original volumes = 104
/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1
Preprocessing:Stage 1
-/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90
+/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/example_func.nii.gz -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90
Option -F ( FEAT version parameter ) selected with argument "6.00"
Option -d ( output directory ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat"
Option -l ( logfile )input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/logs/feat2_pre"
Option -R ( html unwarping report ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/report_unwarp.html"
Option -r ( html registration report ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/report_reg.html"
Option -i ( main input ) input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/example_func.nii.gz"
-Option -h ( high-res structural image ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
+Option -h ( high-res structural image ) selected with argument "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
Option -w ( highres dof ) selected with argument "BBR"
Option -x ( highres search ) selected with argument "90"
Option -s ( standard image ) selected with argument "/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain"
@@ -59,10 +59,10 @@ Progress Report / Log
/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/reg
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head
did not find file: example_func2highres.mat. Generating transform.
@@ -128,9 +128,9 @@ Progress Report / Log
/bin/rm -rf prefiltered_func_data*
Stats
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
cp mc/prefiltered_func_data_mcf.par mc/prefiltered_func_data_mcf_final.par
diff --git a/examples/from_parsers/fsl/fsl_motion_reg_report_log.jsonld b/examples/from_parsers/fsl/fsl_motion_reg_report_log.jsonld
index df932b1fa..bf4ca927b 100644
--- a/examples/from_parsers/fsl/fsl_motion_reg_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_motion_reg_report_log.jsonld
@@ -4,600 +4,609 @@
"Records": {
"Software": [
{
- "@id": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:fsl-q1u8Lfn3",
"@type": "prov:SoftwareAgent",
"Label": "FSL",
- "Version": "xxx"
+ "Version": "xxx",
+ "AltIdentifier": "RRID:SCR_002823"
}
],
"Activities": [
{
- "@id": "urn:f01afec8-8551-4e82-a73e-7b0e7466afdd",
+ "@id": "urn:fslmaths-3e1BW8zk",
"Label": "fslmaths",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
"Used": [
- "urn:89d72914-4200-41f9-a756-1f0024506f14"
+ "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold"
]
},
{
- "@id": "urn:029ff773-b876-4565-854a-eafde9c7aaaa",
+ "@id": "urn:fslroi-P8KgYNMI",
"Label": "fslroi",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1",
"Used": [
- "urn:86b9e119-37bf-49fd-b850-0570cc53c3b8"
+ "bids::prefiltered_func_data"
]
},
{
- "@id": "urn:32abc1e4-0bbf-4ef4-a8e9-c2f67a5eb11c",
+ "@id": "urn:mainfeat-L2O1FWWa",
"Label": "mainfeatreg",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/example_func.nii.gz -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
"Used": [
- "urn:a76bfa82-0ac8-4e80-ac42-ec944929459f",
- "urn:f6fe1240-45ad-4a19-a07d-df7de9f3f96d",
- "urn:fd12a58d-0911-428a-9049-3519c84b23d6"
+ "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/example_func.nii.gz",
+ "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain",
+ "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
]
},
{
- "@id": "urn:55b47535-6244-4008-b24c-b417f36f1a07",
+ "@id": "urn:makedire-081RCxsU",
"Label": "Make directory",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/reg",
"Used": []
},
{
- "@id": "urn:8cb2cdce-390d-44a3-9b79-61baed152e49",
+ "@id": "urn:fslmaths-oZkoFxMk",
"Label": "fslmaths",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
"Used": [
- "urn:fd12a58d-0911-428a-9049-3519c84b23d6"
+ "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
]
},
{
- "@id": "urn:613d4024-978b-4042-8677-856dcd153fdd",
+ "@id": "urn:fslmaths-Di35akWj",
"Label": "fslmaths",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
"Used": [
- "urn:e2b94bbc-7b9d-42b4-a4a8-02abcdf4eafd"
+ "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w"
]
},
{
- "@id": "urn:7bb84456-964c-4314-bb24-10f5018731ab",
+ "@id": "urn:epireg-g2VLNGNl",
"Label": "epi_reg",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/usr/local/packages/fsl-5.0.10/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres",
- "Used": []
+ "Used": [
+ "bids::example_func",
+ "bids::highres",
+ "bids::highres_head"
+ ]
},
{
- "@id": "urn:8e237c8a-8985-456f-ba72-ae41b9f753a0",
+ "@id": "urn:convertx-OwOGE44S",
"Label": "convert_xfm",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/usr/local/packages/fsl-5.0.10/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat",
"Used": [
- "urn:86b35929-f1ee-473d-8639-edd3a207b228"
+ "bids::example_func2highres.mat"
]
},
{
- "@id": "urn:d41c4d7c-7f7f-4c9d-8db0-b3bb3e06f8a7",
+ "@id": "urn:slicer-WDHg7RO5",
"Label": "slicer",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:45e2bca9-7675-4ee6-8c57-7fcd33d51a0e",
- "urn:bf539143-ed61-483a-9a54-b5409615e050"
+ "bids::example_func2highres",
+ "bids::highres"
]
},
{
- "@id": "urn:7d9c5fc6-bbe9-46f4-aa91-a071f2605908",
+ "@id": "urn:pngappen-gg2Ssdze",
"Label": "pngappend",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres1.png",
"Used": [
- "urn:10c6cdeb-975a-41c9-9aaf-33d0116e2f1a",
- "urn:132f3df2-fdac-4638-b3f8-9cd0419c22c1",
- "urn:1fb66b81-602b-4a6f-8d21-c58996c3dc91",
- "urn:5f88ea35-c580-447b-9fcd-a365ca8b1160",
- "urn:81bdbe32-8fd2-4c86-ad90-d75314e52071",
- "urn:820883ac-814d-49c1-95b6-2129629530ef",
- "urn:829059e7-40d3-402e-acd7-52ce046b7263",
- "urn:9c045eed-e0d8-4752-9f38-b03c8961ba54",
- "urn:b43412a0-0f56-4d67-8a7e-634c25544801",
- "urn:bf13f751-1153-4368-91c1-d903622f7d4d",
- "urn:c59e7f5b-8800-43da-9512-3cf33aa2d64f",
- "urn:eeb424ca-31ff-4ca3-b854-306184f22561"
+ "bids::sla.png",
+ "bids::slb.png",
+ "bids::slc.png",
+ "bids::sld.png",
+ "bids::sle.png",
+ "bids::slf.png",
+ "bids::slg.png",
+ "bids::slh.png",
+ "bids::sli.png",
+ "bids::slj.png",
+ "bids::slk.png",
+ "bids::sll.png"
]
},
{
- "@id": "urn:7f373576-0167-4294-9e8a-e15cfad9516b",
+ "@id": "urn:slicer-xfVLnC1i",
"Label": "slicer",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:45e2bca9-7675-4ee6-8c57-7fcd33d51a0e",
- "urn:bf539143-ed61-483a-9a54-b5409615e050"
+ "bids::example_func2highres",
+ "bids::highres"
]
},
{
- "@id": "urn:dfa1c116-dd9b-4a89-b521-148073f45dd4",
+ "@id": "urn:pngappen-DdSGKIgw",
"Label": "pngappend",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres2.png",
"Used": [
- "urn:10c6cdeb-975a-41c9-9aaf-33d0116e2f1a",
- "urn:132f3df2-fdac-4638-b3f8-9cd0419c22c1",
- "urn:1fb66b81-602b-4a6f-8d21-c58996c3dc91",
- "urn:5f88ea35-c580-447b-9fcd-a365ca8b1160",
- "urn:81bdbe32-8fd2-4c86-ad90-d75314e52071",
- "urn:820883ac-814d-49c1-95b6-2129629530ef",
- "urn:829059e7-40d3-402e-acd7-52ce046b7263",
- "urn:9c045eed-e0d8-4752-9f38-b03c8961ba54",
- "urn:b43412a0-0f56-4d67-8a7e-634c25544801",
- "urn:bf13f751-1153-4368-91c1-d903622f7d4d",
- "urn:c59e7f5b-8800-43da-9512-3cf33aa2d64f",
- "urn:eeb424ca-31ff-4ca3-b854-306184f22561"
+ "bids::sla.png",
+ "bids::slb.png",
+ "bids::slc.png",
+ "bids::sld.png",
+ "bids::sle.png",
+ "bids::slf.png",
+ "bids::slg.png",
+ "bids::slh.png",
+ "bids::sli.png",
+ "bids::slj.png",
+ "bids::slk.png",
+ "bids::sll.png"
]
},
{
- "@id": "urn:44317bf6-99a8-4fa3-a1d4-6c5b970ddeda",
+ "@id": "urn:pngappen-AABwFbAU",
"Label": "pngappend",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend example_func2highres1.png example_func2highres2.png example_func2highres.png",
"Used": [
- "urn:5a798d51-b0f0-4d2e-81da-8f835a289d93",
- "urn:d0817bad-4522-48f7-9e50-31e3489d82ae"
+ "bids::example_func2highres1.png",
+ "bids::example_func2highres2.png"
]
},
{
- "@id": "urn:d965b6df-759f-418b-a6e5-0eac46db33da",
+ "@id": "urn:rm-9FeJXu6N",
"Label": "rm",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/bin/rm -f sl?.png example_func2highres2.png",
"Used": [
- "urn:4342af1c-2b81-4c02-b669-ccdebeaafff8",
- "urn:d0817bad-4522-48f7-9e50-31e3489d82ae"
+ "bids::example_func2highres2.png",
+ "bids::sl?.png"
]
},
{
- "@id": "urn:efe55a24-f1b1-4b61-8343-0087b38ed521",
+ "@id": "urn:rm-QeRTve2R",
"Label": "rm",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/bin/rm example_func2highres1.png",
"Used": [
- "urn:5a798d51-b0f0-4d2e-81da-8f835a289d93"
+ "bids::example_func2highres1.png"
]
},
{
- "@id": "urn:6e82ab5e-2cae-4566-b691-f4eb52ac5a93",
+ "@id": "urn:mcflirt-mRIur6l3",
"Label": "mcflirt",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/usr/local/packages/fsl-5.0.10/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs -spline_final",
"Used": [
- "urn:86b9e119-37bf-49fd-b850-0570cc53c3b8"
+ "bids::prefiltered_func_data"
]
},
{
- "@id": "urn:fb0a4cf2-0b8a-445d-b252-7e765e1ba496",
+ "@id": "urn:makedire-AoaD1CwM",
"Label": "Make directory",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/bin/mkdir -p mc",
"Used": []
},
{
- "@id": "urn:f52d0638-4f8b-46ef-911f-4a11a3bd6392",
+ "@id": "urn:mv-2yFPQBIr",
"Label": "mv",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc",
"Used": [
- "urn:406533ba-f5f6-475d-b834-784305e689ce",
- "urn:794883bf-d745-44bf-880c-8341377bd9ec",
- "urn:ca9a4718-ff12-4c49-bc9b-c8e5d0c67304",
- "urn:da0a1900-b8f3-4fff-85b1-b9f700cefdff",
- "urn:ee05cd16-9e60-45d8-9454-736cb892f197",
- "urn:fa8d9523-1bbe-4d63-99df-ddfc0e3f8fd7"
+ "bids::prefiltered_func_data_mcf.mat",
+ "bids::prefiltered_func_data_mcf.par",
+ "bids::prefiltered_func_data_mcf_abs.rms",
+ "bids::prefiltered_func_data_mcf_abs_mean.rms",
+ "bids::prefiltered_func_data_mcf_rel.rms",
+ "bids::prefiltered_func_data_mcf_rel_mean.rms"
]
},
{
- "@id": "urn:f8728d5a-b3f1-4f75-b4cd-73ed82ad1764",
+ "@id": "urn:fsltsplo-J0iwwUfZ",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png",
"Used": [
- "urn:ee05cd16-9e60-45d8-9454-736cb892f197"
+ "bids::prefiltered_func_data_mcf.par"
]
},
{
- "@id": "urn:e5c7fec3-13ac-43b2-b147-e6c89efc06ad",
+ "@id": "urn:fsltsplo-D7UjyFRB",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png",
"Used": [
- "urn:ee05cd16-9e60-45d8-9454-736cb892f197"
+ "bids::prefiltered_func_data_mcf.par"
]
},
{
- "@id": "urn:0105302f-6dee-4f56-b390-8f4c7b70f68b",
+ "@id": "urn:fsltsplo-InC74Sut",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png",
"Used": [
- "urn:43302e4a-2df7-4b56-ba7c-61f14009fe14"
+ "bids::prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms"
]
},
{
- "@id": "urn:482a00bc-4f3f-4866-adff-1ca4914f0f9c",
+ "@id": "urn:fslmaths-R434LBry",
"Label": "fslmaths",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func",
"Used": [
- "urn:32cae31b-c5e5-42d4-a310-416b886eed55"
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:6facd168-6205-4eab-902a-051b05e0d300",
+ "@id": "urn:bet2-WJQyP3oC",
"Label": "bet2",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/usr/local/packages/fsl-5.0.10/bin/bet2 mean_func mask -f 0.3 -n -m",
"Used": [
- "urn:afd3d158-c888-4146-81cc-da7a53e3cd8c"
+ "bids::mean_func"
]
},
{
- "@id": "urn:0840ffaf-344d-4b50-b9b5-1a4dd76fe080",
+ "@id": "urn:immv-4v7jamiF",
"Label": "immv",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/usr/local/packages/fsl-5.0.10/bin/immv mask_mask mask",
"Used": [
- "urn:bf820444-ae9b-4433-98a7-a11014b56ea1"
+ "bids::mask_mask"
]
},
{
- "@id": "urn:fa9c14f8-dc0e-4bf6-a4c1-efa702904c63",
+ "@id": "urn:fslmaths-qYlHII1V",
"Label": "fslmaths",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet",
"Used": [
- "urn:32cae31b-c5e5-42d4-a310-416b886eed55",
- "urn:3a2f1b8e-942c-4178-8f58-491c55c796a7"
+ "bids::mask",
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:65ac2267-948b-4892-afd1-d931dd616401",
+ "@id": "urn:fslstats-4JFp7lV9",
"Label": "fslstats",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_bet -p 2 -p 98",
"Used": [
- "urn:42579cc8-6d6b-44d4-bbb5-b30f3f880bfc"
+ "bids::prefiltered_func_data_bet"
]
},
{
- "@id": "urn:db70a010-5f90-48af-8c31-6be63a2c5d14",
+ "@id": "urn:fslmaths-YUTXrUXd",
"Label": "fslmaths",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_bet -thr 74.4585571 -Tmin -bin mask -odt char",
"Used": [
- "urn:42579cc8-6d6b-44d4-bbb5-b30f3f880bfc"
+ "bids::prefiltered_func_data_bet"
]
},
{
- "@id": "urn:17be67dd-6c13-4769-b68a-36e4a40852c4",
+ "@id": "urn:fslstats-MyWqhTsi",
"Label": "fslstats",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_mcf -k mask -p 50",
"Used": [
- "urn:32cae31b-c5e5-42d4-a310-416b886eed55"
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:2f1d7d43-4b07-48b9-8496-eebbf76893b0",
+ "@id": "urn:fslmaths-wwPgPnYX",
"Label": "fslmaths",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -dilF mask",
"Used": [
- "urn:3a2f1b8e-942c-4178-8f58-491c55c796a7"
+ "bids::mask"
]
},
{
- "@id": "urn:9e154a04-adf5-4892-9856-fd8ce771786a",
+ "@id": "urn:fslmaths-C3yoMH6k",
"Label": "fslmaths",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh",
"Used": [
- "urn:32cae31b-c5e5-42d4-a310-416b886eed55",
- "urn:3a2f1b8e-942c-4178-8f58-491c55c796a7"
+ "bids::mask",
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:ad350bf9-e517-49d8-9019-361963775a0f",
+ "@id": "urn:fslmaths-Cx8FTnEr",
"Label": "fslmaths",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func",
"Used": [
- "urn:5145d4af-4d72-4daa-9067-cb76d89eed9c"
+ "bids::prefiltered_func_data_thresh"
]
},
{
- "@id": "urn:a6ea5103-3e65-49ed-8c46-e7dd0671cb33",
+ "@id": "urn:susan-2AISnNgW",
"Label": "susan",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/usr/local/packages/fsl-5.0.10/bin/susan prefiltered_func_data_thresh 445.8289035 2.54777070064 3 1 1 mean_func 445.8289035 prefiltered_func_data_smooth",
"Used": [
- "urn:5145d4af-4d72-4daa-9067-cb76d89eed9c"
+ "bids::prefiltered_func_data_thresh"
]
},
{
- "@id": "urn:3d1775e1-e6d1-44d4-9cc6-e7b2558fbaec",
+ "@id": "urn:fslmaths-uhxHBqAa",
"Label": "fslmaths",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth",
"Used": [
- "urn:3a2f1b8e-942c-4178-8f58-491c55c796a7",
- "urn:e7b0996d-40d0-4d73-b587-f8982e0c5c55"
+ "bids::mask",
+ "bids::prefiltered_func_data_smooth"
]
},
{
- "@id": "urn:9002f1b5-4239-44e4-8932-7d943f25e6e9",
+ "@id": "urn:fslmaths-OGv4Qr30",
"Label": "fslmaths",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mul 16.8225970571 prefiltered_func_data_intnorm",
"Used": [
- "urn:e7b0996d-40d0-4d73-b587-f8982e0c5c55"
+ "bids::prefiltered_func_data_smooth"
]
},
{
- "@id": "urn:fb916597-66ca-4bbc-b771-b741c3716c95",
+ "@id": "urn:fslmaths-kI7gzSJZ",
"Label": "fslmaths",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean",
"Used": [
- "urn:2c0f03e8-19de-4de6-8318-65d031bacb43"
+ "bids::prefiltered_func_data_intnorm"
]
},
{
- "@id": "urn:3844eec4-0749-4130-aed2-99ca8096e764",
+ "@id": "urn:fslmaths-tmHau3zK",
"Label": "fslmaths",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -bptf 15.0 -1 -add tempMean prefiltered_func_data_tempfilt",
"Used": [
- "urn:2c0f03e8-19de-4de6-8318-65d031bacb43",
- "urn:fcee0b5c-13c9-4567-8f44-629ba9e7a513"
+ "bids::prefiltered_func_data_intnorm",
+ "bids::tempMean"
]
},
{
- "@id": "urn:70a2e9c1-f699-4996-92ea-cc6e5e822379",
+ "@id": "urn:imrm-NX9LduVv",
"Label": "imrm",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/usr/local/packages/fsl-5.0.10/bin/imrm tempMean",
"Used": [
- "urn:fcee0b5c-13c9-4567-8f44-629ba9e7a513"
+ "bids::tempMean"
]
},
{
- "@id": "urn:fa4e18e3-3c2a-48c1-9e6d-9e8c4fea9da6",
+ "@id": "urn:fslmaths-8mzN1fkC",
"Label": "fslmaths",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data",
"Used": [
- "urn:9455faad-b8cd-462a-a17d-795342424c45"
+ "bids::prefiltered_func_data_tempfilt"
]
},
{
- "@id": "urn:77118d6c-abae-4566-a58f-c5813e9b102c",
+ "@id": "urn:fslmaths-tvhntGIA",
"Label": "fslmaths",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths filtered_func_data -Tmean mean_func",
"Used": [
- "urn:e69f21ae-6759-4681-95b6-c8ad39e7de22"
+ "bids::filtered_func_data"
]
},
{
- "@id": "urn:86c6e3c7-7ffe-4555-8dc3-3b571ddee012",
+ "@id": "urn:rm-0HzAUihb",
"Label": "rm",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/bin/rm -rf prefiltered_func_data*",
"Used": [
- "urn:c5c4d138-bb2c-48b5-a3c2-79041dd19565"
+ "bids::prefiltered_func_data*"
]
},
{
- "@id": "urn:9722cc70-09b9-4f29-8d8b-fdbb14cd3513",
+ "@id": "urn:makedire-nVCXGaK7",
"Label": "Make directory",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
- "@id": "urn:f4544d21-aeac-43af-8bee-dce242d6ad99",
+ "@id": "urn:fslfixte-Yaoid2yI",
"Label": "fslFixText",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
"Used": [
- "urn:e0e86ef2-0070-4e6a-a7ef-2048348dca4a"
+ "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt"
]
},
{
- "@id": "urn:dfcbdf85-06e9-4175-ad85-a65841a04ff1",
+ "@id": "urn:makedire-Z7VhBRjC",
"Label": "Make directory",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
- "@id": "urn:243917d6-f1de-4d9b-9a28-5b18b08c2b7d",
+ "@id": "urn:fslfixte-BP3JdcoO",
"Label": "fslFixText",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
"Used": [
- "urn:06dd1a96-a05a-4144-b35a-53463465f137"
+ "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt"
]
},
{
- "@id": "urn:a8a46b77-99a6-42bf-837a-9a8c1c51f833",
+ "@id": "urn:cp-QigRY0AI",
"Label": "cp",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "cp mc/prefiltered_func_data_mcf.par mc/prefiltered_func_data_mcf_final.par",
"Used": [
- "urn:5dd29509-b5b3-44e5-a292-7d62809c22b2"
+ "bids::mc/prefiltered_func_data_mcf.par"
]
},
{
- "@id": "urn:dc20e262-17a0-4086-a588-6fd64f621ed6",
+ "@id": "urn:paste-T2ti4avE",
"Label": "paste",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
- "Command": "paste -d ' ' mc/prefiltered_func_data_mcf_final.par > confoundevs.txt",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
+ "Command": "paste -d ' ' mc/prefiltered_func_data_mcf_final.par > confoundevs.txt",
"Used": []
},
{
- "@id": "urn:d6457024-b31d-4316-a44c-204f5f2b561b",
+ "@id": "urn:featmode-QiHfDLNN",
"Label": "feat_model",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/usr/local/packages/fsl-5.0.10/bin/feat_model design confoundevs.txt",
"Used": [
- "urn:cf1b1419-bbf9-4471-9c0b-f39e9d282890"
+ "bids::design"
]
},
{
- "@id": "urn:93f66e36-dea1-4356-88fe-da648830d7e3",
+ "@id": "urn:filmgls-AynXvtZy",
"Label": "film_gls",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con",
- "Used": []
+ "Used": [
+ "bids::design.con",
+ "bids::design.mat",
+ "bids::filtered_func_data",
+ "bids::stats"
+ ]
},
{
- "@id": "urn:e0e55412-d874-484b-9271-f297fc987ca8",
+ "@id": "urn:smoothes-zejB0NIO",
"Label": "smoothest",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 96 -m mask -r stats/res4d > stats/smoothness",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 96 -m mask -r stats/res4d > stats/smoothness",
"Used": [
- "urn:3a2f1b8e-942c-4178-8f58-491c55c796a7",
- "urn:f6487662-966c-4737-93d3-db7ce991e7ec"
+ "bids::mask",
+ "bids::stats/res4d"
]
},
{
- "@id": "urn:7e2bc2b5-b927-447d-a3ae-8767c2603c26",
+ "@id": "urn:fslmaths-Fs9p1PuI",
"Label": "fslmaths",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1",
"Used": [
- "urn:3a2f1b8e-942c-4178-8f58-491c55c796a7",
- "urn:3e2049c4-7134-443a-bcaa-32771d013ee9"
+ "bids::mask",
+ "bids::stats/zstat1"
]
},
{
- "@id": "urn:2dd4bdd9-81a3-4671-ae2b-3303e79bd597",
+ "@id": "urn:echo-w4Z3IJwq",
"Label": "echo",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "echo 38352 > thresh_zstat1.vol",
"Used": []
},
{
- "@id": "urn:9436c7f5-ce44-4311-8385-1d54351a4e9f",
+ "@id": "urn:ptoz-3z1yNibF",
"Label": "ptoz",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:30833595-df15-473c-9fbc-b51b46f6220f",
+ "@id": "urn:cluster-dQTSoZRU",
"Label": "cluster",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -t 3.090232 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z --voxuncthresh -c stats/cope1 > cluster_zstat1.txt",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -t 3.090232 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z --voxuncthresh -c stats/cope1 > cluster_zstat1.txt",
"Used": [
- "urn:1e422005-3b1a-4f43-9113-dd49f1ddf5b5",
- "urn:ce6d0fcd-9703-44df-9e5e-d126eaee7f4c"
+ "bids::stats/cope1",
+ "bids::thresh_zstat1"
]
},
{
- "@id": "urn:1f9cf81a-a168-4237-ba3c-30f95e1264eb",
+ "@id": "urn:cluster2-ojcUUeuy",
"Label": "cluster2html",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat1",
"Used": [
- "urn:e84ad552-4fd6-4f7a-b61f-af8268dbc4b7"
+ "bids::cluster_zstat1"
]
},
{
- "@id": "urn:50610570-f005-4efe-b967-fb1fe217c163",
+ "@id": "urn:fslstats-FhQi5D0S",
"Label": "fslstats",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat1 -l 0.0001 -R 2>/dev/null",
"Used": [
- "urn:1e422005-3b1a-4f43-9113-dd49f1ddf5b5"
+ "bids::thresh_zstat1"
]
},
{
- "@id": "urn:52dc58df-35c5-4d53-999e-2377d2e2eddd",
+ "@id": "urn:overlay-MQWSN0yZ",
"Label": "overlay",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat1 3.091832 5.263171 rendered_thresh_zstat1",
"Used": []
},
{
- "@id": "urn:b8e10bbb-9865-4396-87b8-69935a2f0a7a",
+ "@id": "urn:slicer-KQKRKhwm",
"Label": "slicer",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat1 -A 750 rendered_thresh_zstat1.png",
"Used": [
- "urn:fb9f4b8d-e79b-4082-952e-839608db3b81"
+ "bids::rendered_thresh_zstat1"
]
},
{
- "@id": "urn:0e383a9f-e4be-447d-baa2-be66cac8bff3",
+ "@id": "urn:cp-2T3xfElR",
"Label": "cp",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/bin/cp /usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif .ramp.gif",
"Used": [
- "urn:b263d905-07d9-4561-8e6f-3642c4753b72"
+ "bids::/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif"
]
},
{
- "@id": "urn:cd4904d9-50f8-40f4-ba37-150beaa53fb0",
+ "@id": "urn:makedire-Ybe9be1w",
"Label": "Make directory",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "mkdir -p tsplot",
"Used": []
},
{
- "@id": "urn:785ab00d-b2b2-4d41-9517-5340e9a6b666",
+ "@id": "urn:tsplot-b6M9Wmgz",
"Label": "tsplot",
- "AssociatedWith": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
+ "AssociatedWith": "urn:fsl-q1u8Lfn3",
"Command": "/usr/local/packages/fsl-5.0.10/bin/tsplot . -f filtered_func_data -o tsplot",
"Used": []
}
],
"Entities": [
{
- "@id": "urn:89d72914-4200-41f9-a756-1f0024506f14",
+ "@id": "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold",
"Label": "sub-01_task-tonecounting_bold",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold",
+ "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold",
"digest": {
- "sha256": "028adf00daa36e78f06a61dcd3cb3526cd8564c1284e80516ab5520701324ac1"
+ "sha256": "33501604ae140e58832facff473a9578d5a549403bdbec53107d2b3eaab898ee"
}
},
{
- "@id": "urn:86b9e119-37bf-49fd-b850-0570cc53c3b8",
+ "@id": "bids::prefiltered_func_data",
"Label": "prefiltered_func_data",
"AtLocation": "prefiltered_func_data",
- "GeneratedBy": "urn:f01afec8-8551-4e82-a73e-7b0e7466afdd",
+ "GeneratedBy": "urn:fslmaths-3e1BW8zk",
"digest": {
"sha256": "2bea6005bace2adbea3534588b8c1b0d1759aa1af85b703b7f5bd2959c961a29"
}
},
{
- "@id": "urn:4abe4996-f2c8-41cc-8561-e4ae6c3e9474",
+ "@id": "bids::example_func",
"Label": "example_func",
"AtLocation": "example_func",
- "GeneratedBy": "urn:029ff773-b876-4565-854a-eafde9c7aaaa",
+ "GeneratedBy": "urn:fslroi-P8KgYNMI",
"digest": {
"sha256": "57841df382242a0e56f4fd1f340b30d4eb3bbd270342825da476367c640135e4"
}
},
{
- "@id": "urn:a76bfa82-0ac8-4e80-ac42-ec944929459f",
+ "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/example_func.nii.gz",
"Label": "example_func.nii.gz",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/example_func.nii.gz",
"digest": {
@@ -605,15 +614,15 @@
}
},
{
- "@id": "urn:fd12a58d-0911-428a-9049-3519c84b23d6",
+ "@id": "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
"Label": "sub-01_T1w_brain",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
+ "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
"digest": {
- "sha256": "ccb9a4d1def67002e358c45bd912034053ffc221ab52c2a19aa55f72c3236279"
+ "sha256": "8f1ae7ba69869c79b2cc5a83ce4ca24a7d666187256c2aa4d61a952b903b05b0"
}
},
{
- "@id": "urn:f6fe1240-45ad-4a19-a07d-df7de9f3f96d",
+ "@id": "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain",
"Label": "MNI152_T1_2mm_brain",
"AtLocation": "/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain",
"digest": {
@@ -621,45 +630,57 @@
}
},
{
- "@id": "urn:186b2014-9458-4f2b-8d8a-31a9b39be1f5",
+ "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat",
"Label": "fsl_motion_reg.feat",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat",
- "GeneratedBy": "urn:32abc1e4-0bbf-4ef4-a8e9-c2f67a5eb11c"
+ "GeneratedBy": "urn:mainfeat-L2O1FWWa"
},
{
- "@id": "urn:c95a9c1f-ad08-4358-a423-8f333dd6e996",
+ "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/reg",
"Label": "reg",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/reg",
- "GeneratedBy": "urn:55b47535-6244-4008-b24c-b417f36f1a07",
+ "GeneratedBy": "urn:makedire-081RCxsU",
"digest": {
"sha256": "2643a484ce1687b1a6162404ddb808150254b6ba544f373e464fb42309393256"
}
},
{
- "@id": "urn:45e2bca9-7675-4ee6-8c57-7fcd33d51a0e",
+ "@id": "bids::highres",
"Label": "highres",
"AtLocation": "highres",
- "GeneratedBy": "urn:8cb2cdce-390d-44a3-9b79-61baed152e49",
+ "GeneratedBy": "urn:fslmaths-oZkoFxMk",
"digest": {
"sha256": "ebf6ec6bd805d571a2e3649be9011bb1924dcf4971d5aab9055ca2434313fb90"
}
},
{
- "@id": "urn:e2b94bbc-7b9d-42b4-a4a8-02abcdf4eafd",
+ "@id": "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
"Label": "sub-01_T1w",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
+ "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
"digest": {
- "sha256": "3be6c69338e200d2a286a56cd9a0030539cf50201f412c910ade833e18354d27"
+ "sha256": "8dd4893a9c9500ce8c516f1a9845abf887087d00c2c47fc3524a17d924e78acf"
}
},
{
- "@id": "urn:3c406d97-e58a-4264-9ea1-cd9cc3009c32",
- "Label": "",
- "AtLocation": "",
- "GeneratedBy": "urn:613d4024-978b-4042-8677-856dcd153fdd"
+ "@id": "bids::highres_head",
+ "Label": "highres_head",
+ "AtLocation": "highres_head",
+ "GeneratedBy": "urn:fslmaths-Di35akWj",
+ "digest": {
+ "sha256": "590f180bade23162ef1567a5a61d86ee93155e4c7dc59c04c8ac5d6b7a20ea51"
+ }
+ },
+ {
+ "@id": "bids::example_func2highres",
+ "Label": "example_func2highres",
+ "AtLocation": "example_func2highres",
+ "GeneratedBy": "urn:epireg-g2VLNGNl",
+ "digest": {
+ "sha256": "00c021d82b83d2dc562c77f76528ece0f7425d4982f292f22021467afce1ba59"
+ }
},
{
- "@id": "urn:86b35929-f1ee-473d-8639-edd3a207b228",
+ "@id": "bids::example_func2highres.mat",
"Label": "example_func2highres.mat",
"AtLocation": "example_func2highres.mat",
"digest": {
@@ -667,267 +688,259 @@
}
},
{
- "@id": "urn:f7a8a677-377a-4757-bd2c-fde4fc3b1150",
+ "@id": "bids::highres2example_func.mat",
"Label": "highres2example_func.mat",
"AtLocation": "highres2example_func.mat",
- "GeneratedBy": "urn:8e237c8a-8985-456f-ba72-ae41b9f753a0",
+ "GeneratedBy": "urn:convertx-OwOGE44S",
"digest": {
"sha256": "cbdf8a350762f7b207544f53517491b745cb2331914d52286fc15ac83ed99677"
}
},
{
- "@id": "urn:bf539143-ed61-483a-9a54-b5409615e050",
- "Label": "example_func2highres",
- "AtLocation": "example_func2highres",
- "digest": {
- "sha256": "00c021d82b83d2dc562c77f76528ece0f7425d4982f292f22021467afce1ba59"
- }
- },
- {
- "@id": "urn:5f88ea35-c580-447b-9fcd-a365ca8b1160",
+ "@id": "bids::sla.png",
"Label": "sla.png",
"AtLocation": "sla.png",
- "GeneratedBy": "urn:d41c4d7c-7f7f-4c9d-8db0-b3bb3e06f8a7",
+ "GeneratedBy": "urn:slicer-WDHg7RO5",
"digest": {
"sha256": "a25ddd3d3c82c797577396f7129c156f3e38ed3bae73238958ea49a977b482fa"
}
},
{
- "@id": "urn:820883ac-814d-49c1-95b6-2129629530ef",
+ "@id": "bids::slb.png",
"Label": "slb.png",
"AtLocation": "slb.png",
- "GeneratedBy": "urn:d41c4d7c-7f7f-4c9d-8db0-b3bb3e06f8a7",
+ "GeneratedBy": "urn:slicer-WDHg7RO5",
"digest": {
"sha256": "c28c7f6a641a9114d0dc7e77621c732ef73a95fda0a560b61526d9c4b35aadae"
}
},
{
- "@id": "urn:bf13f751-1153-4368-91c1-d903622f7d4d",
+ "@id": "bids::slc.png",
"Label": "slc.png",
"AtLocation": "slc.png",
- "GeneratedBy": "urn:d41c4d7c-7f7f-4c9d-8db0-b3bb3e06f8a7",
+ "GeneratedBy": "urn:slicer-WDHg7RO5",
"digest": {
"sha256": "c8477a5e51aedf908e76ac10cade2ab4252d32ea34de718ae1098dc6963aa1e2"
}
},
{
- "@id": "urn:829059e7-40d3-402e-acd7-52ce046b7263",
+ "@id": "bids::sld.png",
"Label": "sld.png",
"AtLocation": "sld.png",
- "GeneratedBy": "urn:d41c4d7c-7f7f-4c9d-8db0-b3bb3e06f8a7",
+ "GeneratedBy": "urn:slicer-WDHg7RO5",
"digest": {
"sha256": "bf84a2ce8a5e5e91e265d647a81fbf29bc65b5a4a9bc7a2f64fe7021797550b8"
}
},
{
- "@id": "urn:c59e7f5b-8800-43da-9512-3cf33aa2d64f",
+ "@id": "bids::sle.png",
"Label": "sle.png",
"AtLocation": "sle.png",
- "GeneratedBy": "urn:d41c4d7c-7f7f-4c9d-8db0-b3bb3e06f8a7",
+ "GeneratedBy": "urn:slicer-WDHg7RO5",
"digest": {
"sha256": "e6500261b9cdd09cafc113e59438f1dfbc04c61d2a37c80732c5bfd6f743a1b5"
}
},
{
- "@id": "urn:81bdbe32-8fd2-4c86-ad90-d75314e52071",
+ "@id": "bids::slf.png",
"Label": "slf.png",
"AtLocation": "slf.png",
- "GeneratedBy": "urn:d41c4d7c-7f7f-4c9d-8db0-b3bb3e06f8a7",
+ "GeneratedBy": "urn:slicer-WDHg7RO5",
"digest": {
"sha256": "2dbf8b64f7d813fa546c74862fafd3ee96db45d8aee8fcb1d193ef92a88e63a4"
}
},
{
- "@id": "urn:eeb424ca-31ff-4ca3-b854-306184f22561",
+ "@id": "bids::slg.png",
"Label": "slg.png",
"AtLocation": "slg.png",
- "GeneratedBy": "urn:d41c4d7c-7f7f-4c9d-8db0-b3bb3e06f8a7",
+ "GeneratedBy": "urn:slicer-WDHg7RO5",
"digest": {
"sha256": "fbb7b25ca44e92f4e9a9335aff73cb16f13b8342127f7c85f5687f7d7f5988a8"
}
},
{
- "@id": "urn:132f3df2-fdac-4638-b3f8-9cd0419c22c1",
+ "@id": "bids::slh.png",
"Label": "slh.png",
"AtLocation": "slh.png",
- "GeneratedBy": "urn:d41c4d7c-7f7f-4c9d-8db0-b3bb3e06f8a7",
+ "GeneratedBy": "urn:slicer-WDHg7RO5",
"digest": {
"sha256": "dab220796c763bdfa0d073b186005b118c51dbe6c13d72eb40556b9d8542108b"
}
},
{
- "@id": "urn:b43412a0-0f56-4d67-8a7e-634c25544801",
+ "@id": "bids::sli.png",
"Label": "sli.png",
"AtLocation": "sli.png",
- "GeneratedBy": "urn:d41c4d7c-7f7f-4c9d-8db0-b3bb3e06f8a7",
+ "GeneratedBy": "urn:slicer-WDHg7RO5",
"digest": {
"sha256": "12b578b66c0305ed3283d229408a1498ea405ccd95b3184ff523d4b36d3bbeca"
}
},
{
- "@id": "urn:1fb66b81-602b-4a6f-8d21-c58996c3dc91",
+ "@id": "bids::slj.png",
"Label": "slj.png",
"AtLocation": "slj.png",
- "GeneratedBy": "urn:d41c4d7c-7f7f-4c9d-8db0-b3bb3e06f8a7",
+ "GeneratedBy": "urn:slicer-WDHg7RO5",
"digest": {
"sha256": "e3417ca0a8c36a7c9572306e68b2837708e4dad049103ac2654e8f21082f261c"
}
},
{
- "@id": "urn:9c045eed-e0d8-4752-9f38-b03c8961ba54",
+ "@id": "bids::slk.png",
"Label": "slk.png",
"AtLocation": "slk.png",
- "GeneratedBy": "urn:d41c4d7c-7f7f-4c9d-8db0-b3bb3e06f8a7",
+ "GeneratedBy": "urn:slicer-WDHg7RO5",
"digest": {
"sha256": "c540df2ed1d697609b08bd955a2ca31f3aeca3395c403edd9b036be63682eb64"
}
},
{
- "@id": "urn:10c6cdeb-975a-41c9-9aaf-33d0116e2f1a",
+ "@id": "bids::sll.png",
"Label": "sll.png",
"AtLocation": "sll.png",
- "GeneratedBy": "urn:d41c4d7c-7f7f-4c9d-8db0-b3bb3e06f8a7",
+ "GeneratedBy": "urn:slicer-WDHg7RO5",
"digest": {
"sha256": "0b9c965bbea7bb7d1f251ea0f2973f485727fbbc91357e30aee25ff9869f5009"
}
},
{
- "@id": "urn:5a798d51-b0f0-4d2e-81da-8f835a289d93",
+ "@id": "bids::example_func2highres1.png",
"Label": "example_func2highres1.png",
"AtLocation": "example_func2highres1.png",
- "GeneratedBy": "urn:7d9c5fc6-bbe9-46f4-aa91-a071f2605908",
+ "GeneratedBy": "urn:pngappen-gg2Ssdze",
"digest": {
"sha256": "0ed1c9f85cce7ae47bc8891995afbe83b93836ae83772e8be1cb884d5ec7d2ca"
}
},
{
- "@id": "urn:114e3532-8f75-43c4-8325-0411b3f2d898",
+ "@id": "bids::sla.png",
"Label": "sla.png",
"AtLocation": "sla.png",
- "GeneratedBy": "urn:7f373576-0167-4294-9e8a-e15cfad9516b",
+ "GeneratedBy": "urn:slicer-xfVLnC1i",
"digest": {
"sha256": "a25ddd3d3c82c797577396f7129c156f3e38ed3bae73238958ea49a977b482fa"
}
},
{
- "@id": "urn:d4caa5e8-8399-4a90-8650-f7ddb831f026",
+ "@id": "bids::slb.png",
"Label": "slb.png",
"AtLocation": "slb.png",
- "GeneratedBy": "urn:7f373576-0167-4294-9e8a-e15cfad9516b",
+ "GeneratedBy": "urn:slicer-xfVLnC1i",
"digest": {
"sha256": "c28c7f6a641a9114d0dc7e77621c732ef73a95fda0a560b61526d9c4b35aadae"
}
},
{
- "@id": "urn:354f9b5f-7299-4cb0-ac4f-d336008774f5",
+ "@id": "bids::slc.png",
"Label": "slc.png",
"AtLocation": "slc.png",
- "GeneratedBy": "urn:7f373576-0167-4294-9e8a-e15cfad9516b",
+ "GeneratedBy": "urn:slicer-xfVLnC1i",
"digest": {
"sha256": "c8477a5e51aedf908e76ac10cade2ab4252d32ea34de718ae1098dc6963aa1e2"
}
},
{
- "@id": "urn:519fc1f0-12e8-4d55-8221-a9a1782415ef",
+ "@id": "bids::sld.png",
"Label": "sld.png",
"AtLocation": "sld.png",
- "GeneratedBy": "urn:7f373576-0167-4294-9e8a-e15cfad9516b",
+ "GeneratedBy": "urn:slicer-xfVLnC1i",
"digest": {
"sha256": "bf84a2ce8a5e5e91e265d647a81fbf29bc65b5a4a9bc7a2f64fe7021797550b8"
}
},
{
- "@id": "urn:9981c55e-0d2a-4cac-8dac-2cbbc84e1fef",
+ "@id": "bids::sle.png",
"Label": "sle.png",
"AtLocation": "sle.png",
- "GeneratedBy": "urn:7f373576-0167-4294-9e8a-e15cfad9516b",
+ "GeneratedBy": "urn:slicer-xfVLnC1i",
"digest": {
"sha256": "e6500261b9cdd09cafc113e59438f1dfbc04c61d2a37c80732c5bfd6f743a1b5"
}
},
{
- "@id": "urn:b3724df6-ae51-4816-9a81-72b912549083",
+ "@id": "bids::slf.png",
"Label": "slf.png",
"AtLocation": "slf.png",
- "GeneratedBy": "urn:7f373576-0167-4294-9e8a-e15cfad9516b",
+ "GeneratedBy": "urn:slicer-xfVLnC1i",
"digest": {
"sha256": "2dbf8b64f7d813fa546c74862fafd3ee96db45d8aee8fcb1d193ef92a88e63a4"
}
},
{
- "@id": "urn:ec3229a5-b849-4c4b-b171-3c3e320464b3",
+ "@id": "bids::slg.png",
"Label": "slg.png",
"AtLocation": "slg.png",
- "GeneratedBy": "urn:7f373576-0167-4294-9e8a-e15cfad9516b",
+ "GeneratedBy": "urn:slicer-xfVLnC1i",
"digest": {
"sha256": "fbb7b25ca44e92f4e9a9335aff73cb16f13b8342127f7c85f5687f7d7f5988a8"
}
},
{
- "@id": "urn:9c9da777-12ff-4a63-9181-3e25fe6bc696",
+ "@id": "bids::slh.png",
"Label": "slh.png",
"AtLocation": "slh.png",
- "GeneratedBy": "urn:7f373576-0167-4294-9e8a-e15cfad9516b",
+ "GeneratedBy": "urn:slicer-xfVLnC1i",
"digest": {
"sha256": "dab220796c763bdfa0d073b186005b118c51dbe6c13d72eb40556b9d8542108b"
}
},
{
- "@id": "urn:b7832027-315a-4c02-a724-80f5aec4ff08",
+ "@id": "bids::sli.png",
"Label": "sli.png",
"AtLocation": "sli.png",
- "GeneratedBy": "urn:7f373576-0167-4294-9e8a-e15cfad9516b",
+ "GeneratedBy": "urn:slicer-xfVLnC1i",
"digest": {
"sha256": "12b578b66c0305ed3283d229408a1498ea405ccd95b3184ff523d4b36d3bbeca"
}
},
{
- "@id": "urn:692f3e44-6c57-4be4-bf7f-74b19df5f43a",
+ "@id": "bids::slj.png",
"Label": "slj.png",
"AtLocation": "slj.png",
- "GeneratedBy": "urn:7f373576-0167-4294-9e8a-e15cfad9516b",
+ "GeneratedBy": "urn:slicer-xfVLnC1i",
"digest": {
"sha256": "e3417ca0a8c36a7c9572306e68b2837708e4dad049103ac2654e8f21082f261c"
}
},
{
- "@id": "urn:153521cf-ee7b-4e10-bd52-013f29c11e90",
+ "@id": "bids::slk.png",
"Label": "slk.png",
"AtLocation": "slk.png",
- "GeneratedBy": "urn:7f373576-0167-4294-9e8a-e15cfad9516b",
+ "GeneratedBy": "urn:slicer-xfVLnC1i",
"digest": {
"sha256": "c540df2ed1d697609b08bd955a2ca31f3aeca3395c403edd9b036be63682eb64"
}
},
{
- "@id": "urn:120c218e-37ec-43c4-bf0b-6e126b10530e",
+ "@id": "bids::sll.png",
"Label": "sll.png",
"AtLocation": "sll.png",
- "GeneratedBy": "urn:7f373576-0167-4294-9e8a-e15cfad9516b",
+ "GeneratedBy": "urn:slicer-xfVLnC1i",
"digest": {
"sha256": "0b9c965bbea7bb7d1f251ea0f2973f485727fbbc91357e30aee25ff9869f5009"
}
},
{
- "@id": "urn:d0817bad-4522-48f7-9e50-31e3489d82ae",
+ "@id": "bids::example_func2highres2.png",
"Label": "example_func2highres2.png",
"AtLocation": "example_func2highres2.png",
- "GeneratedBy": "urn:dfa1c116-dd9b-4a89-b521-148073f45dd4",
+ "GeneratedBy": "urn:pngappen-DdSGKIgw",
"digest": {
"sha256": "4e622cf27c5f4d28786e7ccdc4e88253f4e5a855818d597ceec90fa78f0d437c"
}
},
{
- "@id": "urn:b3739448-eeb9-483a-becc-989cce766a2d",
+ "@id": "bids::example_func2highres.png",
"Label": "example_func2highres.png",
"AtLocation": "example_func2highres.png",
- "GeneratedBy": "urn:44317bf6-99a8-4fa3-a1d4-6c5b970ddeda",
+ "GeneratedBy": "urn:pngappen-AABwFbAU",
"digest": {
"sha256": "31960f4162da045cb9b73a0eb3cac33f09d5a2ec1f146f1e457c4a59f478f3e8"
}
},
{
- "@id": "urn:4342af1c-2b81-4c02-b669-ccdebeaafff8",
+ "@id": "bids::sl?.png",
"Label": "sl?.png",
"AtLocation": "sl?.png",
"digest": {
@@ -935,25 +948,25 @@
}
},
{
- "@id": "urn:32cae31b-c5e5-42d4-a310-416b886eed55",
+ "@id": "bids::prefiltered_func_data_mcf",
"Label": "prefiltered_func_data_mcf",
"AtLocation": "prefiltered_func_data_mcf",
- "GeneratedBy": "urn:6e82ab5e-2cae-4566-b691-f4eb52ac5a93",
+ "GeneratedBy": "urn:mcflirt-mRIur6l3",
"digest": {
"sha256": "83371e264d408de4f678b8182097b39c86bd0a618ca76af6d1dfee5db0903b78"
}
},
{
- "@id": "urn:16dddb2c-906b-4a85-b556-0bb3e7ddaff2",
+ "@id": "bids::mc",
"Label": "mc",
"AtLocation": "mc",
- "GeneratedBy": "urn:fb0a4cf2-0b8a-445d-b252-7e765e1ba496",
+ "GeneratedBy": "urn:makedire-AoaD1CwM",
"digest": {
"sha256": "a1a8fa7b1d2bf5bc0a263e95f926d3d9b656d2572455245d46edf48e93744ffa"
}
},
{
- "@id": "urn:fa8d9523-1bbe-4d63-99df-ddfc0e3f8fd7",
+ "@id": "bids::prefiltered_func_data_mcf.mat",
"Label": "prefiltered_func_data_mcf.mat",
"AtLocation": "prefiltered_func_data_mcf.mat",
"digest": {
@@ -961,7 +974,7 @@
}
},
{
- "@id": "urn:ee05cd16-9e60-45d8-9454-736cb892f197",
+ "@id": "bids::prefiltered_func_data_mcf.par",
"Label": "prefiltered_func_data_mcf.par",
"AtLocation": "prefiltered_func_data_mcf.par",
"digest": {
@@ -969,7 +982,7 @@
}
},
{
- "@id": "urn:ca9a4718-ff12-4c49-bc9b-c8e5d0c67304",
+ "@id": "bids::prefiltered_func_data_mcf_abs.rms",
"Label": "prefiltered_func_data_mcf_abs.rms",
"AtLocation": "prefiltered_func_data_mcf_abs.rms",
"digest": {
@@ -977,7 +990,7 @@
}
},
{
- "@id": "urn:406533ba-f5f6-475d-b834-784305e689ce",
+ "@id": "bids::prefiltered_func_data_mcf_abs_mean.rms",
"Label": "prefiltered_func_data_mcf_abs_mean.rms",
"AtLocation": "prefiltered_func_data_mcf_abs_mean.rms",
"digest": {
@@ -985,7 +998,7 @@
}
},
{
- "@id": "urn:da0a1900-b8f3-4fff-85b1-b9f700cefdff",
+ "@id": "bids::prefiltered_func_data_mcf_rel.rms",
"Label": "prefiltered_func_data_mcf_rel.rms",
"AtLocation": "prefiltered_func_data_mcf_rel.rms",
"digest": {
@@ -993,7 +1006,7 @@
}
},
{
- "@id": "urn:794883bf-d745-44bf-880c-8341377bd9ec",
+ "@id": "bids::prefiltered_func_data_mcf_rel_mean.rms",
"Label": "prefiltered_func_data_mcf_rel_mean.rms",
"AtLocation": "prefiltered_func_data_mcf_rel_mean.rms",
"digest": {
@@ -1001,34 +1014,34 @@
}
},
{
- "@id": "urn:2ec46422-3d77-4635-82fc-107101bfe479",
+ "@id": "bids::mc",
"Label": "mc",
"AtLocation": "mc",
- "GeneratedBy": "urn:f52d0638-4f8b-46ef-911f-4a11a3bd6392",
+ "GeneratedBy": "urn:mv-2yFPQBIr",
"digest": {
"sha256": "a1a8fa7b1d2bf5bc0a263e95f926d3d9b656d2572455245d46edf48e93744ffa"
}
},
{
- "@id": "urn:65fc9308-a754-4214-9ca2-53d26cab2a5f",
+ "@id": "bids::rot.png",
"Label": "rot.png",
"AtLocation": "rot.png",
- "GeneratedBy": "urn:f8728d5a-b3f1-4f75-b4cd-73ed82ad1764",
+ "GeneratedBy": "urn:fsltsplo-J0iwwUfZ",
"digest": {
"sha256": "b8776603f8865a358b2273847d21e63491e7c2e10567fb640608dd47ba721f29"
}
},
{
- "@id": "urn:213ba206-6549-42b3-90f5-5dbaa5443c31",
+ "@id": "bids::trans.png",
"Label": "trans.png",
"AtLocation": "trans.png",
- "GeneratedBy": "urn:e5c7fec3-13ac-43b2-b147-e6c89efc06ad",
+ "GeneratedBy": "urn:fsltsplo-D7UjyFRB",
"digest": {
"sha256": "496eac1d0ac15e80928780c73766c7791a1707291b2b9a6d1781c2f6a38de3cd"
}
},
{
- "@id": "urn:43302e4a-2df7-4b56-ba7c-61f14009fe14",
+ "@id": "bids::prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"Label": "prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"AtLocation": "prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"digest": {
@@ -1036,34 +1049,34 @@
}
},
{
- "@id": "urn:73ac48b8-1ba7-42d9-b8a3-86ad316270d6",
+ "@id": "bids::disp.png",
"Label": "disp.png",
"AtLocation": "disp.png",
- "GeneratedBy": "urn:0105302f-6dee-4f56-b390-8f4c7b70f68b",
+ "GeneratedBy": "urn:fsltsplo-InC74Sut",
"digest": {
"sha256": "c4615e07e04f0c390d969482634cb62e81d47c818d2866ee866ec9c64a5350fd"
}
},
{
- "@id": "urn:afd3d158-c888-4146-81cc-da7a53e3cd8c",
+ "@id": "bids::mean_func",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:482a00bc-4f3f-4866-adff-1ca4914f0f9c",
+ "GeneratedBy": "urn:fslmaths-R434LBry",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:3a2f1b8e-942c-4178-8f58-491c55c796a7",
+ "@id": "bids::mask",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:6facd168-6205-4eab-902a-051b05e0d300",
+ "GeneratedBy": "urn:bet2-WJQyP3oC",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:bf820444-ae9b-4433-98a7-a11014b56ea1",
+ "@id": "bids::mask_mask",
"Label": "mask_mask",
"AtLocation": "mask_mask",
"digest": {
@@ -1071,132 +1084,124 @@
}
},
{
- "@id": "urn:d227a590-b746-4e62-a756-06959e2f290e",
+ "@id": "bids::mask",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:0840ffaf-344d-4b50-b9b5-1a4dd76fe080",
+ "GeneratedBy": "urn:immv-4v7jamiF",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:42579cc8-6d6b-44d4-bbb5-b30f3f880bfc",
+ "@id": "bids::prefiltered_func_data_bet",
"Label": "prefiltered_func_data_bet",
"AtLocation": "prefiltered_func_data_bet",
- "GeneratedBy": "urn:fa9c14f8-dc0e-4bf6-a4c1-efa702904c63",
+ "GeneratedBy": "urn:fslmaths-qYlHII1V",
"digest": {
"sha256": "c01f21947b38d9886528dec14edf23dfb55304b7da67569fe93902472b286cf4"
}
},
{
- "@id": "urn:d3bbe5ef-0da2-4c47-bf61-d804b9ebc44b",
+ "@id": "bids::mask",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:db70a010-5f90-48af-8c31-6be63a2c5d14",
+ "GeneratedBy": "urn:fslmaths-YUTXrUXd",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:a54a7195-0af3-4b2e-bfaf-3740a677b53b",
+ "@id": "bids::mask",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:2f1d7d43-4b07-48b9-8496-eebbf76893b0",
+ "GeneratedBy": "urn:fslmaths-wwPgPnYX",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:5145d4af-4d72-4daa-9067-cb76d89eed9c",
+ "@id": "bids::prefiltered_func_data_thresh",
"Label": "prefiltered_func_data_thresh",
"AtLocation": "prefiltered_func_data_thresh",
- "GeneratedBy": "urn:9e154a04-adf5-4892-9856-fd8ce771786a",
+ "GeneratedBy": "urn:fslmaths-C3yoMH6k",
"digest": {
"sha256": "c5c015a8df079b497bbce596808cbbdc09fb39411f490244de192dfa72d33640"
}
},
{
- "@id": "urn:f3e2b286-a6e2-427e-b5fe-bc4389dea257",
+ "@id": "bids::mean_func",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:ad350bf9-e517-49d8-9019-361963775a0f",
+ "GeneratedBy": "urn:fslmaths-Cx8FTnEr",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:e7b0996d-40d0-4d73-b587-f8982e0c5c55",
+ "@id": "bids::prefiltered_func_data_smooth",
"Label": "prefiltered_func_data_smooth",
"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:a6ea5103-3e65-49ed-8c46-e7dd0671cb33",
+ "GeneratedBy": "urn:susan-2AISnNgW",
"digest": {
"sha256": "2a4901d885fce0b083c9f99364da8dcff184635e74ab011f53a68cfc6827b429"
}
},
{
- "@id": "urn:a6f01e18-f324-4587-938f-b524db505088",
+ "@id": "bids::prefiltered_func_data_smooth",
"Label": "prefiltered_func_data_smooth",
"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:3d1775e1-e6d1-44d4-9cc6-e7b2558fbaec",
+ "GeneratedBy": "urn:fslmaths-uhxHBqAa",
"digest": {
"sha256": "2a4901d885fce0b083c9f99364da8dcff184635e74ab011f53a68cfc6827b429"
}
},
{
- "@id": "urn:2c0f03e8-19de-4de6-8318-65d031bacb43",
+ "@id": "bids::prefiltered_func_data_intnorm",
"Label": "prefiltered_func_data_intnorm",
"AtLocation": "prefiltered_func_data_intnorm",
- "GeneratedBy": "urn:9002f1b5-4239-44e4-8932-7d943f25e6e9",
+ "GeneratedBy": "urn:fslmaths-OGv4Qr30",
"digest": {
"sha256": "0698a276f6f0fdccfb06033926d333a176503a09aaa87b78384fbffbf1c54dee"
}
},
{
- "@id": "urn:fcee0b5c-13c9-4567-8f44-629ba9e7a513",
+ "@id": "bids::tempMean",
"Label": "tempMean",
"AtLocation": "tempMean",
- "GeneratedBy": "urn:fb916597-66ca-4bbc-b771-b741c3716c95",
+ "GeneratedBy": "urn:fslmaths-kI7gzSJZ",
"digest": {
"sha256": "1a01513c76bc17516b60df315a1922789ce79d72e66e105fbf2723df9cb1b038"
}
},
{
- "@id": "urn:4707fc33-7c41-4f66-9b46-e9362b27f739",
- "Label": "15.0",
- "AtLocation": "15.0",
- "GeneratedBy": "urn:3844eec4-0749-4130-aed2-99ca8096e764",
- "digest": {
- "sha256": "552db91328a881034f16ec50203ba34d4af448f52c616eb28db6c07aa575a286"
- }
- },
- {
- "@id": "urn:9455faad-b8cd-462a-a17d-795342424c45",
+ "@id": "bids::prefiltered_func_data_tempfilt",
"Label": "prefiltered_func_data_tempfilt",
"AtLocation": "prefiltered_func_data_tempfilt",
+ "GeneratedBy": "urn:fslmaths-tmHau3zK",
"digest": {
"sha256": "a1836f4694e7ffdb50484626724602498c7b22b4f3cdd1e7d105efd336cbc8bd"
}
},
{
- "@id": "urn:e69f21ae-6759-4681-95b6-c8ad39e7de22",
+ "@id": "bids::filtered_func_data",
"Label": "filtered_func_data",
"AtLocation": "filtered_func_data",
- "GeneratedBy": "urn:fa4e18e3-3c2a-48c1-9e6d-9e8c4fea9da6",
+ "GeneratedBy": "urn:fslmaths-8mzN1fkC",
"digest": {
"sha256": "2a1854e3b48a54f88e063191e25159015a0afbd300d18a1cfda37b4b68a1ee69"
}
},
{
- "@id": "urn:39034638-6c66-4cb9-9372-fde68eb5b1a0",
+ "@id": "bids::mean_func",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:77118d6c-abae-4566-a58f-c5813e9b102c",
+ "GeneratedBy": "urn:fslmaths-tvhntGIA",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:c5c4d138-bb2c-48b5-a3c2-79041dd19565",
+ "@id": "bids::prefiltered_func_data*",
"Label": "prefiltered_func_data*",
"AtLocation": "prefiltered_func_data*",
"digest": {
@@ -1204,64 +1209,64 @@
}
},
{
- "@id": "urn:fef2a43c-eaae-4ebc-b7ef-589205bef810",
+ "@id": "bids::custom_timing_files",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:9722cc70-09b9-4f29-8d8b-fdbb14cd3513",
+ "GeneratedBy": "urn:makedire-nVCXGaK7",
"digest": {
"sha256": "1d7e19792328d5040f2f9fb3c15d59de90fc771785f81c67039a043bd5f2ed20"
}
},
{
- "@id": "urn:e0e86ef2-0070-4e6a-a7ef-2048348dca4a",
+ "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
"Label": "sub-01_tone_counting.txt",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
+ "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
"digest": {
- "sha256": "c120d27b9d5d81a91be0e55f5cb880b2cb7de6c655554d9c15c9c04c6232ea8e"
+ "sha256": "165398224a205d2fc0b19354e15d9b085c6d81e333b69c4697b7894a2549be0b"
}
},
{
- "@id": "urn:2511e06b-b1e2-40db-8fb8-b4b80d6be4f9",
+ "@id": "bids::custom_timing_files/ev1.txt",
"Label": "ev1.txt",
"AtLocation": "custom_timing_files/ev1.txt",
- "GeneratedBy": "urn:f4544d21-aeac-43af-8bee-dce242d6ad99"
+ "GeneratedBy": "urn:fslfixte-Yaoid2yI"
},
{
- "@id": "urn:fdf9bf5c-f5b2-418f-809d-c9ae3fb7c49a",
+ "@id": "bids::custom_timing_files",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:dfcbdf85-06e9-4175-ad85-a65841a04ff1",
+ "GeneratedBy": "urn:makedire-Z7VhBRjC",
"digest": {
"sha256": "1d7e19792328d5040f2f9fb3c15d59de90fc771785f81c67039a043bd5f2ed20"
}
},
{
- "@id": "urn:06dd1a96-a05a-4144-b35a-53463465f137",
+ "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
"Label": "sub-01_tone_counting_probe.txt",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
+ "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
"digest": {
- "sha256": "f09eeb82fa0be8e8759a5269403f36ec2b7dbf2c5b6caba1f0f985cc6cb3f703"
+ "sha256": "8b912293767f1a5e082311f6aaf0c44fc91fe45b0f2ae7f80e368bc2f4c2918a"
}
},
{
- "@id": "urn:d9d80477-49d0-45ec-9721-6439160eab83",
+ "@id": "bids::custom_timing_files/ev2.txt",
"Label": "ev2.txt",
"AtLocation": "custom_timing_files/ev2.txt",
- "GeneratedBy": "urn:243917d6-f1de-4d9b-9a28-5b18b08c2b7d"
+ "GeneratedBy": "urn:fslfixte-BP3JdcoO"
},
{
- "@id": "urn:5dd29509-b5b3-44e5-a292-7d62809c22b2",
+ "@id": "bids::mc/prefiltered_func_data_mcf.par",
"Label": "prefiltered_func_data_mcf.par",
"AtLocation": "mc/prefiltered_func_data_mcf.par"
},
{
- "@id": "urn:30436b61-6099-453e-a5a4-2cabd5f7c9af",
+ "@id": "bids::mc/prefiltered_func_data_mcf_final.par",
"Label": "prefiltered_func_data_mcf_final.par",
"AtLocation": "mc/prefiltered_func_data_mcf_final.par",
- "GeneratedBy": "urn:a8a46b77-99a6-42bf-837a-9a8c1c51f833"
+ "GeneratedBy": "urn:cp-QigRY0AI"
},
{
- "@id": "urn:cf1b1419-bbf9-4471-9c0b-f39e9d282890",
+ "@id": "bids::design",
"Label": "design",
"AtLocation": "design",
"digest": {
@@ -1269,67 +1274,112 @@
}
},
{
- "@id": "urn:f6487662-966c-4737-93d3-db7ce991e7ec",
- "Label": "res4d",
- "AtLocation": "stats/res4d",
+ "@id": "bids::stats",
+ "Label": "stats",
+ "AtLocation": "stats",
"digest": {
- "sha256": "8845286f36caedf891a02afddc4175ea46f18f830b59a8c5026962184a530699"
+ "sha256": "a9f3e135372514a16d11a8038262b3eff94ccd69a9b35c4724b2759cfc944a07"
}
},
{
- "@id": "urn:5a83e6ba-4f1c-459f-8b9f-60f61e9444e5",
- "Label": "smoothness",
- "AtLocation": "stats/smoothness",
- "GeneratedBy": "urn:e0e55412-d874-484b-9271-f297fc987ca8",
+ "@id": "bids::design.mat",
+ "Label": "design.mat",
+ "AtLocation": "design.mat",
"digest": {
- "sha256": "67b0aaf95a257beff60d331b56265034807ca51e67e2d312d481d5835ef0b1d0"
+ "sha256": "1c1a6ef59a355e1f6f81e741e157784ccbe066ba3594a07aa9b16781e3d5bb25"
}
},
{
- "@id": "urn:3e2049c4-7134-443a-bcaa-32771d013ee9",
- "Label": "zstat1",
- "AtLocation": "stats/zstat1",
+ "@id": "bids::design.con",
+ "Label": "design.con",
+ "AtLocation": "design.con",
"digest": {
- "sha256": "70ae47cee1ea1d3f1f6f8aa7ac51f2641cb2fcb745dfd8cc54a389346e6fa094"
+ "sha256": "5808d1be37dd8f2a4906b710bb384fbee62faa4a46b2bc6847afc8962ed4eb54"
}
},
{
- "@id": "urn:1e422005-3b1a-4f43-9113-dd49f1ddf5b5",
+ "@id": "bids::stats",
+ "Label": "stats",
+ "AtLocation": "stats",
+ "GeneratedBy": "urn:filmgls-AynXvtZy",
+ "digest": {
+ "sha256": "a9f3e135372514a16d11a8038262b3eff94ccd69a9b35c4724b2759cfc944a07"
+ }
+ },
+ {
+ "@id": "bids::stats/res4d",
+ "Label": "res4d",
+ "AtLocation": "stats/res4d"
+ },
+ {
+ "@id": "bids::stats/smoothness",
+ "Label": "smoothness",
+ "AtLocation": "stats/smoothness",
+ "GeneratedBy": "urn:smoothes-zejB0NIO"
+ },
+ {
+ "@id": "bids::stats/zstat1",
+ "Label": "zstat1",
+ "AtLocation": "stats/zstat1"
+ },
+ {
+ "@id": "bids::thresh_zstat1",
"Label": "thresh_zstat1",
"AtLocation": "thresh_zstat1",
- "GeneratedBy": "urn:7e2bc2b5-b927-447d-a3ae-8767c2603c26",
+ "GeneratedBy": "urn:fslmaths-Fs9p1PuI",
"digest": {
"sha256": "662e7ba670e124d15bb3cc18b818868f76604578034b524c8882f35fc5db413f"
}
},
{
- "@id": "urn:ce6d0fcd-9703-44df-9e5e-d126eaee7f4c",
+ "@id": "bids::stats/cope1",
"Label": "cope1",
- "AtLocation": "stats/cope1",
- "digest": {
- "sha256": "bf3b603569da6dbe3d6f0e8667d346f3ac943c9d01d2fc9743ce17abeb1547fb"
- }
+ "AtLocation": "stats/cope1"
},
{
- "@id": "urn:035f1ae5-a898-46bd-a450-430331b8b987",
+ "@id": "bids::cluster_mask_zstat1",
"Label": "cluster_mask_zstat1",
"AtLocation": "cluster_mask_zstat1",
- "GeneratedBy": "urn:30833595-df15-473c-9fbc-b51b46f6220f",
+ "GeneratedBy": "urn:cluster-dQTSoZRU",
"digest": {
"sha256": "b28c170e33d2917cac55183786616a9e976e5e7f30dc7c8666341f12ed6d0277"
}
},
{
- "@id": "urn:8f05debd-39ba-4706-8450-7e506af5b91c",
+ "@id": "bids::thresh_zstat1",
+ "Label": "thresh_zstat1",
+ "AtLocation": "thresh_zstat1",
+ "GeneratedBy": "urn:cluster-dQTSoZRU",
+ "digest": {
+ "sha256": "662e7ba670e124d15bb3cc18b818868f76604578034b524c8882f35fc5db413f"
+ }
+ },
+ {
+ "@id": "bids::lmax_zstat1.txt",
+ "Label": "lmax_zstat1.txt",
+ "AtLocation": "lmax_zstat1.txt",
+ "GeneratedBy": "urn:cluster-dQTSoZRU",
+ "digest": {
+ "sha256": "d44ee21719775397a1a95ede6778d25404b50e8bd259dbdf02d2fde635fc81a5"
+ }
+ },
+ {
+ "@id": "bids::stats/cope1",
"Label": "cope1",
"AtLocation": "stats/cope1",
- "GeneratedBy": "urn:30833595-df15-473c-9fbc-b51b46f6220f",
+ "GeneratedBy": "urn:cluster-dQTSoZRU"
+ },
+ {
+ "@id": "bids::cluster_zstat1.txt",
+ "Label": "cluster_zstat1.txt",
+ "AtLocation": "cluster_zstat1.txt",
+ "GeneratedBy": "urn:cluster-dQTSoZRU",
"digest": {
- "sha256": "bf3b603569da6dbe3d6f0e8667d346f3ac943c9d01d2fc9743ce17abeb1547fb"
+ "sha256": "b06695ff4f0a8158fa439b1ddf224b58d344606d400885c177390d09506e8e4c"
}
},
{
- "@id": "urn:e84ad552-4fd6-4f7a-b61f-af8268dbc4b7",
+ "@id": "bids::cluster_zstat1",
"Label": "cluster_zstat1",
"AtLocation": "cluster_zstat1",
"digest": {
@@ -1337,25 +1387,25 @@
}
},
{
- "@id": "urn:fb9f4b8d-e79b-4082-952e-839608db3b81",
+ "@id": "bids::rendered_thresh_zstat1",
"Label": "rendered_thresh_zstat1",
"AtLocation": "rendered_thresh_zstat1",
- "GeneratedBy": "urn:52dc58df-35c5-4d53-999e-2377d2e2eddd",
+ "GeneratedBy": "urn:overlay-MQWSN0yZ",
"digest": {
"sha256": "de5b9d44d95f4252f491eb45c76a0ae2b4d2c75b58664fc0df7d9153810c0bf6"
}
},
{
- "@id": "urn:79ddf8b9-1b42-46e8-ae11-c94065e05fa1",
+ "@id": "bids::rendered_thresh_zstat1.png",
"Label": "rendered_thresh_zstat1.png",
"AtLocation": "rendered_thresh_zstat1.png",
- "GeneratedBy": "urn:b8e10bbb-9865-4396-87b8-69935a2f0a7a",
+ "GeneratedBy": "urn:slicer-KQKRKhwm",
"digest": {
"sha256": "15d6a8bf7a902df8c5feeb7468a3d0caacf9eb3067c0840c2f4763f5e2301527"
}
},
{
- "@id": "urn:b263d905-07d9-4561-8e6f-3642c4753b72",
+ "@id": "bids::/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif",
"Label": "ramp.gif",
"AtLocation": "/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif",
"digest": {
@@ -1363,28 +1413,28 @@
}
},
{
- "@id": "urn:51621115-ddfd-4b47-a945-1f41a2d2d1ae",
+ "@id": "bids::.ramp.gif",
"Label": ".ramp.gif",
"AtLocation": ".ramp.gif",
- "GeneratedBy": "urn:0e383a9f-e4be-447d-baa2-be66cac8bff3",
+ "GeneratedBy": "urn:cp-2T3xfElR",
"digest": {
"sha256": "93f4284ccb854d5a41401d9360a13223017b67479cb289a33d83836922e028a4"
}
},
{
- "@id": "urn:522057cf-87c1-4b9f-bbd3-24f853426872",
+ "@id": "bids::tsplot",
"Label": "tsplot",
"AtLocation": "tsplot",
- "GeneratedBy": "urn:cd4904d9-50f8-40f4-ba37-150beaa53fb0",
+ "GeneratedBy": "urn:makedire-Ybe9be1w",
"digest": {
"sha256": "2a74042f4edf02288edf16961307f741651efb4346e102a04b7603e781d1625e"
}
},
{
- "@id": "urn:e12bd186-f854-46a0-89c9-d7035a31bd5d",
+ "@id": "bids::tsplot",
"Label": "tsplot",
"AtLocation": "tsplot",
- "GeneratedBy": "urn:785ab00d-b2b2-4d41-9517-5340e9a6b666",
+ "GeneratedBy": "urn:tsplot-b6M9Wmgz",
"digest": {
"sha256": "2a74042f4edf02288edf16961307f741651efb4346e102a04b7603e781d1625e"
}
diff --git a/examples/from_parsers/fsl/fsl_motion_reg_report_log.png b/examples/from_parsers/fsl/fsl_motion_reg_report_log.png
index 887b76db9..642ab7f7a 100644
Binary files a/examples/from_parsers/fsl/fsl_motion_reg_report_log.png and b/examples/from_parsers/fsl/fsl_motion_reg_report_log.png differ
diff --git a/examples/from_parsers/fsl/fsl_thr_clustfwep05_report_log.html b/examples/from_parsers/fsl/fsl_thr_clustfwep05_report_log.html
index 4324db37c..35beaa16b 100644
--- a/examples/from_parsers/fsl/fsl_thr_clustfwep05_report_log.html
+++ b/examples/from_parsers/fsl/fsl_thr_clustfwep05_report_log.html
@@ -35,20 +35,20 @@ Progress Report / Log
326951
Initialisation
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
Total original volumes = 104
/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1
Preprocessing:Stage 1
-/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90
+/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/example_func.nii.gz -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90
Option -F ( FEAT version parameter ) selected with argument "6.00"
Option -d ( output directory ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat"
Option -l ( logfile )input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/logs/feat2_pre"
Option -R ( html unwarping report ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/report_unwarp.html"
Option -r ( html registration report ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/report_reg.html"
Option -i ( main input ) input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/example_func.nii.gz"
-Option -h ( high-res structural image ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
+Option -h ( high-res structural image ) selected with argument "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
Option -w ( highres dof ) selected with argument "BBR"
Option -x ( highres search ) selected with argument "90"
Option -s ( standard image ) selected with argument "/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain"
@@ -59,10 +59,10 @@ Progress Report / Log
/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/reg
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head
did not find file: example_func2highres.mat. Generating transform.
@@ -128,9 +128,9 @@ Progress Report / Log
/bin/rm -rf prefiltered_func_data*
Stats
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
/usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con
Log directory is: stats
diff --git a/examples/from_parsers/fsl/fsl_thr_clustfwep05_report_log.jsonld b/examples/from_parsers/fsl/fsl_thr_clustfwep05_report_log.jsonld
index a4fc4cfe2..181ffab64 100644
--- a/examples/from_parsers/fsl/fsl_thr_clustfwep05_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_thr_clustfwep05_report_log.jsonld
@@ -4,568 +4,577 @@
"Records": {
"Software": [
{
- "@id": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:fsl-z2mBRkGk",
"@type": "prov:SoftwareAgent",
"Label": "FSL",
- "Version": "xxx"
+ "Version": "xxx",
+ "AltIdentifier": "RRID:SCR_002823"
}
],
"Activities": [
{
- "@id": "urn:b9abc1ea-bd24-4d11-9265-b47515b60018",
+ "@id": "urn:fslmaths-CQbxzFTw",
"Label": "fslmaths",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
"Used": [
- "urn:9c7c6f27-48e0-4fea-9462-0562a157958e"
+ "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold"
]
},
{
- "@id": "urn:6ec6582b-5a64-41b9-b74a-d118936b0284",
+ "@id": "urn:fslroi-wGZBqcbE",
"Label": "fslroi",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1",
"Used": [
- "urn:e64b9468-e646-4716-a449-e734edd20283"
+ "bids::prefiltered_func_data"
]
},
{
- "@id": "urn:876c515d-0b2c-4896-a395-f5208dbee953",
+ "@id": "urn:mainfeat-Z5CbKU9F",
"Label": "mainfeatreg",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/example_func.nii.gz -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
"Used": [
- "urn:287cbf00-f101-4375-ad78-e61d0f8c648f",
- "urn:4ea6317a-4ae1-4f30-b5a2-4e01539d929e",
- "urn:ad185281-72cb-4c30-9556-4af3978bbe83"
+ "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/example_func.nii.gz",
+ "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain",
+ "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
]
},
{
- "@id": "urn:5a20644f-8235-42e5-b56f-e86bb7753ecd",
+ "@id": "urn:makedire-NOEtFviS",
"Label": "Make directory",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/reg",
"Used": []
},
{
- "@id": "urn:37121a7c-b567-4f85-a500-bb3562563a9d",
+ "@id": "urn:fslmaths-T1fVWMQu",
"Label": "fslmaths",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
"Used": [
- "urn:4ea6317a-4ae1-4f30-b5a2-4e01539d929e"
+ "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
]
},
{
- "@id": "urn:580b968d-c1ef-4ea6-a72c-b4a7646d5ee4",
+ "@id": "urn:fslmaths-2vYi9QDl",
"Label": "fslmaths",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
"Used": [
- "urn:281f3d24-626f-4c05-b06f-01ed8c009bdc"
+ "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w"
]
},
{
- "@id": "urn:d604d4b1-3ba4-4569-a3e2-e89c6cb6b835",
+ "@id": "urn:epireg-B1VKnLMt",
"Label": "epi_reg",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres",
- "Used": []
+ "Used": [
+ "bids::example_func",
+ "bids::highres",
+ "bids::highres_head"
+ ]
},
{
- "@id": "urn:25126a8b-b6aa-45e0-b05b-aaddcb7793c8",
+ "@id": "urn:convertx-gcVgFYO6",
"Label": "convert_xfm",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat",
"Used": [
- "urn:f429e94a-e5cc-4796-835d-4fc7ba1917d1"
+ "bids::example_func2highres.mat"
]
},
{
- "@id": "urn:8d91aa22-22f8-4ea2-9ca5-42d0f4643f4f",
+ "@id": "urn:slicer-9NGIvNbx",
"Label": "slicer",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:52c07d8f-2a53-4bf0-bf9e-c5a1656c9deb",
- "urn:863f1088-36af-4ae7-8a09-4c5ee8c5559f"
+ "bids::example_func2highres",
+ "bids::highres"
]
},
{
- "@id": "urn:0b2b92bb-d5a0-481b-b286-f5524c5174c7",
+ "@id": "urn:pngappen-SVwn1wOf",
"Label": "pngappend",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres1.png",
"Used": [
- "urn:053445f1-731c-4b12-ad78-83c800e44f52",
- "urn:16e3f814-261e-426c-ac40-a4112a65d10d",
- "urn:170a2642-1f39-449a-b52c-43a3f96332f4",
- "urn:5ca8b30b-941d-4623-abe9-cd9d43ac941c",
- "urn:7ec370f6-7fa0-4fe6-b172-78531415e913",
- "urn:8d4a17dd-0272-4c84-abd0-49fe8c41c0ee",
- "urn:947fc159-4080-408c-90d8-9c082ab4f5db",
- "urn:9e439a85-3103-4992-96af-be574019827e",
- "urn:acda275a-b3d5-4117-b8e2-02e26364ba33",
- "urn:affc4ea6-1cd3-4deb-bf21-c01b7d788de1",
- "urn:c3fef51d-5762-42e0-b208-60c41cb88f9e",
- "urn:e263f16e-cedc-4489-bc9a-a3b69f9a926e"
+ "bids::sla.png",
+ "bids::slb.png",
+ "bids::slc.png",
+ "bids::sld.png",
+ "bids::sle.png",
+ "bids::slf.png",
+ "bids::slg.png",
+ "bids::slh.png",
+ "bids::sli.png",
+ "bids::slj.png",
+ "bids::slk.png",
+ "bids::sll.png"
]
},
{
- "@id": "urn:a011f4d3-bcb4-49b9-92b5-60d54964a1d2",
+ "@id": "urn:slicer-aUDIirTp",
"Label": "slicer",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:52c07d8f-2a53-4bf0-bf9e-c5a1656c9deb",
- "urn:863f1088-36af-4ae7-8a09-4c5ee8c5559f"
+ "bids::example_func2highres",
+ "bids::highres"
]
},
{
- "@id": "urn:00125f77-6342-48bb-963c-4dae68613589",
+ "@id": "urn:pngappen-HDABNtYq",
"Label": "pngappend",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres2.png",
"Used": [
- "urn:053445f1-731c-4b12-ad78-83c800e44f52",
- "urn:16e3f814-261e-426c-ac40-a4112a65d10d",
- "urn:170a2642-1f39-449a-b52c-43a3f96332f4",
- "urn:5ca8b30b-941d-4623-abe9-cd9d43ac941c",
- "urn:7ec370f6-7fa0-4fe6-b172-78531415e913",
- "urn:8d4a17dd-0272-4c84-abd0-49fe8c41c0ee",
- "urn:947fc159-4080-408c-90d8-9c082ab4f5db",
- "urn:9e439a85-3103-4992-96af-be574019827e",
- "urn:acda275a-b3d5-4117-b8e2-02e26364ba33",
- "urn:affc4ea6-1cd3-4deb-bf21-c01b7d788de1",
- "urn:c3fef51d-5762-42e0-b208-60c41cb88f9e",
- "urn:e263f16e-cedc-4489-bc9a-a3b69f9a926e"
+ "bids::sla.png",
+ "bids::slb.png",
+ "bids::slc.png",
+ "bids::sld.png",
+ "bids::sle.png",
+ "bids::slf.png",
+ "bids::slg.png",
+ "bids::slh.png",
+ "bids::sli.png",
+ "bids::slj.png",
+ "bids::slk.png",
+ "bids::sll.png"
]
},
{
- "@id": "urn:940a024f-3e2f-4682-85f1-a12ff1028ab6",
+ "@id": "urn:pngappen-du46OFzf",
"Label": "pngappend",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend example_func2highres1.png example_func2highres2.png example_func2highres.png",
"Used": [
- "urn:68ebae99-927e-455f-b2a6-5123f2ef2fba",
- "urn:915e32b4-c652-48ce-8660-ecf7a007269e"
+ "bids::example_func2highres1.png",
+ "bids::example_func2highres2.png"
]
},
{
- "@id": "urn:7a473662-ee47-4397-a8ae-b2bf8e1d4409",
+ "@id": "urn:rm-iBAEppWw",
"Label": "rm",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/bin/rm -f sl?.png example_func2highres2.png",
"Used": [
- "urn:189beb08-e9a2-4516-9240-a715584e0031",
- "urn:915e32b4-c652-48ce-8660-ecf7a007269e"
+ "bids::example_func2highres2.png",
+ "bids::sl?.png"
]
},
{
- "@id": "urn:9ba21a89-ed35-4419-a682-3263f7dac0fb",
+ "@id": "urn:rm-ULp49SaM",
"Label": "rm",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/bin/rm example_func2highres1.png",
"Used": [
- "urn:68ebae99-927e-455f-b2a6-5123f2ef2fba"
+ "bids::example_func2highres1.png"
]
},
{
- "@id": "urn:ff2a2443-83b2-4529-a30f-d2d858c75ea9",
+ "@id": "urn:mcflirt-VrAGRiNW",
"Label": "mcflirt",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs -spline_final",
"Used": [
- "urn:e64b9468-e646-4716-a449-e734edd20283"
+ "bids::prefiltered_func_data"
]
},
{
- "@id": "urn:e750f6bc-d97a-4a51-ac11-ae1720f99d12",
+ "@id": "urn:makedire-rsmkMsdJ",
"Label": "Make directory",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/bin/mkdir -p mc",
"Used": []
},
{
- "@id": "urn:5023c995-0b5c-4c5d-8e82-318ef6c185f8",
+ "@id": "urn:mv-eJZYi4bU",
"Label": "mv",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc",
"Used": [
- "urn:2bd63b48-4475-4f80-9b48-bceab9a6454c",
- "urn:2d697161-8067-4c48-9479-bf87530c9fe0",
- "urn:3dbdc0d0-6ed7-4673-adb7-bf7ee0e10c5f",
- "urn:4a8f29c1-4ba1-4ea3-a128-eccc5bc20519",
- "urn:86bc195e-ddf4-49cd-a722-c44af7f51739",
- "urn:cd671cbd-c42d-4719-81c8-0a9e3e044d7b"
+ "bids::prefiltered_func_data_mcf.mat",
+ "bids::prefiltered_func_data_mcf.par",
+ "bids::prefiltered_func_data_mcf_abs.rms",
+ "bids::prefiltered_func_data_mcf_abs_mean.rms",
+ "bids::prefiltered_func_data_mcf_rel.rms",
+ "bids::prefiltered_func_data_mcf_rel_mean.rms"
]
},
{
- "@id": "urn:0ec054dc-b03d-4682-86e2-3ce489e221cf",
+ "@id": "urn:fsltsplo-jfXPMkZi",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png",
"Used": [
- "urn:cd671cbd-c42d-4719-81c8-0a9e3e044d7b"
+ "bids::prefiltered_func_data_mcf.par"
]
},
{
- "@id": "urn:a3127220-c9fb-4c52-99d6-9a7bfb95a855",
+ "@id": "urn:fsltsplo-tVA4OWyL",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png",
"Used": [
- "urn:cd671cbd-c42d-4719-81c8-0a9e3e044d7b"
+ "bids::prefiltered_func_data_mcf.par"
]
},
{
- "@id": "urn:bd3cda7f-ebb1-4668-8946-9c8ecc7be163",
+ "@id": "urn:fsltsplo-CVpNhDKM",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png",
"Used": [
- "urn:e5e18b59-a90b-4ac9-9254-d5a18b92d307"
+ "bids::prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms"
]
},
{
- "@id": "urn:a842c4e3-7553-4db1-8f80-c8490a6d2342",
+ "@id": "urn:fslmaths-PCDp4ETS",
"Label": "fslmaths",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func",
"Used": [
- "urn:e4185d45-0bcd-48f6-91a2-839587f71001"
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:83d9775b-d095-4fa1-9c97-3eb1ccbcc82c",
+ "@id": "urn:bet2-zwxs3XiV",
"Label": "bet2",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/bet2 mean_func mask -f 0.3 -n -m",
"Used": [
- "urn:860299cd-8a5e-476b-8b87-e045551bc294"
+ "bids::mean_func"
]
},
{
- "@id": "urn:9dcd837c-b805-482e-ada6-bc351c6279b5",
+ "@id": "urn:immv-aNaAxFct",
"Label": "immv",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/immv mask_mask mask",
"Used": [
- "urn:0b89b54b-b2af-4483-a3e0-94cf7ae5c951"
+ "bids::mask_mask"
]
},
{
- "@id": "urn:693a8ebf-4876-42b8-b3e6-39bc58fb9175",
+ "@id": "urn:fslmaths-mR5ox17n",
"Label": "fslmaths",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet",
"Used": [
- "urn:5b04f058-84b0-4900-86d8-ba5bda1ed793",
- "urn:e4185d45-0bcd-48f6-91a2-839587f71001"
+ "bids::mask",
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:738325f4-ebfd-4fbd-b9ab-981a80357af0",
+ "@id": "urn:fslstats-DM7S9Mpc",
"Label": "fslstats",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_bet -p 2 -p 98",
"Used": [
- "urn:39403e4d-45b5-4582-9d37-258d3e64847d"
+ "bids::prefiltered_func_data_bet"
]
},
{
- "@id": "urn:929a3f98-4314-480f-b888-01bdcf215560",
+ "@id": "urn:fslmaths-WkfiIcbD",
"Label": "fslmaths",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_bet -thr 74.4585571 -Tmin -bin mask -odt char",
"Used": [
- "urn:39403e4d-45b5-4582-9d37-258d3e64847d"
+ "bids::prefiltered_func_data_bet"
]
},
{
- "@id": "urn:f2e84dd6-35d9-45be-bd69-95e73d210f05",
+ "@id": "urn:fslstats-aG1XtjHz",
"Label": "fslstats",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_mcf -k mask -p 50",
"Used": [
- "urn:e4185d45-0bcd-48f6-91a2-839587f71001"
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:8d94fd93-014b-4548-b541-9601585ac784",
+ "@id": "urn:fslmaths-CtpyYKuB",
"Label": "fslmaths",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -dilF mask",
"Used": [
- "urn:5b04f058-84b0-4900-86d8-ba5bda1ed793"
+ "bids::mask"
]
},
{
- "@id": "urn:1e2be37d-557a-44bf-b9c6-d6adcd9fb278",
+ "@id": "urn:fslmaths-2WC0lJN1",
"Label": "fslmaths",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh",
"Used": [
- "urn:5b04f058-84b0-4900-86d8-ba5bda1ed793",
- "urn:e4185d45-0bcd-48f6-91a2-839587f71001"
+ "bids::mask",
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:bff29ae7-06a5-47af-89d8-c7b5a76718ce",
+ "@id": "urn:fslmaths-khNo5iOT",
"Label": "fslmaths",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func",
"Used": [
- "urn:bfdaeecc-9a20-4732-acf7-ebc9e8c2d4c1"
+ "bids::prefiltered_func_data_thresh"
]
},
{
- "@id": "urn:2603df19-39bf-4946-8d17-6e5611b01406",
+ "@id": "urn:susan-HnfKAKRm",
"Label": "susan",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/susan prefiltered_func_data_thresh 445.8289035 2.54777070064 3 1 1 mean_func 445.8289035 prefiltered_func_data_smooth",
"Used": [
- "urn:bfdaeecc-9a20-4732-acf7-ebc9e8c2d4c1"
+ "bids::prefiltered_func_data_thresh"
]
},
{
- "@id": "urn:6004db50-d525-4e60-b9d9-0f6cb3513e69",
+ "@id": "urn:fslmaths-bhbGoy1D",
"Label": "fslmaths",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth",
"Used": [
- "urn:5b04f058-84b0-4900-86d8-ba5bda1ed793",
- "urn:f8fc8443-30d8-4435-8ef5-98fd326b0325"
+ "bids::mask",
+ "bids::prefiltered_func_data_smooth"
]
},
{
- "@id": "urn:196eab7a-3e2b-410e-a4c3-89f706ae8db3",
+ "@id": "urn:fslmaths-v1t2Tib0",
"Label": "fslmaths",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mul 16.8225970571 prefiltered_func_data_intnorm",
"Used": [
- "urn:f8fc8443-30d8-4435-8ef5-98fd326b0325"
+ "bids::prefiltered_func_data_smooth"
]
},
{
- "@id": "urn:0c860fc3-fbed-464c-a458-8e2221e88652",
+ "@id": "urn:fslmaths-f5vk8v8D",
"Label": "fslmaths",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean",
"Used": [
- "urn:bc1d54d7-90b4-444e-8ad4-93948efd48fd"
+ "bids::prefiltered_func_data_intnorm"
]
},
{
- "@id": "urn:0613b8de-2123-4f1e-9661-006a4bb01370",
+ "@id": "urn:fslmaths-syGOJJLj",
"Label": "fslmaths",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -bptf 15.0 -1 -add tempMean prefiltered_func_data_tempfilt",
"Used": [
- "urn:bc1d54d7-90b4-444e-8ad4-93948efd48fd",
- "urn:fe3e4131-9b71-4cde-ae30-0c848b08a6d6"
+ "bids::prefiltered_func_data_intnorm",
+ "bids::tempMean"
]
},
{
- "@id": "urn:1094048a-35c9-4b7e-a180-70ace816a1b5",
+ "@id": "urn:imrm-hHibgoES",
"Label": "imrm",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/imrm tempMean",
"Used": [
- "urn:fe3e4131-9b71-4cde-ae30-0c848b08a6d6"
+ "bids::tempMean"
]
},
{
- "@id": "urn:c32b3dea-3bb5-460f-836b-f0d37c0c92f4",
+ "@id": "urn:fslmaths-e9nQDxGR",
"Label": "fslmaths",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data",
"Used": [
- "urn:dfe214b8-a7ec-45f5-90bd-927c66e253c2"
+ "bids::prefiltered_func_data_tempfilt"
]
},
{
- "@id": "urn:1e06fa49-f568-4a8d-95b1-1b00344d42c2",
+ "@id": "urn:fslmaths-oR3LoS44",
"Label": "fslmaths",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths filtered_func_data -Tmean mean_func",
"Used": [
- "urn:bcca5728-ee7a-4910-b04e-4afe1f0100d4"
+ "bids::filtered_func_data"
]
},
{
- "@id": "urn:1e97af62-8e80-4922-b801-9fbfd1c08e95",
+ "@id": "urn:rm-UBJlqLmj",
"Label": "rm",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/bin/rm -rf prefiltered_func_data*",
"Used": [
- "urn:dd59d2c2-9e43-4dac-b1d2-71a3db038952"
+ "bids::prefiltered_func_data*"
]
},
{
- "@id": "urn:df8b62e7-fee0-43de-bb45-e25ae1a262f2",
+ "@id": "urn:makedire-GyMaT50A",
"Label": "Make directory",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
- "@id": "urn:7a60ceed-9253-40d3-ab98-9dbcceac5361",
+ "@id": "urn:fslfixte-EtMronL8",
"Label": "fslFixText",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
"Used": [
- "urn:95ca1050-f815-482f-a5d5-50df9eb5fcc6"
+ "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt"
]
},
{
- "@id": "urn:c49d5a06-0a28-4dff-8d3f-b322c4f36291",
+ "@id": "urn:makedire-5sWMxcHV",
"Label": "Make directory",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
- "@id": "urn:fac26c4d-38f9-49b0-9faf-062fe892a8ff",
+ "@id": "urn:fslfixte-IQqtsVCJ",
"Label": "fslFixText",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
"Used": [
- "urn:308e722d-3011-4493-b217-f569373f2c39"
+ "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt"
]
},
{
- "@id": "urn:fe99ab29-ca34-4fb3-a31c-865b7fde6579",
+ "@id": "urn:filmgls-Ynnm5y4b",
"Label": "film_gls",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con",
- "Used": []
+ "Used": [
+ "bids::design.con",
+ "bids::design.mat",
+ "bids::filtered_func_data",
+ "bids::stats"
+ ]
},
{
- "@id": "urn:9e7316c6-b46b-4b93-b667-1785f7503f51",
+ "@id": "urn:smoothes-M85mOmBI",
"Label": "smoothest",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 102 -m mask -r stats/res4d > stats/smoothness",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 102 -m mask -r stats/res4d > stats/smoothness",
"Used": [
- "urn:5b04f058-84b0-4900-86d8-ba5bda1ed793",
- "urn:65c14f0f-4471-4ee4-b76b-0837fffadfee"
+ "bids::mask",
+ "bids::stats/res4d"
]
},
{
- "@id": "urn:69ce85f3-e1c3-45a4-9eea-f36fac8b7522",
+ "@id": "urn:fslmaths-u2OKI4tM",
"Label": "fslmaths",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1",
"Used": [
- "urn:3dbc753d-ec5f-4933-816b-b57d17bdb32d",
- "urn:5b04f058-84b0-4900-86d8-ba5bda1ed793"
+ "bids::mask",
+ "bids::stats/zstat1"
]
},
{
- "@id": "urn:0df558d3-86a4-4596-82b9-2026fa148678",
+ "@id": "urn:echo-O7bBldSG",
"Label": "echo",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "echo 38352 > thresh_zstat1.vol",
"Used": []
},
{
- "@id": "urn:0255aa2c-31b4-488c-97f8-7e4e7a35295e",
+ "@id": "urn:cluster-arWUdanS",
"Label": "cluster",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -t 2.3 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z -p 0.05 -d 0.70114 --volume=38352 -c stats/cope1 > cluster_zstat1.txt",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -t 2.3 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z -p 0.05 -d 0.70114 --volume=38352 -c stats/cope1 > cluster_zstat1.txt",
"Used": [
- "urn:7a75f677-aee4-4241-bc66-2169ae57d63d",
- "urn:9f51d912-394a-4bb7-8858-1674aed5be7c"
+ "bids::stats/cope1",
+ "bids::thresh_zstat1"
]
},
{
- "@id": "urn:a7de91f4-6659-4288-9fa1-daeb0fd5f01b",
+ "@id": "urn:cluster2-SSw3QWij",
"Label": "cluster2html",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat1",
"Used": [
- "urn:48c32de6-d8cc-4932-9033-005392de7601"
+ "bids::cluster_zstat1"
]
},
{
- "@id": "urn:6591f358-d675-4355-a6fa-74c22467f6bf",
+ "@id": "urn:fslstats-vYUU0538",
"Label": "fslstats",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat1 -l 0.0001 -R 2>/dev/null",
"Used": [
- "urn:9f51d912-394a-4bb7-8858-1674aed5be7c"
+ "bids::thresh_zstat1"
]
},
{
- "@id": "urn:83b8a0a0-af45-4d8f-9a2e-35c24bcb3c0c",
+ "@id": "urn:overlay-ingy4BcX",
"Label": "overlay",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat1 2.300208 7.488793 rendered_thresh_zstat1",
"Used": []
},
{
- "@id": "urn:9409d309-6e12-4b1c-94b2-7bee390b752e",
+ "@id": "urn:slicer-mTcDkz7J",
"Label": "slicer",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat1 -A 750 rendered_thresh_zstat1.png",
"Used": [
- "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc"
+ "bids::rendered_thresh_zstat1"
]
},
{
- "@id": "urn:837c6c1f-5c41-4ce9-8bf6-5ee96151ec45",
+ "@id": "urn:cp-PR5EAyjU",
"Label": "cp",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/bin/cp /usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif .ramp.gif",
"Used": [
- "urn:2d9ff369-4529-4847-81b1-9444562e5d64"
+ "bids::/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif"
]
},
{
- "@id": "urn:33c75be3-aa4e-406c-baeb-c6b0c73dd6e4",
+ "@id": "urn:makedire-ZUoir1kH",
"Label": "Make directory",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "mkdir -p tsplot",
"Used": []
},
{
- "@id": "urn:9a05342f-5bd5-43c7-ad4c-c0335f9a38fb",
+ "@id": "urn:tsplot-3cwiWj6a",
"Label": "tsplot",
- "AssociatedWith": "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
+ "AssociatedWith": "urn:fsl-z2mBRkGk",
"Command": "/usr/local/packages/fsl-5.0.10/bin/tsplot . -f filtered_func_data -o tsplot",
"Used": []
}
],
"Entities": [
{
- "@id": "urn:9c7c6f27-48e0-4fea-9462-0562a157958e",
+ "@id": "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold",
"Label": "sub-01_task-tonecounting_bold",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold",
+ "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold",
"digest": {
- "sha256": "028adf00daa36e78f06a61dcd3cb3526cd8564c1284e80516ab5520701324ac1"
+ "sha256": "33501604ae140e58832facff473a9578d5a549403bdbec53107d2b3eaab898ee"
}
},
{
- "@id": "urn:e64b9468-e646-4716-a449-e734edd20283",
+ "@id": "bids::prefiltered_func_data",
"Label": "prefiltered_func_data",
"AtLocation": "prefiltered_func_data",
- "GeneratedBy": "urn:b9abc1ea-bd24-4d11-9265-b47515b60018",
+ "GeneratedBy": "urn:fslmaths-CQbxzFTw",
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}
},
{
- "@id": "urn:cd3e9e9a-6f09-400c-9eef-126515d808a8",
+ "@id": "bids::example_func",
"Label": "example_func",
"AtLocation": "example_func",
- "GeneratedBy": "urn:6ec6582b-5a64-41b9-b74a-d118936b0284",
+ "GeneratedBy": "urn:fslroi-wGZBqcbE",
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- "@id": "urn:ad185281-72cb-4c30-9556-4af3978bbe83",
+ "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/example_func.nii.gz",
"Label": "example_func.nii.gz",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/example_func.nii.gz",
"digest": {
@@ -573,15 +582,15 @@
}
},
{
- "@id": "urn:4ea6317a-4ae1-4f30-b5a2-4e01539d929e",
+ "@id": "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
"Label": "sub-01_T1w_brain",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
+ "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
"digest": {
- "sha256": "ccb9a4d1def67002e358c45bd912034053ffc221ab52c2a19aa55f72c3236279"
+ "sha256": "8f1ae7ba69869c79b2cc5a83ce4ca24a7d666187256c2aa4d61a952b903b05b0"
}
},
{
- "@id": "urn:287cbf00-f101-4375-ad78-e61d0f8c648f",
+ "@id": "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain",
"Label": "MNI152_T1_2mm_brain",
"AtLocation": "/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain",
"digest": {
@@ -589,45 +598,57 @@
}
},
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- "@id": "urn:c4a84cc8-b43e-4379-8adc-83c8d4b5727e",
+ "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat",
"Label": "fsl_cluster_p005.feat",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat",
- "GeneratedBy": "urn:876c515d-0b2c-4896-a395-f5208dbee953"
+ "GeneratedBy": "urn:mainfeat-Z5CbKU9F"
},
{
- "@id": "urn:77b26c36-1727-41bd-92d1-903d0fd511c9",
+ "@id": "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/reg",
"Label": "reg",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/reg",
- "GeneratedBy": "urn:5a20644f-8235-42e5-b56f-e86bb7753ecd",
+ "GeneratedBy": "urn:makedire-NOEtFviS",
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{
- "@id": "urn:863f1088-36af-4ae7-8a09-4c5ee8c5559f",
+ "@id": "bids::highres",
"Label": "highres",
"AtLocation": "highres",
- "GeneratedBy": "urn:37121a7c-b567-4f85-a500-bb3562563a9d",
+ "GeneratedBy": "urn:fslmaths-T1fVWMQu",
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- "@id": "urn:281f3d24-626f-4c05-b06f-01ed8c009bdc",
+ "@id": "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
"Label": "sub-01_T1w",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
+ "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
"digest": {
- "sha256": "3be6c69338e200d2a286a56cd9a0030539cf50201f412c910ade833e18354d27"
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- "Label": "",
- "AtLocation": "",
- "GeneratedBy": "urn:580b968d-c1ef-4ea6-a72c-b4a7646d5ee4"
+ "@id": "bids::highres_head",
+ "Label": "highres_head",
+ "AtLocation": "highres_head",
+ "GeneratedBy": "urn:fslmaths-2vYi9QDl",
+ "digest": {
+ "sha256": "590f180bade23162ef1567a5a61d86ee93155e4c7dc59c04c8ac5d6b7a20ea51"
+ }
+ },
+ {
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+ "Label": "example_func2highres",
+ "AtLocation": "example_func2highres",
+ "GeneratedBy": "urn:epireg-B1VKnLMt",
+ "digest": {
+ "sha256": "00c021d82b83d2dc562c77f76528ece0f7425d4982f292f22021467afce1ba59"
+ }
},
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- "@id": "urn:f429e94a-e5cc-4796-835d-4fc7ba1917d1",
+ "@id": "bids::example_func2highres.mat",
"Label": "example_func2highres.mat",
"AtLocation": "example_func2highres.mat",
"digest": {
@@ -635,267 +656,259 @@
}
},
{
- "@id": "urn:d15366f1-fcfc-4689-94f3-936e235b3bdd",
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"AtLocation": "highres2example_func.mat",
- "GeneratedBy": "urn:25126a8b-b6aa-45e0-b05b-aaddcb7793c8",
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"Label": "sla.png",
"AtLocation": "sla.png",
- "GeneratedBy": "urn:8d91aa22-22f8-4ea2-9ca5-42d0f4643f4f",
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"AtLocation": "slb.png",
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{
- "@id": "urn:947fc159-4080-408c-90d8-9c082ab4f5db",
+ "@id": "bids::slc.png",
"Label": "slc.png",
"AtLocation": "slc.png",
- "GeneratedBy": "urn:8d91aa22-22f8-4ea2-9ca5-42d0f4643f4f",
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{
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"AtLocation": "example_func2highres1.png",
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- "GeneratedBy": "urn:a011f4d3-bcb4-49b9-92b5-60d54964a1d2",
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- "GeneratedBy": "urn:a011f4d3-bcb4-49b9-92b5-60d54964a1d2",
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- "GeneratedBy": "urn:a011f4d3-bcb4-49b9-92b5-60d54964a1d2",
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{
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- "GeneratedBy": "urn:a011f4d3-bcb4-49b9-92b5-60d54964a1d2",
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- "GeneratedBy": "urn:a011f4d3-bcb4-49b9-92b5-60d54964a1d2",
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- "GeneratedBy": "urn:a011f4d3-bcb4-49b9-92b5-60d54964a1d2",
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{
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- "GeneratedBy": "urn:a011f4d3-bcb4-49b9-92b5-60d54964a1d2",
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{
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- "GeneratedBy": "urn:a011f4d3-bcb4-49b9-92b5-60d54964a1d2",
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- "GeneratedBy": "urn:a011f4d3-bcb4-49b9-92b5-60d54964a1d2",
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{
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- "GeneratedBy": "urn:a011f4d3-bcb4-49b9-92b5-60d54964a1d2",
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{
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"AtLocation": "example_func2highres2.png",
- "GeneratedBy": "urn:00125f77-6342-48bb-963c-4dae68613589",
+ "GeneratedBy": "urn:pngappen-HDABNtYq",
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"AtLocation": "example_func2highres.png",
- "GeneratedBy": "urn:940a024f-3e2f-4682-85f1-a12ff1028ab6",
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{
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+ "@id": "bids::sl?.png",
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"digest": {
@@ -903,25 +916,25 @@
}
},
{
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"AtLocation": "prefiltered_func_data_mcf",
- "GeneratedBy": "urn:ff2a2443-83b2-4529-a30f-d2d858c75ea9",
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{
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+ "GeneratedBy": "urn:makedire-rsmkMsdJ",
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{
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@@ -929,7 +942,7 @@
}
},
{
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"digest": {
@@ -937,7 +950,7 @@
}
},
{
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"digest": {
@@ -945,7 +958,7 @@
}
},
{
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@@ -953,7 +966,7 @@
}
},
{
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@@ -961,7 +974,7 @@
}
},
{
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"digest": {
@@ -969,34 +982,34 @@
}
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{
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- "GeneratedBy": "urn:5023c995-0b5c-4c5d-8e82-318ef6c185f8",
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{
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- "GeneratedBy": "urn:0ec054dc-b03d-4682-86e2-3ce489e221cf",
+ "GeneratedBy": "urn:fsltsplo-jfXPMkZi",
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{
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- "GeneratedBy": "urn:a3127220-c9fb-4c52-99d6-9a7bfb95a855",
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{
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@@ -1004,34 +1017,34 @@
}
},
{
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- "GeneratedBy": "urn:bd3cda7f-ebb1-4668-8946-9c8ecc7be163",
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{
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"AtLocation": "mean_func",
- "GeneratedBy": "urn:a842c4e3-7553-4db1-8f80-c8490a6d2342",
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{
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- "GeneratedBy": "urn:83d9775b-d095-4fa1-9c97-3eb1ccbcc82c",
+ "GeneratedBy": "urn:bet2-zwxs3XiV",
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{
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@@ -1039,132 +1052,124 @@
}
},
{
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{
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"AtLocation": "prefiltered_func_data_bet",
- "GeneratedBy": "urn:693a8ebf-4876-42b8-b3e6-39bc58fb9175",
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{
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{
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"AtLocation": "prefiltered_func_data_thresh",
- "GeneratedBy": "urn:1e2be37d-557a-44bf-b9c6-d6adcd9fb278",
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{
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"AtLocation": "mean_func",
- "GeneratedBy": "urn:bff29ae7-06a5-47af-89d8-c7b5a76718ce",
+ "GeneratedBy": "urn:fslmaths-khNo5iOT",
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{
- "@id": "urn:f8fc8443-30d8-4435-8ef5-98fd326b0325",
+ "@id": "bids::prefiltered_func_data_smooth",
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"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:2603df19-39bf-4946-8d17-6e5611b01406",
+ "GeneratedBy": "urn:susan-HnfKAKRm",
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{
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"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:6004db50-d525-4e60-b9d9-0f6cb3513e69",
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{
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"AtLocation": "prefiltered_func_data_intnorm",
- "GeneratedBy": "urn:196eab7a-3e2b-410e-a4c3-89f706ae8db3",
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{
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"AtLocation": "tempMean",
- "GeneratedBy": "urn:0c860fc3-fbed-464c-a458-8e2221e88652",
+ "GeneratedBy": "urn:fslmaths-f5vk8v8D",
"digest": {
"sha256": "1a01513c76bc17516b60df315a1922789ce79d72e66e105fbf2723df9cb1b038"
}
},
{
- "@id": "urn:2c2a2a5f-12d9-443d-8307-038476e05738",
- "Label": "15.0",
- "AtLocation": "15.0",
- "GeneratedBy": "urn:0613b8de-2123-4f1e-9661-006a4bb01370",
- "digest": {
- "sha256": "552db91328a881034f16ec50203ba34d4af448f52c616eb28db6c07aa575a286"
- }
- },
- {
- "@id": "urn:dfe214b8-a7ec-45f5-90bd-927c66e253c2",
+ "@id": "bids::prefiltered_func_data_tempfilt",
"Label": "prefiltered_func_data_tempfilt",
"AtLocation": "prefiltered_func_data_tempfilt",
+ "GeneratedBy": "urn:fslmaths-syGOJJLj",
"digest": {
"sha256": "a1836f4694e7ffdb50484626724602498c7b22b4f3cdd1e7d105efd336cbc8bd"
}
},
{
- "@id": "urn:bcca5728-ee7a-4910-b04e-4afe1f0100d4",
+ "@id": "bids::filtered_func_data",
"Label": "filtered_func_data",
"AtLocation": "filtered_func_data",
- "GeneratedBy": "urn:c32b3dea-3bb5-460f-836b-f0d37c0c92f4",
+ "GeneratedBy": "urn:fslmaths-e9nQDxGR",
"digest": {
"sha256": "2a1854e3b48a54f88e063191e25159015a0afbd300d18a1cfda37b4b68a1ee69"
}
},
{
- "@id": "urn:dbb3dfce-3c0a-4c43-89f6-c10b5c5dacb7",
+ "@id": "bids::mean_func",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:1e06fa49-f568-4a8d-95b1-1b00344d42c2",
+ "GeneratedBy": "urn:fslmaths-oR3LoS44",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:dd59d2c2-9e43-4dac-b1d2-71a3db038952",
+ "@id": "bids::prefiltered_func_data*",
"Label": "prefiltered_func_data*",
"AtLocation": "prefiltered_func_data*",
"digest": {
@@ -1172,113 +1177,158 @@
}
},
{
- "@id": "urn:e085e4ed-61ad-41bb-8450-cffef55b7cc8",
+ "@id": "bids::custom_timing_files",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:df8b62e7-fee0-43de-bb45-e25ae1a262f2",
+ "GeneratedBy": "urn:makedire-GyMaT50A",
"digest": {
"sha256": "1d7e19792328d5040f2f9fb3c15d59de90fc771785f81c67039a043bd5f2ed20"
}
},
{
- "@id": "urn:95ca1050-f815-482f-a5d5-50df9eb5fcc6",
+ "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
"Label": "sub-01_tone_counting.txt",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
+ "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
"digest": {
- "sha256": "c120d27b9d5d81a91be0e55f5cb880b2cb7de6c655554d9c15c9c04c6232ea8e"
+ "sha256": "165398224a205d2fc0b19354e15d9b085c6d81e333b69c4697b7894a2549be0b"
}
},
{
- "@id": "urn:b000ce49-ee34-4b4a-a104-841943e9bc11",
+ "@id": "bids::custom_timing_files/ev1.txt",
"Label": "ev1.txt",
"AtLocation": "custom_timing_files/ev1.txt",
- "GeneratedBy": "urn:7a60ceed-9253-40d3-ab98-9dbcceac5361"
+ "GeneratedBy": "urn:fslfixte-EtMronL8"
},
{
- "@id": "urn:e4e35b1a-0ffb-4b69-91ed-079440711b3b",
+ "@id": "bids::custom_timing_files",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:c49d5a06-0a28-4dff-8d3f-b322c4f36291",
+ "GeneratedBy": "urn:makedire-5sWMxcHV",
"digest": {
"sha256": "1d7e19792328d5040f2f9fb3c15d59de90fc771785f81c67039a043bd5f2ed20"
}
},
{
- "@id": "urn:308e722d-3011-4493-b217-f569373f2c39",
+ "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
"Label": "sub-01_tone_counting_probe.txt",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
+ "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
"digest": {
- "sha256": "f09eeb82fa0be8e8759a5269403f36ec2b7dbf2c5b6caba1f0f985cc6cb3f703"
+ "sha256": "8b912293767f1a5e082311f6aaf0c44fc91fe45b0f2ae7f80e368bc2f4c2918a"
}
},
{
- "@id": "urn:65a49861-ebb5-4b47-b2f8-400979e419dc",
+ "@id": "bids::custom_timing_files/ev2.txt",
"Label": "ev2.txt",
"AtLocation": "custom_timing_files/ev2.txt",
- "GeneratedBy": "urn:fac26c4d-38f9-49b0-9faf-062fe892a8ff"
+ "GeneratedBy": "urn:fslfixte-IQqtsVCJ"
},
{
- "@id": "urn:65c14f0f-4471-4ee4-b76b-0837fffadfee",
- "Label": "res4d",
- "AtLocation": "stats/res4d",
+ "@id": "bids::stats",
+ "Label": "stats",
+ "AtLocation": "stats",
"digest": {
- "sha256": "8845286f36caedf891a02afddc4175ea46f18f830b59a8c5026962184a530699"
+ "sha256": "a9f3e135372514a16d11a8038262b3eff94ccd69a9b35c4724b2759cfc944a07"
}
},
{
- "@id": "urn:9293b57e-bed7-40ac-b1e7-d6552e21881c",
- "Label": "smoothness",
- "AtLocation": "stats/smoothness",
- "GeneratedBy": "urn:9e7316c6-b46b-4b93-b667-1785f7503f51",
+ "@id": "bids::design.mat",
+ "Label": "design.mat",
+ "AtLocation": "design.mat",
"digest": {
- "sha256": "67b0aaf95a257beff60d331b56265034807ca51e67e2d312d481d5835ef0b1d0"
+ "sha256": "1c1a6ef59a355e1f6f81e741e157784ccbe066ba3594a07aa9b16781e3d5bb25"
}
},
{
- "@id": "urn:3dbc753d-ec5f-4933-816b-b57d17bdb32d",
- "Label": "zstat1",
- "AtLocation": "stats/zstat1",
+ "@id": "bids::design.con",
+ "Label": "design.con",
+ "AtLocation": "design.con",
"digest": {
- "sha256": "70ae47cee1ea1d3f1f6f8aa7ac51f2641cb2fcb745dfd8cc54a389346e6fa094"
+ "sha256": "5808d1be37dd8f2a4906b710bb384fbee62faa4a46b2bc6847afc8962ed4eb54"
}
},
{
- "@id": "urn:9f51d912-394a-4bb7-8858-1674aed5be7c",
+ "@id": "bids::stats",
+ "Label": "stats",
+ "AtLocation": "stats",
+ "GeneratedBy": "urn:filmgls-Ynnm5y4b",
+ "digest": {
+ "sha256": "a9f3e135372514a16d11a8038262b3eff94ccd69a9b35c4724b2759cfc944a07"
+ }
+ },
+ {
+ "@id": "bids::stats/res4d",
+ "Label": "res4d",
+ "AtLocation": "stats/res4d"
+ },
+ {
+ "@id": "bids::stats/smoothness",
+ "Label": "smoothness",
+ "AtLocation": "stats/smoothness",
+ "GeneratedBy": "urn:smoothes-M85mOmBI"
+ },
+ {
+ "@id": "bids::stats/zstat1",
+ "Label": "zstat1",
+ "AtLocation": "stats/zstat1"
+ },
+ {
+ "@id": "bids::thresh_zstat1",
"Label": "thresh_zstat1",
"AtLocation": "thresh_zstat1",
- "GeneratedBy": "urn:69ce85f3-e1c3-45a4-9eea-f36fac8b7522",
+ "GeneratedBy": "urn:fslmaths-u2OKI4tM",
"digest": {
"sha256": "662e7ba670e124d15bb3cc18b818868f76604578034b524c8882f35fc5db413f"
}
},
{
- "@id": "urn:7a75f677-aee4-4241-bc66-2169ae57d63d",
+ "@id": "bids::stats/cope1",
"Label": "cope1",
- "AtLocation": "stats/cope1",
- "digest": {
- "sha256": "bf3b603569da6dbe3d6f0e8667d346f3ac943c9d01d2fc9743ce17abeb1547fb"
- }
+ "AtLocation": "stats/cope1"
},
{
- "@id": "urn:041f3508-d4c5-4ef0-947d-4fc6d5de0a0f",
+ "@id": "bids::cluster_mask_zstat1",
"Label": "cluster_mask_zstat1",
"AtLocation": "cluster_mask_zstat1",
- "GeneratedBy": "urn:0255aa2c-31b4-488c-97f8-7e4e7a35295e",
+ "GeneratedBy": "urn:cluster-arWUdanS",
"digest": {
"sha256": "b28c170e33d2917cac55183786616a9e976e5e7f30dc7c8666341f12ed6d0277"
}
},
{
- "@id": "urn:695318d9-1169-4e52-a4e7-75d46de608a2",
+ "@id": "bids::thresh_zstat1",
+ "Label": "thresh_zstat1",
+ "AtLocation": "thresh_zstat1",
+ "GeneratedBy": "urn:cluster-arWUdanS",
+ "digest": {
+ "sha256": "662e7ba670e124d15bb3cc18b818868f76604578034b524c8882f35fc5db413f"
+ }
+ },
+ {
+ "@id": "bids::lmax_zstat1.txt",
+ "Label": "lmax_zstat1.txt",
+ "AtLocation": "lmax_zstat1.txt",
+ "GeneratedBy": "urn:cluster-arWUdanS",
+ "digest": {
+ "sha256": "d44ee21719775397a1a95ede6778d25404b50e8bd259dbdf02d2fde635fc81a5"
+ }
+ },
+ {
+ "@id": "bids::stats/cope1",
"Label": "cope1",
"AtLocation": "stats/cope1",
- "GeneratedBy": "urn:0255aa2c-31b4-488c-97f8-7e4e7a35295e",
+ "GeneratedBy": "urn:cluster-arWUdanS"
+ },
+ {
+ "@id": "bids::cluster_zstat1.txt",
+ "Label": "cluster_zstat1.txt",
+ "AtLocation": "cluster_zstat1.txt",
+ "GeneratedBy": "urn:cluster-arWUdanS",
"digest": {
- "sha256": "bf3b603569da6dbe3d6f0e8667d346f3ac943c9d01d2fc9743ce17abeb1547fb"
+ "sha256": "b06695ff4f0a8158fa439b1ddf224b58d344606d400885c177390d09506e8e4c"
}
},
{
- "@id": "urn:48c32de6-d8cc-4932-9033-005392de7601",
+ "@id": "bids::cluster_zstat1",
"Label": "cluster_zstat1",
"AtLocation": "cluster_zstat1",
"digest": {
@@ -1286,25 +1336,25 @@
}
},
{
- "@id": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
+ "@id": "bids::rendered_thresh_zstat1",
"Label": "rendered_thresh_zstat1",
"AtLocation": "rendered_thresh_zstat1",
- "GeneratedBy": "urn:83b8a0a0-af45-4d8f-9a2e-35c24bcb3c0c",
+ "GeneratedBy": "urn:overlay-ingy4BcX",
"digest": {
"sha256": "de5b9d44d95f4252f491eb45c76a0ae2b4d2c75b58664fc0df7d9153810c0bf6"
}
},
{
- "@id": "urn:19ab30f4-d471-4bcc-9a78-eec044705c90",
+ "@id": "bids::rendered_thresh_zstat1.png",
"Label": "rendered_thresh_zstat1.png",
"AtLocation": "rendered_thresh_zstat1.png",
- "GeneratedBy": "urn:9409d309-6e12-4b1c-94b2-7bee390b752e",
+ "GeneratedBy": "urn:slicer-mTcDkz7J",
"digest": {
"sha256": "15d6a8bf7a902df8c5feeb7468a3d0caacf9eb3067c0840c2f4763f5e2301527"
}
},
{
- "@id": "urn:2d9ff369-4529-4847-81b1-9444562e5d64",
+ "@id": "bids::/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif",
"Label": "ramp.gif",
"AtLocation": "/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif",
"digest": {
@@ -1312,28 +1362,28 @@
}
},
{
- "@id": "urn:e6787718-533c-4ee0-9c8b-804f603f9942",
+ "@id": "bids::.ramp.gif",
"Label": ".ramp.gif",
"AtLocation": ".ramp.gif",
- "GeneratedBy": "urn:837c6c1f-5c41-4ce9-8bf6-5ee96151ec45",
+ "GeneratedBy": "urn:cp-PR5EAyjU",
"digest": {
"sha256": "93f4284ccb854d5a41401d9360a13223017b67479cb289a33d83836922e028a4"
}
},
{
- "@id": "urn:7e90b8aa-1787-46fb-88cf-ae5ddc1b0750",
+ "@id": "bids::tsplot",
"Label": "tsplot",
"AtLocation": "tsplot",
- "GeneratedBy": "urn:33c75be3-aa4e-406c-baeb-c6b0c73dd6e4",
+ "GeneratedBy": "urn:makedire-ZUoir1kH",
"digest": {
"sha256": "2a74042f4edf02288edf16961307f741651efb4346e102a04b7603e781d1625e"
}
},
{
- "@id": "urn:fefe30f0-2f4a-4307-9cad-d79ba9e76530",
+ "@id": "bids::tsplot",
"Label": "tsplot",
"AtLocation": "tsplot",
- "GeneratedBy": "urn:9a05342f-5bd5-43c7-ad4c-c0335f9a38fb",
+ "GeneratedBy": "urn:tsplot-3cwiWj6a",
"digest": {
"sha256": "2a74042f4edf02288edf16961307f741651efb4346e102a04b7603e781d1625e"
}
diff --git a/examples/from_parsers/fsl/fsl_thr_clustfwep05_report_log.png b/examples/from_parsers/fsl/fsl_thr_clustfwep05_report_log.png
index 2792861af..14eee83b2 100644
Binary files a/examples/from_parsers/fsl/fsl_thr_clustfwep05_report_log.png and b/examples/from_parsers/fsl/fsl_thr_clustfwep05_report_log.png differ
diff --git a/examples/from_parsers/fsl/fsl_thr_voxelfwep05_report_log.html b/examples/from_parsers/fsl/fsl_thr_voxelfwep05_report_log.html
index e902e09ad..6103f229a 100644
--- a/examples/from_parsers/fsl/fsl_thr_voxelfwep05_report_log.html
+++ b/examples/from_parsers/fsl/fsl_thr_voxelfwep05_report_log.html
@@ -35,20 +35,20 @@ Progress Report / Log
326956
Initialisation
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float
Total original volumes = 104
/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1
Preprocessing:Stage 1
-/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90
+/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/example_func.nii.gz -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90
Option -F ( FEAT version parameter ) selected with argument "6.00"
Option -d ( output directory ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat"
Option -l ( logfile )input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/logs/feat2_pre"
Option -R ( html unwarping report ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/report_unwarp.html"
Option -r ( html registration report ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/report_reg.html"
Option -i ( main input ) input with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/example_func.nii.gz"
-Option -h ( high-res structural image ) selected with argument "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
+Option -h ( high-res structural image ) selected with argument "ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
Option -w ( highres dof ) selected with argument "BBR"
Option -x ( highres search ) selected with argument "90"
Option -s ( standard image ) selected with argument "/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain"
@@ -59,10 +59,10 @@ Progress Report / Log
/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/reg
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres
-/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head
+/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head
did not find file: example_func2highres.mat. Generating transform.
@@ -128,9 +128,9 @@ Progress Report / Log
/bin/rm -rf prefiltered_func_data*
Stats
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt
-mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
+mkdir -p custom_timing_files ; /usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt
/usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con
Log directory is: stats
diff --git a/examples/from_parsers/fsl/fsl_thr_voxelfwep05_report_log.jsonld b/examples/from_parsers/fsl/fsl_thr_voxelfwep05_report_log.jsonld
index 7f6b4a9b1..396c9382b 100644
--- a/examples/from_parsers/fsl/fsl_thr_voxelfwep05_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_thr_voxelfwep05_report_log.jsonld
@@ -4,575 +4,584 @@
"Records": {
"Software": [
{
- "@id": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:fsl-un0J9v6I",
"@type": "prov:SoftwareAgent",
"Label": "FSL",
- "Version": "xxx"
+ "Version": "xxx",
+ "AltIdentifier": "RRID:SCR_002823"
}
],
"Activities": [
{
- "@id": "urn:96a73f71-358d-457f-8892-670c9b5e4c54",
+ "@id": "urn:fslmaths-0UEDBgwF",
"Label": "fslmaths",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
"Used": [
- "urn:9723d944-903b-4c04-8a8f-b4d78556e8b4"
+ "bids::ds011/sub-01/func/sub-01_task-tonecounting_bold"
]
},
{
- "@id": "urn:f018e574-c168-4881-888c-9219e4b677b5",
+ "@id": "urn:fslroi-BiurVc38",
"Label": "fslroi",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1",
"Used": [
- "urn:a49c2b75-473b-4726-93c3-d0327ef97cd4"
+ "bids::prefiltered_func_data"
]
},
{
- "@id": "urn:1b781f3e-d5fd-400c-89de-ff3f0fa207a7",
+ "@id": "urn:mainfeat-MbvgcKNU",
"Label": "mainfeatreg",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/example_func.nii.gz -h ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
"Used": [
- "urn:57568e78-c209-4703-8379-c145283e032f",
- "urn:c6a468b6-cc4a-43b3-ac27-31554da9d2fc",
- "urn:d371b84e-3f72-47e0-815d-60bda0e0ea20"
+ "bids::/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/example_func.nii.gz",
+ "bids::/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain",
+ "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
]
},
{
- "@id": "urn:834348f8-d41c-407b-a7dd-0209297427d4",
+ "@id": "urn:makedire-XQJb6bN7",
"Label": "Make directory",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/reg",
"Used": []
},
{
- "@id": "urn:0bbb1294-8273-4059-89d9-af92f4a71b99",
+ "@id": "urn:fslmaths-wVW9AYbV",
"Label": "fslmaths",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
"Used": [
- "urn:d371b84e-3f72-47e0-815d-60bda0e0ea20"
+ "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain"
]
},
{
- "@id": "urn:6d71a816-eb5c-40c8-abd0-ba55ee51be5c",
+ "@id": "urn:fslmaths-zVtrpznD",
"Label": "fslmaths",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
"Used": [
- "urn:17e338e3-78a3-420f-ab4b-f48e30cbd207"
+ "bids::ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w"
]
},
{
- "@id": "urn:0f4d707a-72e8-42d9-bfe8-0c2db37553b3",
+ "@id": "urn:epireg-oMUx8O4H",
"Label": "epi_reg",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/usr/local/packages/fsl-5.0.10/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres",
- "Used": []
+ "Used": [
+ "bids::example_func",
+ "bids::highres",
+ "bids::highres_head"
+ ]
},
{
- "@id": "urn:24d65676-5458-4491-b14d-afc59bdc3e7c",
+ "@id": "urn:convertx-CpKNgCUu",
"Label": "convert_xfm",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/usr/local/packages/fsl-5.0.10/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat",
"Used": [
- "urn:91e6e90d-7fd9-4fe3-9c65-1029ada5d21f"
+ "bids::example_func2highres.mat"
]
},
{
- "@id": "urn:f4d3c9da-afba-4300-bdb6-8b2eddc90883",
+ "@id": "urn:slicer-kSvyNzUC",
"Label": "slicer",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:02ad2de3-ed26-4828-86dd-5090741065b4",
- "urn:ac767057-e6a1-4207-8818-bbb01d04b597"
+ "bids::example_func2highres",
+ "bids::highres"
]
},
{
- "@id": "urn:b7bd3c57-1d8d-4cd8-9a1c-67c8b0962dfc",
+ "@id": "urn:pngappen-YzcHp6V7",
"Label": "pngappend",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres1.png",
"Used": [
- "urn:081c6ba0-20ae-4769-9fbe-9f1c0d3a0380",
- "urn:0b111a92-c24b-463f-b287-d4090823ed0c",
- "urn:25b260b1-6825-40d3-b423-c05cca0747fb",
- "urn:43044f87-e488-43eb-8305-0ff802654d36",
- "urn:4a25fd24-f3f5-4e89-8aec-1df8d599a71b",
- "urn:61060efc-571a-4d70-8b50-c0d29a64aa93",
- "urn:7b677c0f-e7cb-44b6-8ff2-15ba74368f4d",
- "urn:c71c3c10-c978-44ab-9ef6-ddf0ccebe5cf",
- "urn:f19ccc20-154f-4cee-9abd-ec0a43848b3d",
- "urn:f22c9f55-f2c2-4817-92f3-730166d502e6",
- "urn:f58b2410-1003-4339-820b-f8d53e229a17",
- "urn:fb7367d2-16c2-4df8-b59a-428cf588b529"
+ "bids::sla.png",
+ "bids::slb.png",
+ "bids::slc.png",
+ "bids::sld.png",
+ "bids::sle.png",
+ "bids::slf.png",
+ "bids::slg.png",
+ "bids::slh.png",
+ "bids::sli.png",
+ "bids::slj.png",
+ "bids::slk.png",
+ "bids::sll.png"
]
},
{
- "@id": "urn:4d096062-937a-423a-b156-281a3a0a9777",
+ "@id": "urn:slicer-KvB5HBpn",
"Label": "slicer",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:02ad2de3-ed26-4828-86dd-5090741065b4",
- "urn:ac767057-e6a1-4207-8818-bbb01d04b597"
+ "bids::example_func2highres",
+ "bids::highres"
]
},
{
- "@id": "urn:71a50c02-85cf-4542-9253-938bf96ac20e",
+ "@id": "urn:pngappen-RZLqGcTy",
"Label": "pngappend",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres2.png",
"Used": [
- "urn:081c6ba0-20ae-4769-9fbe-9f1c0d3a0380",
- "urn:0b111a92-c24b-463f-b287-d4090823ed0c",
- "urn:25b260b1-6825-40d3-b423-c05cca0747fb",
- "urn:43044f87-e488-43eb-8305-0ff802654d36",
- "urn:4a25fd24-f3f5-4e89-8aec-1df8d599a71b",
- "urn:61060efc-571a-4d70-8b50-c0d29a64aa93",
- "urn:7b677c0f-e7cb-44b6-8ff2-15ba74368f4d",
- "urn:c71c3c10-c978-44ab-9ef6-ddf0ccebe5cf",
- "urn:f19ccc20-154f-4cee-9abd-ec0a43848b3d",
- "urn:f22c9f55-f2c2-4817-92f3-730166d502e6",
- "urn:f58b2410-1003-4339-820b-f8d53e229a17",
- "urn:fb7367d2-16c2-4df8-b59a-428cf588b529"
+ "bids::sla.png",
+ "bids::slb.png",
+ "bids::slc.png",
+ "bids::sld.png",
+ "bids::sle.png",
+ "bids::slf.png",
+ "bids::slg.png",
+ "bids::slh.png",
+ "bids::sli.png",
+ "bids::slj.png",
+ "bids::slk.png",
+ "bids::sll.png"
]
},
{
- "@id": "urn:2a39471a-4d01-4594-9f52-1bc9808a9542",
+ "@id": "urn:pngappen-WgIoMyNq",
"Label": "pngappend",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend example_func2highres1.png example_func2highres2.png example_func2highres.png",
"Used": [
- "urn:1fb8b55b-7e5a-4562-a76a-8de3078be908",
- "urn:b3d4192a-b913-4511-8128-ed5d464529f5"
+ "bids::example_func2highres1.png",
+ "bids::example_func2highres2.png"
]
},
{
- "@id": "urn:18ce82e3-98b1-4bc1-8d21-6baecf8def51",
+ "@id": "urn:rm-CAgyyYms",
"Label": "rm",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/bin/rm -f sl?.png example_func2highres2.png",
"Used": [
- "urn:7bba9bc4-f141-4036-bfe9-719e2f2f674d",
- "urn:b3d4192a-b913-4511-8128-ed5d464529f5"
+ "bids::example_func2highres2.png",
+ "bids::sl?.png"
]
},
{
- "@id": "urn:7db798dd-6c0b-44c4-9157-25acc6391ff8",
+ "@id": "urn:rm-SlsnfD6L",
"Label": "rm",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/bin/rm example_func2highres1.png",
"Used": [
- "urn:1fb8b55b-7e5a-4562-a76a-8de3078be908"
+ "bids::example_func2highres1.png"
]
},
{
- "@id": "urn:36c1aece-90bf-4233-9092-29463e67e4db",
+ "@id": "urn:mcflirt-jKj3SG5l",
"Label": "mcflirt",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/usr/local/packages/fsl-5.0.10/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs -spline_final",
"Used": [
- "urn:a49c2b75-473b-4726-93c3-d0327ef97cd4"
+ "bids::prefiltered_func_data"
]
},
{
- "@id": "urn:75548ade-ead8-4b08-8c99-a4b85a134c18",
+ "@id": "urn:makedire-tHA0cfqk",
"Label": "Make directory",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/bin/mkdir -p mc",
"Used": []
},
{
- "@id": "urn:aee6ccfc-49bc-4c7f-b671-bca972835626",
+ "@id": "urn:mv-N7HIMtzW",
"Label": "mv",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc",
"Used": [
- "urn:2a4a9ce0-2c65-4c7e-8f1a-491602520a96",
- "urn:3713f68d-b817-4393-88f4-7fa93ad934ec",
- "urn:3a33d095-10bb-43e7-b187-27cf4b1e9e46",
- "urn:5c26155a-ec3f-4b9a-b84e-494c4aacb8ea",
- "urn:7fff857f-dabf-408d-af75-bf7637c2e7ca",
- "urn:c424e895-a3c1-481a-8fdc-27f12b374808"
+ "bids::prefiltered_func_data_mcf.mat",
+ "bids::prefiltered_func_data_mcf.par",
+ "bids::prefiltered_func_data_mcf_abs.rms",
+ "bids::prefiltered_func_data_mcf_abs_mean.rms",
+ "bids::prefiltered_func_data_mcf_rel.rms",
+ "bids::prefiltered_func_data_mcf_rel_mean.rms"
]
},
{
- "@id": "urn:55f70081-d3f4-4826-a9ac-8efad3908bfd",
+ "@id": "urn:fsltsplo-SmYBfYdR",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png",
"Used": [
- "urn:5c26155a-ec3f-4b9a-b84e-494c4aacb8ea"
+ "bids::prefiltered_func_data_mcf.par"
]
},
{
- "@id": "urn:987d4ecb-adbd-4da2-bee7-80c8e1c21133",
+ "@id": "urn:fsltsplo-72Yhjlf3",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png",
"Used": [
- "urn:5c26155a-ec3f-4b9a-b84e-494c4aacb8ea"
+ "bids::prefiltered_func_data_mcf.par"
]
},
{
- "@id": "urn:38551fef-e588-44a6-b934-93cb671a56f6",
+ "@id": "urn:fsltsplo-ujOqVhKN",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png",
"Used": [
- "urn:1a83e7f6-a856-4c18-85fd-ad5fae8e1954"
+ "bids::prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms"
]
},
{
- "@id": "urn:077d73ee-2b99-43bb-8424-92d76d6ace15",
+ "@id": "urn:fslmaths-mM2GOkAg",
"Label": "fslmaths",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func",
"Used": [
- "urn:0ed73b37-71c2-4ec8-bedf-7dbda5dbf534"
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:f8bf025a-bf6e-49f7-a38c-ca65385dd71d",
+ "@id": "urn:bet2-xTMutGSF",
"Label": "bet2",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/usr/local/packages/fsl-5.0.10/bin/bet2 mean_func mask -f 0.3 -n -m",
"Used": [
- "urn:a22a0a26-9679-4208-a173-4e8e87fa031c"
+ "bids::mean_func"
]
},
{
- "@id": "urn:3c91a86f-673d-40f3-b844-24466965e0c9",
+ "@id": "urn:immv-YxptIEZG",
"Label": "immv",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/usr/local/packages/fsl-5.0.10/bin/immv mask_mask mask",
"Used": [
- "urn:9254ee69-c36c-4f52-a2d5-9b6f37782f50"
+ "bids::mask_mask"
]
},
{
- "@id": "urn:041e9560-07b0-4ac8-84af-83551a8abcd5",
+ "@id": "urn:fslmaths-s8nkMei9",
"Label": "fslmaths",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet",
"Used": [
- "urn:0ed73b37-71c2-4ec8-bedf-7dbda5dbf534",
- "urn:c83de79e-f16d-4a1a-8038-2d36fe3e1a8a"
+ "bids::mask",
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:d93acab0-193e-49b6-a16f-d6b155678698",
+ "@id": "urn:fslstats-vXvx6lY9",
"Label": "fslstats",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_bet -p 2 -p 98",
"Used": [
- "urn:dbde917c-9ba0-4d04-bd2d-fd2c34c2d061"
+ "bids::prefiltered_func_data_bet"
]
},
{
- "@id": "urn:349bfb32-1123-4a2f-8fe3-09f4f6f984ec",
+ "@id": "urn:fslmaths-H7MMEeHy",
"Label": "fslmaths",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_bet -thr 74.4585571 -Tmin -bin mask -odt char",
"Used": [
- "urn:dbde917c-9ba0-4d04-bd2d-fd2c34c2d061"
+ "bids::prefiltered_func_data_bet"
]
},
{
- "@id": "urn:7762d334-53ef-4c9a-8721-c344e757d3bd",
+ "@id": "urn:fslstats-FeBt6eRG",
"Label": "fslstats",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_mcf -k mask -p 50",
"Used": [
- "urn:0ed73b37-71c2-4ec8-bedf-7dbda5dbf534"
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:5a5ed666-cf2f-4213-b4c3-9fb49c784d57",
+ "@id": "urn:fslmaths-NIhmMG59",
"Label": "fslmaths",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -dilF mask",
"Used": [
- "urn:c83de79e-f16d-4a1a-8038-2d36fe3e1a8a"
+ "bids::mask"
]
},
{
- "@id": "urn:f0bdef22-eca3-4681-b767-71d5b60df1bc",
+ "@id": "urn:fslmaths-p6fahobq",
"Label": "fslmaths",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh",
"Used": [
- "urn:0ed73b37-71c2-4ec8-bedf-7dbda5dbf534",
- "urn:c83de79e-f16d-4a1a-8038-2d36fe3e1a8a"
+ "bids::mask",
+ "bids::prefiltered_func_data_mcf"
]
},
{
- "@id": "urn:4582228c-5c9e-4362-af4f-037553005fcb",
+ "@id": "urn:fslmaths-LQpiwNy6",
"Label": "fslmaths",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func",
"Used": [
- "urn:a3534236-e1a6-40b2-8f8f-b033d89a9d0d"
+ "bids::prefiltered_func_data_thresh"
]
},
{
- "@id": "urn:b6aa3e9a-7625-4de7-a443-a1d0caffeedb",
+ "@id": "urn:susan-K3ufRWdA",
"Label": "susan",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/usr/local/packages/fsl-5.0.10/bin/susan prefiltered_func_data_thresh 445.8289035 2.54777070064 3 1 1 mean_func 445.8289035 prefiltered_func_data_smooth",
"Used": [
- "urn:a3534236-e1a6-40b2-8f8f-b033d89a9d0d"
+ "bids::prefiltered_func_data_thresh"
]
},
{
- "@id": "urn:a8cb53b6-104c-4d2f-be09-f14150ec2a23",
+ "@id": "urn:fslmaths-iraiJEXd",
"Label": "fslmaths",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth",
"Used": [
- "urn:12b01b25-f812-4a96-b44f-5de5c04b952a",
- "urn:c83de79e-f16d-4a1a-8038-2d36fe3e1a8a"
+ "bids::mask",
+ "bids::prefiltered_func_data_smooth"
]
},
{
- "@id": "urn:fa2200bb-fb7c-4e93-af75-14a37b278ed7",
+ "@id": "urn:fslmaths-fjFdgb7Z",
"Label": "fslmaths",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mul 16.8225970571 prefiltered_func_data_intnorm",
"Used": [
- "urn:12b01b25-f812-4a96-b44f-5de5c04b952a"
+ "bids::prefiltered_func_data_smooth"
]
},
{
- "@id": "urn:309094d0-38c7-4b73-b683-aebd81f546ff",
+ "@id": "urn:fslmaths-Ug0ahjSo",
"Label": "fslmaths",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean",
"Used": [
- "urn:1e43c0bd-9af8-46ce-8a5e-b016598773e4"
+ "bids::prefiltered_func_data_intnorm"
]
},
{
- "@id": "urn:3c62785c-8c8b-41d2-8681-a25cfc8feab1",
+ "@id": "urn:fslmaths-f2LRAapL",
"Label": "fslmaths",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -bptf 15.0 -1 -add tempMean prefiltered_func_data_tempfilt",
"Used": [
- "urn:1e43c0bd-9af8-46ce-8a5e-b016598773e4",
- "urn:4f27d341-e215-49f8-a605-583e638b76ac"
+ "bids::prefiltered_func_data_intnorm",
+ "bids::tempMean"
]
},
{
- "@id": "urn:25eaecbc-9e22-47b3-bb25-bc1cd9c184a9",
+ "@id": "urn:imrm-QaqXCLYu",
"Label": "imrm",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/usr/local/packages/fsl-5.0.10/bin/imrm tempMean",
"Used": [
- "urn:4f27d341-e215-49f8-a605-583e638b76ac"
+ "bids::tempMean"
]
},
{
- "@id": "urn:5ab6aa9e-0882-49b0-8c88-f1d550948dd0",
+ "@id": "urn:fslmaths-O6KmaYGx",
"Label": "fslmaths",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data",
"Used": [
- "urn:efc88b68-bb5c-4444-9fbc-2714e3c64014"
+ "bids::prefiltered_func_data_tempfilt"
]
},
{
- "@id": "urn:ed65201d-3e77-467d-849e-678c12d4b06f",
+ "@id": "urn:fslmaths-gbe18HHZ",
"Label": "fslmaths",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths filtered_func_data -Tmean mean_func",
"Used": [
- "urn:456e30ed-525d-48d5-b2b9-99e3b490e311"
+ "bids::filtered_func_data"
]
},
{
- "@id": "urn:4c293e1b-55b8-482c-a455-c0a603fbb1e8",
+ "@id": "urn:rm-7ucPRlke",
"Label": "rm",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/bin/rm -rf prefiltered_func_data*",
"Used": [
- "urn:f412825a-5429-4836-bf9d-85636db4b661"
+ "bids::prefiltered_func_data*"
]
},
{
- "@id": "urn:63f29e1b-4b6c-4457-80a6-3d1fbd4cce36",
+ "@id": "urn:makedire-8EO8Aqpg",
"Label": "Make directory",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
- "@id": "urn:226d6375-1bcb-497b-bbc5-2839fa204101",
+ "@id": "urn:fslfixte-Jw0fO03v",
"Label": "fslFixText",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
"Used": [
- "urn:0d4c627b-47f0-41e5-b910-3deee2f35763"
+ "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt"
]
},
{
- "@id": "urn:d58429c6-9e63-4f00-8a81-abaf77c48ec4",
+ "@id": "urn:makedire-gXxLy0nh",
"Label": "Make directory",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
- "@id": "urn:091391a5-1062-44cc-b7b6-4e2e5f2e005a",
+ "@id": "urn:fslfixte-yrsiSJkG",
"Label": "fslFixText",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
"Used": [
- "urn:2656f2fc-32a0-4db6-82a3-1bee8c7c1262"
+ "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt"
]
},
{
- "@id": "urn:da5aa1af-62a9-4d38-b211-b84e477282bf",
+ "@id": "urn:filmgls-5qTK83BP",
"Label": "film_gls",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con",
- "Used": []
+ "Used": [
+ "bids::design.con",
+ "bids::design.mat",
+ "bids::filtered_func_data",
+ "bids::stats"
+ ]
},
{
- "@id": "urn:b4572bdc-7d32-497b-95a3-6bfac197ab0d",
+ "@id": "urn:smoothes-87cHdl82",
"Label": "smoothest",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 102 -m mask -r stats/res4d > stats/smoothness",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 102 -m mask -r stats/res4d > stats/smoothness",
"Used": [
- "urn:b9f762ec-b84c-448f-8d10-a7ce9720420d",
- "urn:c83de79e-f16d-4a1a-8038-2d36fe3e1a8a"
+ "bids::mask",
+ "bids::stats/res4d"
]
},
{
- "@id": "urn:0b7078ea-8347-47e3-943c-d5b2a5b008b7",
+ "@id": "urn:fslmaths-ANaeZf8r",
"Label": "fslmaths",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1",
"Used": [
- "urn:c83de79e-f16d-4a1a-8038-2d36fe3e1a8a",
- "urn:fb8aec64-0092-4cf1-afe3-07ed664020c4"
+ "bids::mask",
+ "bids::stats/zstat1"
]
},
{
- "@id": "urn:c0281cc6-41ae-4afb-8712-bdddf923860a",
+ "@id": "urn:echo-TuxoJVVO",
"Label": "echo",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "echo 38352 > thresh_zstat1.vol",
"Used": []
},
{
- "@id": "urn:7c054844-b870-48f3-a56d-0958618d172d",
+ "@id": "urn:ptoz-HpAgX3aE",
"Label": "ptoz",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.05 -g 5805",
"Used": []
},
{
- "@id": "urn:8e8d84c6-ac64-47ec-8655-dbebf6578a78",
+ "@id": "urn:cluster-PZLrv8qv",
"Label": "cluster",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
- "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -t 5.042313 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z -r 6.60665 --voxthresh -c stats/cope1 > cluster_zstat1.txt",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
+ "Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -t 5.042313 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z -r 6.60665 --voxthresh -c stats/cope1 > cluster_zstat1.txt",
"Used": [
- "urn:27cbef79-02e5-4f56-a288-ea546ba6a2b1",
- "urn:d73a5f7e-245a-4b50-acff-02c0d6f3c66b"
+ "bids::stats/cope1",
+ "bids::thresh_zstat1"
]
},
{
- "@id": "urn:52020508-61e6-4dfe-a196-64f7e40dc726",
+ "@id": "urn:cluster2-jDBjYNPn",
"Label": "cluster2html",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat1",
"Used": [
- "urn:c2cf42dc-0dd5-4be2-8ffc-e5d8352d94ed"
+ "bids::cluster_zstat1"
]
},
{
- "@id": "urn:077324da-6b60-44f7-925b-9c45937d10db",
+ "@id": "urn:fslstats-8hlZCrqU",
"Label": "fslstats",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat1 -l 0.0001 -R 2>/dev/null",
"Used": [
- "urn:d73a5f7e-245a-4b50-acff-02c0d6f3c66b"
+ "bids::thresh_zstat1"
]
},
{
- "@id": "urn:aa180f27-8256-4664-bbdd-0d6d7ebf1cdb",
+ "@id": "urn:overlay-Dpx5cD5B",
"Label": "overlay",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat1 5.043745 7.488793 rendered_thresh_zstat1",
"Used": []
},
{
- "@id": "urn:1cbd5316-e669-4ad5-8a60-7933b80ed67c",
+ "@id": "urn:slicer-DY4kWvOe",
"Label": "slicer",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat1 -A 750 rendered_thresh_zstat1.png",
"Used": [
- "urn:2956e891-bc2d-4540-acbf-aa3927057795"
+ "bids::rendered_thresh_zstat1"
]
},
{
- "@id": "urn:6efa21e0-6d91-4904-86e8-79b259347c7f",
+ "@id": "urn:cp-2ftxTogj",
"Label": "cp",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
"Command": "/bin/cp /usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif .ramp.gif",
"Used": [
- "urn:4342d03a-e0ae-4a54-9564-cb1ca4398e50"
+ "bids::/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif"
]
},
{
- "@id": "urn:439ab190-6f31-45d3-b781-9cd272040fb4",
+ "@id": "urn:makedire-CA7AqUTd",
"Label": "Make directory",
- "AssociatedWith": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
+ "AssociatedWith": "urn:fsl-un0J9v6I",
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@@ -580,15 +589,15 @@
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@@ -596,45 +605,57 @@
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@@ -642,267 +663,259 @@
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+ "GeneratedBy": "urn:pngappen-RZLqGcTy",
"digest": {
"sha256": "4e622cf27c5f4d28786e7ccdc4e88253f4e5a855818d597ceec90fa78f0d437c"
}
},
{
- "@id": "urn:7d2dcce3-c3b7-477d-a23e-00d6160827be",
+ "@id": "bids::example_func2highres.png",
"Label": "example_func2highres.png",
"AtLocation": "example_func2highres.png",
- "GeneratedBy": "urn:2a39471a-4d01-4594-9f52-1bc9808a9542",
+ "GeneratedBy": "urn:pngappen-WgIoMyNq",
"digest": {
"sha256": "31960f4162da045cb9b73a0eb3cac33f09d5a2ec1f146f1e457c4a59f478f3e8"
}
},
{
- "@id": "urn:7bba9bc4-f141-4036-bfe9-719e2f2f674d",
+ "@id": "bids::sl?.png",
"Label": "sl?.png",
"AtLocation": "sl?.png",
"digest": {
@@ -910,25 +923,25 @@
}
},
{
- "@id": "urn:0ed73b37-71c2-4ec8-bedf-7dbda5dbf534",
+ "@id": "bids::prefiltered_func_data_mcf",
"Label": "prefiltered_func_data_mcf",
"AtLocation": "prefiltered_func_data_mcf",
- "GeneratedBy": "urn:36c1aece-90bf-4233-9092-29463e67e4db",
+ "GeneratedBy": "urn:mcflirt-jKj3SG5l",
"digest": {
"sha256": "83371e264d408de4f678b8182097b39c86bd0a618ca76af6d1dfee5db0903b78"
}
},
{
- "@id": "urn:9c584d26-c686-439f-a800-9300d989a27b",
+ "@id": "bids::mc",
"Label": "mc",
"AtLocation": "mc",
- "GeneratedBy": "urn:75548ade-ead8-4b08-8c99-a4b85a134c18",
+ "GeneratedBy": "urn:makedire-tHA0cfqk",
"digest": {
"sha256": "a1a8fa7b1d2bf5bc0a263e95f926d3d9b656d2572455245d46edf48e93744ffa"
}
},
{
- "@id": "urn:7fff857f-dabf-408d-af75-bf7637c2e7ca",
+ "@id": "bids::prefiltered_func_data_mcf.mat",
"Label": "prefiltered_func_data_mcf.mat",
"AtLocation": "prefiltered_func_data_mcf.mat",
"digest": {
@@ -936,7 +949,7 @@
}
},
{
- "@id": "urn:5c26155a-ec3f-4b9a-b84e-494c4aacb8ea",
+ "@id": "bids::prefiltered_func_data_mcf.par",
"Label": "prefiltered_func_data_mcf.par",
"AtLocation": "prefiltered_func_data_mcf.par",
"digest": {
@@ -944,7 +957,7 @@
}
},
{
- "@id": "urn:3713f68d-b817-4393-88f4-7fa93ad934ec",
+ "@id": "bids::prefiltered_func_data_mcf_abs.rms",
"Label": "prefiltered_func_data_mcf_abs.rms",
"AtLocation": "prefiltered_func_data_mcf_abs.rms",
"digest": {
@@ -952,7 +965,7 @@
}
},
{
- "@id": "urn:c424e895-a3c1-481a-8fdc-27f12b374808",
+ "@id": "bids::prefiltered_func_data_mcf_abs_mean.rms",
"Label": "prefiltered_func_data_mcf_abs_mean.rms",
"AtLocation": "prefiltered_func_data_mcf_abs_mean.rms",
"digest": {
@@ -960,7 +973,7 @@
}
},
{
- "@id": "urn:2a4a9ce0-2c65-4c7e-8f1a-491602520a96",
+ "@id": "bids::prefiltered_func_data_mcf_rel.rms",
"Label": "prefiltered_func_data_mcf_rel.rms",
"AtLocation": "prefiltered_func_data_mcf_rel.rms",
"digest": {
@@ -968,7 +981,7 @@
}
},
{
- "@id": "urn:3a33d095-10bb-43e7-b187-27cf4b1e9e46",
+ "@id": "bids::prefiltered_func_data_mcf_rel_mean.rms",
"Label": "prefiltered_func_data_mcf_rel_mean.rms",
"AtLocation": "prefiltered_func_data_mcf_rel_mean.rms",
"digest": {
@@ -976,34 +989,34 @@
}
},
{
- "@id": "urn:61c7bd3a-5bdf-448f-9deb-d13ead4dd708",
+ "@id": "bids::mc",
"Label": "mc",
"AtLocation": "mc",
- "GeneratedBy": "urn:aee6ccfc-49bc-4c7f-b671-bca972835626",
+ "GeneratedBy": "urn:mv-N7HIMtzW",
"digest": {
"sha256": "a1a8fa7b1d2bf5bc0a263e95f926d3d9b656d2572455245d46edf48e93744ffa"
}
},
{
- "@id": "urn:a745a2fb-4636-4f0f-829b-76e7ea216015",
+ "@id": "bids::rot.png",
"Label": "rot.png",
"AtLocation": "rot.png",
- "GeneratedBy": "urn:55f70081-d3f4-4826-a9ac-8efad3908bfd",
+ "GeneratedBy": "urn:fsltsplo-SmYBfYdR",
"digest": {
"sha256": "b8776603f8865a358b2273847d21e63491e7c2e10567fb640608dd47ba721f29"
}
},
{
- "@id": "urn:d81a5c5b-8b03-48f8-92ae-3e9895636e1e",
+ "@id": "bids::trans.png",
"Label": "trans.png",
"AtLocation": "trans.png",
- "GeneratedBy": "urn:987d4ecb-adbd-4da2-bee7-80c8e1c21133",
+ "GeneratedBy": "urn:fsltsplo-72Yhjlf3",
"digest": {
"sha256": "496eac1d0ac15e80928780c73766c7791a1707291b2b9a6d1781c2f6a38de3cd"
}
},
{
- "@id": "urn:1a83e7f6-a856-4c18-85fd-ad5fae8e1954",
+ "@id": "bids::prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"Label": "prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"AtLocation": "prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"digest": {
@@ -1011,34 +1024,34 @@
}
},
{
- "@id": "urn:c3ce6ca2-204a-4e32-bd85-d7fe6eaf08a9",
+ "@id": "bids::disp.png",
"Label": "disp.png",
"AtLocation": "disp.png",
- "GeneratedBy": "urn:38551fef-e588-44a6-b934-93cb671a56f6",
+ "GeneratedBy": "urn:fsltsplo-ujOqVhKN",
"digest": {
"sha256": "c4615e07e04f0c390d969482634cb62e81d47c818d2866ee866ec9c64a5350fd"
}
},
{
- "@id": "urn:a22a0a26-9679-4208-a173-4e8e87fa031c",
+ "@id": "bids::mean_func",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:077d73ee-2b99-43bb-8424-92d76d6ace15",
+ "GeneratedBy": "urn:fslmaths-mM2GOkAg",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:c83de79e-f16d-4a1a-8038-2d36fe3e1a8a",
+ "@id": "bids::mask",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:f8bf025a-bf6e-49f7-a38c-ca65385dd71d",
+ "GeneratedBy": "urn:bet2-xTMutGSF",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:9254ee69-c36c-4f52-a2d5-9b6f37782f50",
+ "@id": "bids::mask_mask",
"Label": "mask_mask",
"AtLocation": "mask_mask",
"digest": {
@@ -1046,132 +1059,124 @@
}
},
{
- "@id": "urn:d2ec1e1f-6b72-4cd0-8bdd-015b1729e259",
+ "@id": "bids::mask",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:3c91a86f-673d-40f3-b844-24466965e0c9",
+ "GeneratedBy": "urn:immv-YxptIEZG",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:dbde917c-9ba0-4d04-bd2d-fd2c34c2d061",
+ "@id": "bids::prefiltered_func_data_bet",
"Label": "prefiltered_func_data_bet",
"AtLocation": "prefiltered_func_data_bet",
- "GeneratedBy": "urn:041e9560-07b0-4ac8-84af-83551a8abcd5",
+ "GeneratedBy": "urn:fslmaths-s8nkMei9",
"digest": {
"sha256": "c01f21947b38d9886528dec14edf23dfb55304b7da67569fe93902472b286cf4"
}
},
{
- "@id": "urn:6d0e42e6-fee1-4138-92a2-dc17b126e960",
+ "@id": "bids::mask",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:349bfb32-1123-4a2f-8fe3-09f4f6f984ec",
+ "GeneratedBy": "urn:fslmaths-H7MMEeHy",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:5bd09178-6596-403f-afa9-3c62d7e3b3aa",
+ "@id": "bids::mask",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:5a5ed666-cf2f-4213-b4c3-9fb49c784d57",
+ "GeneratedBy": "urn:fslmaths-NIhmMG59",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:a3534236-e1a6-40b2-8f8f-b033d89a9d0d",
+ "@id": "bids::prefiltered_func_data_thresh",
"Label": "prefiltered_func_data_thresh",
"AtLocation": "prefiltered_func_data_thresh",
- "GeneratedBy": "urn:f0bdef22-eca3-4681-b767-71d5b60df1bc",
+ "GeneratedBy": "urn:fslmaths-p6fahobq",
"digest": {
"sha256": "c5c015a8df079b497bbce596808cbbdc09fb39411f490244de192dfa72d33640"
}
},
{
- "@id": "urn:bbc46cf1-2945-44ae-a29d-9453d9dc7d90",
+ "@id": "bids::mean_func",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:4582228c-5c9e-4362-af4f-037553005fcb",
+ "GeneratedBy": "urn:fslmaths-LQpiwNy6",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:12b01b25-f812-4a96-b44f-5de5c04b952a",
+ "@id": "bids::prefiltered_func_data_smooth",
"Label": "prefiltered_func_data_smooth",
"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:b6aa3e9a-7625-4de7-a443-a1d0caffeedb",
+ "GeneratedBy": "urn:susan-K3ufRWdA",
"digest": {
"sha256": "2a4901d885fce0b083c9f99364da8dcff184635e74ab011f53a68cfc6827b429"
}
},
{
- "@id": "urn:fda80bd6-96ea-4376-bd3f-195279a3d29a",
+ "@id": "bids::prefiltered_func_data_smooth",
"Label": "prefiltered_func_data_smooth",
"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:a8cb53b6-104c-4d2f-be09-f14150ec2a23",
+ "GeneratedBy": "urn:fslmaths-iraiJEXd",
"digest": {
"sha256": "2a4901d885fce0b083c9f99364da8dcff184635e74ab011f53a68cfc6827b429"
}
},
{
- "@id": "urn:1e43c0bd-9af8-46ce-8a5e-b016598773e4",
+ "@id": "bids::prefiltered_func_data_intnorm",
"Label": "prefiltered_func_data_intnorm",
"AtLocation": "prefiltered_func_data_intnorm",
- "GeneratedBy": "urn:fa2200bb-fb7c-4e93-af75-14a37b278ed7",
+ "GeneratedBy": "urn:fslmaths-fjFdgb7Z",
"digest": {
"sha256": "0698a276f6f0fdccfb06033926d333a176503a09aaa87b78384fbffbf1c54dee"
}
},
{
- "@id": "urn:4f27d341-e215-49f8-a605-583e638b76ac",
+ "@id": "bids::tempMean",
"Label": "tempMean",
"AtLocation": "tempMean",
- "GeneratedBy": "urn:309094d0-38c7-4b73-b683-aebd81f546ff",
+ "GeneratedBy": "urn:fslmaths-Ug0ahjSo",
"digest": {
"sha256": "1a01513c76bc17516b60df315a1922789ce79d72e66e105fbf2723df9cb1b038"
}
},
{
- "@id": "urn:98b8d939-2139-43fe-9809-aff688aedb64",
- "Label": "15.0",
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- "GeneratedBy": "urn:3c62785c-8c8b-41d2-8681-a25cfc8feab1",
- "digest": {
- "sha256": "552db91328a881034f16ec50203ba34d4af448f52c616eb28db6c07aa575a286"
- }
- },
- {
- "@id": "urn:efc88b68-bb5c-4444-9fbc-2714e3c64014",
+ "@id": "bids::prefiltered_func_data_tempfilt",
"Label": "prefiltered_func_data_tempfilt",
"AtLocation": "prefiltered_func_data_tempfilt",
+ "GeneratedBy": "urn:fslmaths-f2LRAapL",
"digest": {
"sha256": "a1836f4694e7ffdb50484626724602498c7b22b4f3cdd1e7d105efd336cbc8bd"
}
},
{
- "@id": "urn:456e30ed-525d-48d5-b2b9-99e3b490e311",
+ "@id": "bids::filtered_func_data",
"Label": "filtered_func_data",
"AtLocation": "filtered_func_data",
- "GeneratedBy": "urn:5ab6aa9e-0882-49b0-8c88-f1d550948dd0",
+ "GeneratedBy": "urn:fslmaths-O6KmaYGx",
"digest": {
"sha256": "2a1854e3b48a54f88e063191e25159015a0afbd300d18a1cfda37b4b68a1ee69"
}
},
{
- "@id": "urn:531e70b4-61fd-4d25-bc4f-81879f3e6a8b",
+ "@id": "bids::mean_func",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:ed65201d-3e77-467d-849e-678c12d4b06f",
+ "GeneratedBy": "urn:fslmaths-gbe18HHZ",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:f412825a-5429-4836-bf9d-85636db4b661",
+ "@id": "bids::prefiltered_func_data*",
"Label": "prefiltered_func_data*",
"AtLocation": "prefiltered_func_data*",
"digest": {
@@ -1179,113 +1184,158 @@
}
},
{
- "@id": "urn:e2baa3ee-4e71-4167-8fa6-2a24869d3bf3",
+ "@id": "bids::custom_timing_files",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:63f29e1b-4b6c-4457-80a6-3d1fbd4cce36",
+ "GeneratedBy": "urn:makedire-8EO8Aqpg",
"digest": {
"sha256": "1d7e19792328d5040f2f9fb3c15d59de90fc771785f81c67039a043bd5f2ed20"
}
},
{
- "@id": "urn:0d4c627b-47f0-41e5-b910-3deee2f35763",
+ "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
"Label": "sub-01_tone_counting.txt",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
+ "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting.txt",
"digest": {
- "sha256": "c120d27b9d5d81a91be0e55f5cb880b2cb7de6c655554d9c15c9c04c6232ea8e"
+ "sha256": "165398224a205d2fc0b19354e15d9b085c6d81e333b69c4697b7894a2549be0b"
}
},
{
- "@id": "urn:989551bd-89f0-41fd-b83d-ff7f03e47600",
+ "@id": "bids::custom_timing_files/ev1.txt",
"Label": "ev1.txt",
"AtLocation": "custom_timing_files/ev1.txt",
- "GeneratedBy": "urn:226d6375-1bcb-497b-bbc5-2839fa204101"
+ "GeneratedBy": "urn:fslfixte-Jw0fO03v"
},
{
- "@id": "urn:fffc11f4-7b98-4d70-b7a4-666db1428765",
+ "@id": "bids::custom_timing_files",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:d58429c6-9e63-4f00-8a81-abaf77c48ec4",
+ "GeneratedBy": "urn:makedire-gXxLy0nh",
"digest": {
"sha256": "1d7e19792328d5040f2f9fb3c15d59de90fc771785f81c67039a043bd5f2ed20"
}
},
{
- "@id": "urn:2656f2fc-32a0-4db6-82a3-1bee8c7c1262",
+ "@id": "bids::ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
"Label": "sub-01_tone_counting_probe.txt",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
+ "AtLocation": "ds011/derivatives/FSL/ONSETS/sub-01_tone_counting_probe.txt",
"digest": {
- "sha256": "f09eeb82fa0be8e8759a5269403f36ec2b7dbf2c5b6caba1f0f985cc6cb3f703"
+ "sha256": "8b912293767f1a5e082311f6aaf0c44fc91fe45b0f2ae7f80e368bc2f4c2918a"
}
},
{
- "@id": "urn:f7097c96-3c16-4787-89da-87315bb9ca69",
+ "@id": "bids::custom_timing_files/ev2.txt",
"Label": "ev2.txt",
"AtLocation": "custom_timing_files/ev2.txt",
- "GeneratedBy": "urn:091391a5-1062-44cc-b7b6-4e2e5f2e005a"
+ "GeneratedBy": "urn:fslfixte-yrsiSJkG"
},
{
- "@id": "urn:b9f762ec-b84c-448f-8d10-a7ce9720420d",
- "Label": "res4d",
- "AtLocation": "stats/res4d",
+ "@id": "bids::stats",
+ "Label": "stats",
+ "AtLocation": "stats",
"digest": {
- "sha256": "8845286f36caedf891a02afddc4175ea46f18f830b59a8c5026962184a530699"
+ "sha256": "a9f3e135372514a16d11a8038262b3eff94ccd69a9b35c4724b2759cfc944a07"
}
},
{
- "@id": "urn:875ab4a4-5a87-49db-9e85-dd972fb37cd5",
- "Label": "smoothness",
- "AtLocation": "stats/smoothness",
- "GeneratedBy": "urn:b4572bdc-7d32-497b-95a3-6bfac197ab0d",
+ "@id": "bids::design.mat",
+ "Label": "design.mat",
+ "AtLocation": "design.mat",
"digest": {
- "sha256": "67b0aaf95a257beff60d331b56265034807ca51e67e2d312d481d5835ef0b1d0"
+ "sha256": "1c1a6ef59a355e1f6f81e741e157784ccbe066ba3594a07aa9b16781e3d5bb25"
}
},
{
- "@id": "urn:fb8aec64-0092-4cf1-afe3-07ed664020c4",
- "Label": "zstat1",
- "AtLocation": "stats/zstat1",
+ "@id": "bids::design.con",
+ "Label": "design.con",
+ "AtLocation": "design.con",
"digest": {
- "sha256": "70ae47cee1ea1d3f1f6f8aa7ac51f2641cb2fcb745dfd8cc54a389346e6fa094"
+ "sha256": "5808d1be37dd8f2a4906b710bb384fbee62faa4a46b2bc6847afc8962ed4eb54"
}
},
{
- "@id": "urn:d73a5f7e-245a-4b50-acff-02c0d6f3c66b",
+ "@id": "bids::stats",
+ "Label": "stats",
+ "AtLocation": "stats",
+ "GeneratedBy": "urn:filmgls-5qTK83BP",
+ "digest": {
+ "sha256": "a9f3e135372514a16d11a8038262b3eff94ccd69a9b35c4724b2759cfc944a07"
+ }
+ },
+ {
+ "@id": "bids::stats/res4d",
+ "Label": "res4d",
+ "AtLocation": "stats/res4d"
+ },
+ {
+ "@id": "bids::stats/smoothness",
+ "Label": "smoothness",
+ "AtLocation": "stats/smoothness",
+ "GeneratedBy": "urn:smoothes-87cHdl82"
+ },
+ {
+ "@id": "bids::stats/zstat1",
+ "Label": "zstat1",
+ "AtLocation": "stats/zstat1"
+ },
+ {
+ "@id": "bids::thresh_zstat1",
"Label": "thresh_zstat1",
"AtLocation": "thresh_zstat1",
- "GeneratedBy": "urn:0b7078ea-8347-47e3-943c-d5b2a5b008b7",
+ "GeneratedBy": "urn:fslmaths-ANaeZf8r",
"digest": {
"sha256": "662e7ba670e124d15bb3cc18b818868f76604578034b524c8882f35fc5db413f"
}
},
{
- "@id": "urn:27cbef79-02e5-4f56-a288-ea546ba6a2b1",
+ "@id": "bids::stats/cope1",
"Label": "cope1",
- "AtLocation": "stats/cope1",
- "digest": {
- "sha256": "bf3b603569da6dbe3d6f0e8667d346f3ac943c9d01d2fc9743ce17abeb1547fb"
- }
+ "AtLocation": "stats/cope1"
},
{
- "@id": "urn:38c736a6-4fc6-4073-bb81-f2c369f76e4c",
+ "@id": "bids::cluster_mask_zstat1",
"Label": "cluster_mask_zstat1",
"AtLocation": "cluster_mask_zstat1",
- "GeneratedBy": "urn:8e8d84c6-ac64-47ec-8655-dbebf6578a78",
+ "GeneratedBy": "urn:cluster-PZLrv8qv",
"digest": {
"sha256": "b28c170e33d2917cac55183786616a9e976e5e7f30dc7c8666341f12ed6d0277"
}
},
{
- "@id": "urn:f9655809-f177-40cc-84aa-562f4ab32877",
+ "@id": "bids::thresh_zstat1",
+ "Label": "thresh_zstat1",
+ "AtLocation": "thresh_zstat1",
+ "GeneratedBy": "urn:cluster-PZLrv8qv",
+ "digest": {
+ "sha256": "662e7ba670e124d15bb3cc18b818868f76604578034b524c8882f35fc5db413f"
+ }
+ },
+ {
+ "@id": "bids::lmax_zstat1.txt",
+ "Label": "lmax_zstat1.txt",
+ "AtLocation": "lmax_zstat1.txt",
+ "GeneratedBy": "urn:cluster-PZLrv8qv",
+ "digest": {
+ "sha256": "d44ee21719775397a1a95ede6778d25404b50e8bd259dbdf02d2fde635fc81a5"
+ }
+ },
+ {
+ "@id": "bids::stats/cope1",
"Label": "cope1",
"AtLocation": "stats/cope1",
- "GeneratedBy": "urn:8e8d84c6-ac64-47ec-8655-dbebf6578a78",
+ "GeneratedBy": "urn:cluster-PZLrv8qv"
+ },
+ {
+ "@id": "bids::cluster_zstat1.txt",
+ "Label": "cluster_zstat1.txt",
+ "AtLocation": "cluster_zstat1.txt",
+ "GeneratedBy": "urn:cluster-PZLrv8qv",
"digest": {
- "sha256": "bf3b603569da6dbe3d6f0e8667d346f3ac943c9d01d2fc9743ce17abeb1547fb"
+ "sha256": "b06695ff4f0a8158fa439b1ddf224b58d344606d400885c177390d09506e8e4c"
}
},
{
- "@id": "urn:c2cf42dc-0dd5-4be2-8ffc-e5d8352d94ed",
+ "@id": "bids::cluster_zstat1",
"Label": "cluster_zstat1",
"AtLocation": "cluster_zstat1",
"digest": {
@@ -1293,25 +1343,25 @@
}
},
{
- "@id": "urn:2956e891-bc2d-4540-acbf-aa3927057795",
+ "@id": "bids::rendered_thresh_zstat1",
"Label": "rendered_thresh_zstat1",
"AtLocation": "rendered_thresh_zstat1",
- "GeneratedBy": "urn:aa180f27-8256-4664-bbdd-0d6d7ebf1cdb",
+ "GeneratedBy": "urn:overlay-Dpx5cD5B",
"digest": {
"sha256": "de5b9d44d95f4252f491eb45c76a0ae2b4d2c75b58664fc0df7d9153810c0bf6"
}
},
{
- "@id": "urn:48807715-825b-46b4-b198-c4820efdf562",
+ "@id": "bids::rendered_thresh_zstat1.png",
"Label": "rendered_thresh_zstat1.png",
"AtLocation": "rendered_thresh_zstat1.png",
- "GeneratedBy": "urn:1cbd5316-e669-4ad5-8a60-7933b80ed67c",
+ "GeneratedBy": "urn:slicer-DY4kWvOe",
"digest": {
"sha256": "15d6a8bf7a902df8c5feeb7468a3d0caacf9eb3067c0840c2f4763f5e2301527"
}
},
{
- "@id": "urn:4342d03a-e0ae-4a54-9564-cb1ca4398e50",
+ "@id": "bids::/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif",
"Label": "ramp.gif",
"AtLocation": "/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif",
"digest": {
@@ -1319,28 +1369,28 @@
}
},
{
- "@id": "urn:9af51269-2e27-4c5d-959d-c8ffae1ee4d9",
+ "@id": "bids::.ramp.gif",
"Label": ".ramp.gif",
"AtLocation": ".ramp.gif",
- "GeneratedBy": "urn:6efa21e0-6d91-4904-86e8-79b259347c7f",
+ "GeneratedBy": "urn:cp-2ftxTogj",
"digest": {
"sha256": "93f4284ccb854d5a41401d9360a13223017b67479cb289a33d83836922e028a4"
}
},
{
- "@id": "urn:9ec090b1-06df-470a-99fc-447da824a36f",
+ "@id": "bids::tsplot",
"Label": "tsplot",
"AtLocation": "tsplot",
- "GeneratedBy": "urn:439ab190-6f31-45d3-b781-9cd272040fb4",
+ "GeneratedBy": "urn:makedire-CA7AqUTd",
"digest": {
"sha256": "2a74042f4edf02288edf16961307f741651efb4346e102a04b7603e781d1625e"
}
},
{
- "@id": "urn:d8cbec8d-e8ab-497a-8905-72c41e247e8a",
+ "@id": "bids::tsplot",
"Label": "tsplot",
"AtLocation": "tsplot",
- "GeneratedBy": "urn:1cb0b710-db77-4b58-aaa5-ad2f0c1455fb",
+ "GeneratedBy": "urn:tsplot-dRxmDBIq",
"digest": {
"sha256": "2a74042f4edf02288edf16961307f741651efb4346e102a04b7603e781d1625e"
}
diff --git a/examples/from_parsers/fsl/fsl_thr_voxelfwep05_report_log.png b/examples/from_parsers/fsl/fsl_thr_voxelfwep05_report_log.png
index 45f139062..03533b543 100644
Binary files a/examples/from_parsers/fsl/fsl_thr_voxelfwep05_report_log.png and b/examples/from_parsers/fsl/fsl_thr_voxelfwep05_report_log.png differ
diff --git a/examples/from_parsers/spm/spm_2_t_test_batch.jsonld b/examples/from_parsers/spm/spm_2_t_test_batch.jsonld
index bcd5fb494..e2d064c36 100644
--- a/examples/from_parsers/spm/spm_2_t_test_batch.jsonld
+++ b/examples/from_parsers/spm/spm_2_t_test_batch.jsonld
@@ -4,63 +4,63 @@
"Records": {
"Software": [
{
- "@id": "urn:7f43852f-2d85-4cbc-9406-b5d27f469302",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:spm-Oku8US2z",
"@type": "prov:SoftwareAgent",
"Label": "SPM",
- "Version": "SPM12r7224"
+ "Version": "SPM12r7224",
+ "AltIdentifier": "RRID:SCR_007037"
}
],
"Activities": [
{
- "@id": "urn:a85a4a11-bd99-4e4a-b3dc-e021689042d4",
+ "@id": "urn:movefile-BRVbHU21",
"Label": "Move file",
"Used": [
- "urn:d8335e2a-2948-4271-a9f9-e4b5155b8a41"
+ "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
],
- "AssociatedWith": "urn:7f43852f-2d85-4cbc-9406-b5d27f469302",
- "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
+ "AssociatedWith": "urn:spm-Oku8US2z",
+ "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};",
"Parameters": {
- "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
+ "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'}"
}
},
{
- "@id": "urn:29c076d5-a462-4488-977b-958e22f360a9",
+ "@id": "urn:movefile-HaY5ANd7",
"Label": "Move file",
"Used": [
- "urn:0d27f1fd-4f17-4470-bcec-00f31d32585c"
+ "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz"
],
- "AssociatedWith": "urn:7f43852f-2d85-4cbc-9406-b5d27f469302",
- "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
+ "AssociatedWith": "urn:spm-Oku8US2z",
+ "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};",
"Parameters": {
- "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
+ "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'}"
}
},
{
- "@id": "urn:e3fa7976-f584-405e-adc8-f130bfa9a62d",
+ "@id": "urn:gunzip3-UO8GnUKh",
"Label": "Gunzip",
"Used": [
- "urn:c0e2232b-3121-49e4-9765-abca3e931e90"
+ "urn:uuid:d899ee07-a7c3-4f6e-9e05-69ecc85c4e56"
],
- "AssociatedWith": "urn:7f43852f-2d85-4cbc-9406-b5d27f469302",
+ "AssociatedWith": "urn:spm-Oku8US2z",
"Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:2d51e9fa-272d-4370-9bf2-a03e47ea78e6",
+ "@id": "urn:gunzip4-IZN4lsQP",
"Label": "Gunzip",
"Used": [
- "urn:dde44a92-ce46-45ad-8ab0-30c4c6a3ff5e"
+ "urn:uuid:df7eff64-3f23-4fda-824e-e2dcafc46f75"
],
- "AssociatedWith": "urn:7f43852f-2d85-4cbc-9406-b5d27f469302",
+ "AssociatedWith": "urn:spm-Oku8US2z",
"Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:9256a39d-9dd7-4cc1-9cf9-d82a3e799545",
+ "@id": "urn:realign5-DeZnPU9e",
"Label": "Realign",
"Used": [
- "urn:7caef081-9c3e-4cb6-b7db-69e7470b5478"
+ "urn:uuid:397ff0ef-8a7f-4cb3-943f-2c5d419808cb"
],
- "AssociatedWith": "urn:7f43852f-2d85-4cbc-9406-b5d27f469302",
+ "AssociatedWith": "urn:spm-Oku8US2z",
"Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
"Parameters": {
"eoptions.quality": "0.9",
@@ -78,13 +78,13 @@
}
},
{
- "@id": "urn:1ff61e29-8a62-4b6d-9ab3-66b4131f429b",
+ "@id": "urn:coregist-ZC1W9X09",
"Label": "Coregister",
"Used": [
- "urn:88b6394b-ab36-4212-ada9-3823354cec18",
- "urn:cd69bdd6-87b9-4324-8e15-9dfa7d9948bc"
+ "urn:uuid:9daef47f-1c26-402a-8d50-e4c33b798080",
+ "urn:uuid:b2b6b61f-325a-497d-99b3-d85a41230778"
],
- "AssociatedWith": "urn:7f43852f-2d85-4cbc-9406-b5d27f469302",
+ "AssociatedWith": "urn:spm-Oku8US2z",
"Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
"Parameters": {
"other": "{''}",
@@ -95,12 +95,12 @@
}
},
{
- "@id": "urn:1163e644-4c67-4a4a-8632-fef54fc43897",
+ "@id": "urn:segment7-jPXOheEj",
"Label": "Segment",
"Used": [
- "urn:88b6394b-ab36-4212-ada9-3823354cec18"
+ "urn:uuid:b2b6b61f-325a-497d-99b3-d85a41230778"
],
- "AssociatedWith": "urn:7f43852f-2d85-4cbc-9406-b5d27f469302",
+ "AssociatedWith": "urn:spm-Oku8US2z",
"Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
"Parameters": {
"channel.biasreg": "0.001",
@@ -140,13 +140,13 @@
}
},
{
- "@id": "urn:32da1042-3bfe-4549-b418-b69a601dbad5",
+ "@id": "urn:normaliz-533EtjkJ",
"Label": "Normalize",
"Used": [
- "urn:98813b04-86b8-43e8-b7c1-7b79dc16b682",
- "urn:cd69bdd6-87b9-4324-8e15-9dfa7d9948bc"
+ "bids::c1anat_sub-01_T1w.nii",
+ "urn:uuid:9daef47f-1c26-402a-8d50-e4c33b798080"
],
- "AssociatedWith": "urn:7f43852f-2d85-4cbc-9406-b5d27f469302",
+ "AssociatedWith": "urn:spm-Oku8US2z",
"Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -156,12 +156,12 @@
}
},
{
- "@id": "urn:64ce8c11-0547-45c6-9800-a2a392488900",
+ "@id": "urn:normaliz-pl28hrz0",
"Label": "Normalize",
"Used": [
- "urn:98813b04-86b8-43e8-b7c1-7b79dc16b682"
+ "bids::c1anat_sub-01_T1w.nii"
],
- "AssociatedWith": "urn:7f43852f-2d85-4cbc-9406-b5d27f469302",
+ "AssociatedWith": "urn:spm-Oku8US2z",
"Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -171,12 +171,12 @@
}
},
{
- "@id": "urn:72750923-73e5-4a3c-9092-b4aea4286e27",
+ "@id": "urn:smooth10-2wysnGlF",
"Label": "Smooth",
"Used": [
- "urn:8dc7b7dd-1c2d-4de6-af43-49413cef05bf"
+ "urn:uuid:558a08f8-cc0f-4f64-9587-c734cd72d4fe"
],
- "AssociatedWith": "urn:7f43852f-2d85-4cbc-9406-b5d27f469302",
+ "AssociatedWith": "urn:spm-Oku8US2z",
"Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
"Parameters": {
"fwhm": "[6, 6, 6]",
@@ -186,14 +186,14 @@
}
},
{
- "@id": "urn:332fb2ea-36f4-43c9-baea-0b38ef2a2179",
+ "@id": "urn:statdesi-8ZekFNLz",
"Label": "Stat Design",
"Used": [
- "urn:fcac9d40-80b9-4b4b-83e3-a11d7f74a441",
- "urn:c933e975-7f89-4ed1-8131-48cef7b2aa42"
+ "urn:uuid:1c70ac4f-9d4a-4682-8331-00f1fe6826ab",
+ "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
],
- "AssociatedWith": "urn:7f43852f-2d85-4cbc-9406-b5d27f469302",
- "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_2_T_test'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
+ "AssociatedWith": "urn:spm-Oku8US2z",
+ "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_2_T_test'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
"Parameters": {
"dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_2_T_test'}",
"timing.units": "'secs'",
@@ -214,12 +214,12 @@
}
},
{
- "@id": "urn:02fb5596-8669-4c2a-9df6-600488e892b5",
+ "@id": "urn:estimate-f2SVF2No",
"Label": "Estimate stat.",
"Used": [
- "urn:c8b07e4a-29df-4360-bb6b-0d4b76d035a2"
+ "urn:uuid:22cb89fb-8b91-4b72-802a-a29236185147"
],
- "AssociatedWith": "urn:7f43852f-2d85-4cbc-9406-b5d27f469302",
+ "AssociatedWith": "urn:spm-Oku8US2z",
"Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
"Parameters": {
"write_residuals": "0",
@@ -227,12 +227,12 @@
}
},
{
- "@id": "urn:12132d02-f825-4fad-a4be-15d0cf2a31f1",
+ "@id": "urn:estimate-c1PezHBa",
"Label": "Estimate contrast",
"Used": [
- "urn:1320e946-ac94-4740-9e0c-b6f97ad0d99b"
+ "urn:uuid:283181d2-881e-4fb3-af47-1f44af243625"
],
- "AssociatedWith": "urn:7f43852f-2d85-4cbc-9406-b5d27f469302",
+ "AssociatedWith": "urn:spm-Oku8US2z",
"Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.name = 'tone counting probe vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.weights = [0 1];\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
"Parameters": {
"consess{1}.tcon.name": "'tone counting vs baseline'",
@@ -245,12 +245,12 @@
}
},
{
- "@id": "urn:8db107d7-034d-4963-a81d-edf6a4c19ab2",
+ "@id": "urn:threshol-ZHDSgbEP",
"Label": "Threshold",
"Used": [
- "urn:59ad2686-bf03-4c54-ab58-52d3e36e159d"
+ "urn:uuid:237a2ba0-568c-40f8-b707-c49ba5e24f4e"
],
- "AssociatedWith": "urn:7f43852f-2d85-4cbc-9406-b5d27f469302",
+ "AssociatedWith": "urn:spm-Oku8US2z",
"Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.none = 1;",
"Parameters": {
"conspec.titlestr": "''",
@@ -268,98 +268,96 @@
],
"Entities": [
{
- "@id": "urn:d8335e2a-2948-4271-a9f9-e4b5155b8a41",
+ "@id": "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+ "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"digest": {
- "sha256": "52cc2a3822512db5be3accc8263f2ac1338f32fad8af63cc81fb5af2f335c509"
+ "sha256": "b3d8382360fbbc58cbd8c9e654ddda30b9f0318cf04ebd7539ec75bd724041d2"
}
},
{
- "@id": "urn:0d27f1fd-4f17-4470-bcec-00f31d32585c",
+ "@id": "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz",
"Label": "anat_sub-01_T1w.nii.gz",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+ "AtLocation": "ds011/sub-01/anat/sub-01_T1w.nii.gz",
"digest": {
- "sha256": "3d9457fa7712b355d6569522ca80a6dfd70a40b82e6aa0a9364513cf04916dbb"
+ "sha256": "70b9327067cc5200330e04e70b22a41db5aa3b78f978060f61f49bd3a45d125e"
}
},
{
- "@id": "urn:c0e2232b-3121-49e4-9765-abca3e931e90",
+ "@id": "urn:uuid:d899ee07-a7c3-4f6e-9e05-69ecc85c4e56",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "GeneratedBy": "urn:a85a4a11-bd99-4e4a-b3dc-e021689042d4"
+ "GeneratedBy": "urn:movefile-BRVbHU21"
},
{
- "@id": "urn:dde44a92-ce46-45ad-8ab0-30c4c6a3ff5e",
+ "@id": "urn:uuid:df7eff64-3f23-4fda-824e-e2dcafc46f75",
"Label": "anat_sub-01_T1w.nii.gz",
- "GeneratedBy": "urn:29c076d5-a462-4488-977b-958e22f360a9"
+ "GeneratedBy": "urn:movefile-HaY5ANd7"
},
{
- "@id": "urn:7caef081-9c3e-4cb6-b7db-69e7470b5478",
+ "@id": "urn:uuid:397ff0ef-8a7f-4cb3-943f-2c5d419808cb",
"Label": "func_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:e3fa7976-f584-405e-adc8-f130bfa9a62d"
+ "GeneratedBy": "urn:gunzip3-UO8GnUKh"
},
{
- "@id": "urn:cd69bdd6-87b9-4324-8e15-9dfa7d9948bc",
+ "@id": "urn:uuid:9daef47f-1c26-402a-8d50-e4c33b798080",
"Label": "meanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:9256a39d-9dd7-4cc1-9cf9-d82a3e799545"
+ "GeneratedBy": "urn:realign5-DeZnPU9e"
},
{
- "@id": "urn:88b6394b-ab36-4212-ada9-3823354cec18",
+ "@id": "urn:uuid:b2b6b61f-325a-497d-99b3-d85a41230778",
"Label": "anat_sub-01_T1w.nii",
- "GeneratedBy": "urn:2d51e9fa-272d-4370-9bf2-a03e47ea78e6"
+ "GeneratedBy": "urn:gunzip4-IZN4lsQP"
},
{
- "@id": "urn:98813b04-86b8-43e8-b7c1-7b79dc16b682",
+ "@id": "bids::c1anat_sub-01_T1w.nii",
"Label": "segment1",
- "Atlocation": "c1xxx.nii.gz",
- "GeneratedBy": "urn:1163e644-4c67-4a4a-8632-fef54fc43897",
"AtLocation": "c1anat_sub-01_T1w.nii",
+ "GeneratedBy": "urn:segment7-jPXOheEj",
"digest": {
"sha256": "61ca923955d0a5c9088df9e258f41644067ec964e1c9a83284ba03b0515079b0"
}
},
{
- "@id": "urn:49a2c107-7e29-4508-b66a-759397b637be",
+ "@id": "bids::c2anat_sub-01_T1w.nii",
"Label": "segment2",
- "Atlocation": "c2xxx.nii.gz",
- "GeneratedBy": "urn:1163e644-4c67-4a4a-8632-fef54fc43897",
"AtLocation": "c2anat_sub-01_T1w.nii",
+ "GeneratedBy": "urn:segment7-jPXOheEj",
"digest": {
"sha256": "10ad88ebeebebd0bd03ccbdd4df92d500d28d14715fa5375fd35589caddf49a6"
}
},
{
- "@id": "urn:8dc7b7dd-1c2d-4de6-af43-49413cef05bf",
+ "@id": "urn:uuid:558a08f8-cc0f-4f64-9587-c734cd72d4fe",
"Label": "wsegment1",
- "GeneratedBy": "urn:32da1042-3bfe-4549-b418-b69a601dbad5"
+ "GeneratedBy": "urn:normaliz-533EtjkJ"
},
{
- "@id": "urn:c933e975-7f89-4ed1-8131-48cef7b2aa42",
+ "@id": "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"Label": "ONSETS_sub-01-MultiCond.mat",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+ "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"digest": {
- "sha256": "be4671d4f9dc480dd3e5be19aeeab2756f7afdc3b32d81e071685d7a4eafcfed"
+ "sha256": "5599e80629bb4d66cdbfb357511c04060bd3d37cdbfe2a4cd701a2979e9f6610"
}
},
{
- "@id": "urn:fcac9d40-80b9-4b4b-83e3-a11d7f74a441",
+ "@id": "urn:uuid:1c70ac4f-9d4a-4682-8331-00f1fe6826ab",
"Label": "swsegment1",
- "GeneratedBy": "urn:72750923-73e5-4a3c-9092-b4aea4286e27"
+ "GeneratedBy": "urn:smooth10-2wysnGlF"
},
{
- "@id": "urn:c8b07e4a-29df-4360-bb6b-0d4b76d035a2",
+ "@id": "urn:uuid:22cb89fb-8b91-4b72-802a-a29236185147",
"Label": "SPM.mat",
- "GeneratedBy": "urn:332fb2ea-36f4-43c9-baea-0b38ef2a2179"
+ "GeneratedBy": "urn:statdesi-8ZekFNLz"
},
{
- "@id": "urn:1320e946-ac94-4740-9e0c-b6f97ad0d99b",
+ "@id": "urn:uuid:283181d2-881e-4fb3-af47-1f44af243625",
"Label": "SPM.mat",
- "GeneratedBy": "urn:02fb5596-8669-4c2a-9df6-600488e892b5"
+ "GeneratedBy": "urn:estimate-f2SVF2No"
},
{
- "@id": "urn:59ad2686-bf03-4c54-ab58-52d3e36e159d",
+ "@id": "urn:uuid:237a2ba0-568c-40f8-b707-c49ba5e24f4e",
"Label": "SPM.mat",
- "GeneratedBy": "urn:12132d02-f825-4fad-a4be-15d0cf2a31f1"
+ "GeneratedBy": "urn:estimate-c1PezHBa"
}
]
}
diff --git a/examples/from_parsers/spm/spm_2_t_test_batch.m b/examples/from_parsers/spm/spm_2_t_test_batch.m
index 330b898a6..db07861a0 100644
--- a/examples/from_parsers/spm/spm_2_t_test_batch.m
+++ b/examples/from_parsers/spm/spm_2_t_test_batch.m
@@ -3,10 +3,10 @@
% spm SPM - SPM12 (12.1)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------
-matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};
-matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};
-matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};
-matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};
+matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};
+matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};
+matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};
+matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};
matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));
@@ -90,7 +90,7 @@
matlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;
matlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});
-matlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};
+matlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};
matlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});
matlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};
matlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;
diff --git a/examples/from_parsers/spm/spm_2_t_test_batch.png b/examples/from_parsers/spm/spm_2_t_test_batch.png
index 62ff0424d..632199482 100644
Binary files a/examples/from_parsers/spm/spm_2_t_test_batch.png and b/examples/from_parsers/spm/spm_2_t_test_batch.png differ
diff --git a/examples/from_parsers/spm/spm_HRF_informed_basis_batch.jsonld b/examples/from_parsers/spm/spm_HRF_informed_basis_batch.jsonld
index b5fbb069d..c8f25d9e6 100644
--- a/examples/from_parsers/spm/spm_HRF_informed_basis_batch.jsonld
+++ b/examples/from_parsers/spm/spm_HRF_informed_basis_batch.jsonld
@@ -4,63 +4,63 @@
"Records": {
"Software": [
{
- "@id": "urn:3ffb5f05-4a19-4865-b981-909b041426bb",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:spm-acOHF07M",
"@type": "prov:SoftwareAgent",
"Label": "SPM",
- "Version": "SPM12r7224"
+ "Version": "SPM12r7224",
+ "AltIdentifier": "RRID:SCR_007037"
}
],
"Activities": [
{
- "@id": "urn:d867fd7f-631d-420b-900e-78f8937f4436",
+ "@id": "urn:movefile-gzlPmudm",
"Label": "Move file",
"Used": [
- "urn:065fd0da-dec5-43b9-89bd-2e28490b2920"
+ "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
],
- "AssociatedWith": "urn:3ffb5f05-4a19-4865-b981-909b041426bb",
- "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
+ "AssociatedWith": "urn:spm-acOHF07M",
+ "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};",
"Parameters": {
- "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
+ "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'}"
}
},
{
- "@id": "urn:10f8b075-1fca-472e-b140-189ba027fbad",
+ "@id": "urn:movefile-ybi7EcAT",
"Label": "Move file",
"Used": [
- "urn:6f2a8768-dd51-49f4-b29b-badf9cbd2355"
+ "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz"
],
- "AssociatedWith": "urn:3ffb5f05-4a19-4865-b981-909b041426bb",
- "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
+ "AssociatedWith": "urn:spm-acOHF07M",
+ "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};",
"Parameters": {
- "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
+ "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'}"
}
},
{
- "@id": "urn:4f8e64ff-f2e7-4b80-b21d-aab197e3b643",
+ "@id": "urn:gunzip3-yNT9tbr5",
"Label": "Gunzip",
"Used": [
- "urn:d3ee1eb9-ba34-4c1b-be52-8fb9737bcae5"
+ "urn:uuid:747672f0-0684-4712-88d7-7caece60c42c"
],
- "AssociatedWith": "urn:3ffb5f05-4a19-4865-b981-909b041426bb",
+ "AssociatedWith": "urn:spm-acOHF07M",
"Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:c612758d-292e-4c5c-9f22-09f64fa14d84",
+ "@id": "urn:gunzip4-YMI34NTy",
"Label": "Gunzip",
"Used": [
- "urn:f6388f61-a430-4ddb-8dc8-558e2ef8b0ac"
+ "urn:uuid:36203fcb-8c36-4398-8626-9fb725695b3a"
],
- "AssociatedWith": "urn:3ffb5f05-4a19-4865-b981-909b041426bb",
+ "AssociatedWith": "urn:spm-acOHF07M",
"Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:29e1c19f-538c-4342-9e76-a6866ccd580f",
+ "@id": "urn:realign5-mYV2jEjf",
"Label": "Realign",
"Used": [
- "urn:fe757dd9-4588-4498-813e-a29905e30b56"
+ "urn:uuid:dda513d4-ddb2-4de3-8f87-fb8621f2b48e"
],
- "AssociatedWith": "urn:3ffb5f05-4a19-4865-b981-909b041426bb",
+ "AssociatedWith": "urn:spm-acOHF07M",
"Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
"Parameters": {
"eoptions.quality": "0.9",
@@ -78,13 +78,13 @@
}
},
{
- "@id": "urn:b30a0c58-4263-4d7f-be30-876f71d4d2d0",
+ "@id": "urn:coregist-UoUbKniV",
"Label": "Coregister",
"Used": [
- "urn:717e6e9d-b97e-467c-aab3-ae4f15459b31",
- "urn:d27d94c1-784a-4d97-94ff-b674103f64e8"
+ "urn:uuid:00b87638-397e-4a77-9523-896dc7559560",
+ "urn:uuid:c410a960-d03c-4151-87b8-f58dab758b29"
],
- "AssociatedWith": "urn:3ffb5f05-4a19-4865-b981-909b041426bb",
+ "AssociatedWith": "urn:spm-acOHF07M",
"Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
"Parameters": {
"other": "{''}",
@@ -95,12 +95,12 @@
}
},
{
- "@id": "urn:e255be3b-54f2-4438-a0c3-73a0866a113e",
+ "@id": "urn:segment7-cEoNDdlV",
"Label": "Segment",
"Used": [
- "urn:d27d94c1-784a-4d97-94ff-b674103f64e8"
+ "urn:uuid:00b87638-397e-4a77-9523-896dc7559560"
],
- "AssociatedWith": "urn:3ffb5f05-4a19-4865-b981-909b041426bb",
+ "AssociatedWith": "urn:spm-acOHF07M",
"Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
"Parameters": {
"channel.biasreg": "0.001",
@@ -140,13 +140,13 @@
}
},
{
- "@id": "urn:92706503-83a5-42fd-b68e-7dba8a30c693",
+ "@id": "urn:normaliz-ZR78Z1Z8",
"Label": "Normalize",
"Used": [
- "urn:2fc6ed9f-b90f-4833-a80d-770788678427",
- "urn:717e6e9d-b97e-467c-aab3-ae4f15459b31"
+ "bids::c1anat_sub-01_T1w.nii",
+ "urn:uuid:c410a960-d03c-4151-87b8-f58dab758b29"
],
- "AssociatedWith": "urn:3ffb5f05-4a19-4865-b981-909b041426bb",
+ "AssociatedWith": "urn:spm-acOHF07M",
"Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -156,12 +156,12 @@
}
},
{
- "@id": "urn:e1e59516-0eed-4c3c-84d8-68271d7d9ac8",
+ "@id": "urn:normaliz-ZEdAv6uD",
"Label": "Normalize",
"Used": [
- "urn:2fc6ed9f-b90f-4833-a80d-770788678427"
+ "bids::c1anat_sub-01_T1w.nii"
],
- "AssociatedWith": "urn:3ffb5f05-4a19-4865-b981-909b041426bb",
+ "AssociatedWith": "urn:spm-acOHF07M",
"Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -171,12 +171,12 @@
}
},
{
- "@id": "urn:39992d62-da1f-4153-b77c-a96fe95f8555",
+ "@id": "urn:smooth10-IadoLaCi",
"Label": "Smooth",
"Used": [
- "urn:aaa99efc-93c1-456f-a46e-49bb69396a9d"
+ "urn:uuid:037e6a92-83f4-4faa-992b-6e18e31af216"
],
- "AssociatedWith": "urn:3ffb5f05-4a19-4865-b981-909b041426bb",
+ "AssociatedWith": "urn:spm-acOHF07M",
"Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
"Parameters": {
"fwhm": "[6, 6, 6]",
@@ -186,14 +186,14 @@
}
},
{
- "@id": "urn:eefd5f21-3c8d-40a0-bac6-7edd58d696ea",
+ "@id": "urn:statdesi-myWd5TJA",
"Label": "Stat Design",
"Used": [
- "urn:1abedd81-306e-4748-aebb-1f5e42437347",
- "urn:73ab640b-ef65-4907-abc4-6d68bf3b2bf8"
+ "urn:uuid:f8863426-2990-49f3-8228-7c70ae2e41fb",
+ "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
],
- "AssociatedWith": "urn:3ffb5f05-4a19-4865-b981-909b041426bb",
- "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_HRF_informed_basis'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [1 1];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
+ "AssociatedWith": "urn:spm-acOHF07M",
+ "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_HRF_informed_basis'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [1 1];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
"Parameters": {
"dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_HRF_informed_basis'}",
"timing.units": "'secs'",
@@ -214,12 +214,12 @@
}
},
{
- "@id": "urn:eca62f47-2d02-415d-bf7d-769f76277959",
+ "@id": "urn:estimate-ToFAvQwO",
"Label": "Estimate stat.",
"Used": [
- "urn:e9ee1116-9225-47b0-8405-d050722eeb4e"
+ "urn:uuid:acced37c-e797-480a-bb60-90518dd89a5a"
],
- "AssociatedWith": "urn:3ffb5f05-4a19-4865-b981-909b041426bb",
+ "AssociatedWith": "urn:spm-acOHF07M",
"Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
"Parameters": {
"write_residuals": "0",
@@ -227,12 +227,12 @@
}
},
{
- "@id": "urn:9b7413de-84c5-4192-89bf-80266e1ab5ee",
+ "@id": "urn:estimate-E0P2nF9m",
"Label": "Estimate contrast",
"Used": [
- "urn:839c0971-255e-4c75-9e1a-542046cca671"
+ "urn:uuid:99fb6d5b-1d5e-4460-9a59-b669a7b1f326"
],
- "AssociatedWith": "urn:3ffb5f05-4a19-4865-b981-909b041426bb",
+ "AssociatedWith": "urn:spm-acOHF07M",
"Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0 0 0 0 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
"Parameters": {
"consess{1}.tcon.name": "'tone counting vs baseline'",
@@ -242,12 +242,12 @@
}
},
{
- "@id": "urn:86ad9869-3e33-4e42-bd8f-b9b8e8f7a3a2",
+ "@id": "urn:threshol-FFHQAaYA",
"Label": "Threshold",
"Used": [
- "urn:b10473eb-5f57-4126-b12a-75a8302c7d6c"
+ "urn:uuid:9585246b-56b1-478a-84ba-6cf5cb399a11"
],
- "AssociatedWith": "urn:3ffb5f05-4a19-4865-b981-909b041426bb",
+ "AssociatedWith": "urn:spm-acOHF07M",
"Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.tspm.basename = 'thresh';",
"Parameters": {
"conspec.titlestr": "''",
@@ -265,98 +265,96 @@
],
"Entities": [
{
- "@id": "urn:065fd0da-dec5-43b9-89bd-2e28490b2920",
+ "@id": "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+ "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"digest": {
- "sha256": "52cc2a3822512db5be3accc8263f2ac1338f32fad8af63cc81fb5af2f335c509"
+ "sha256": "b3d8382360fbbc58cbd8c9e654ddda30b9f0318cf04ebd7539ec75bd724041d2"
}
},
{
- "@id": "urn:6f2a8768-dd51-49f4-b29b-badf9cbd2355",
+ "@id": "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz",
"Label": "anat_sub-01_T1w.nii.gz",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+ "AtLocation": "ds011/sub-01/anat/sub-01_T1w.nii.gz",
"digest": {
- "sha256": "3d9457fa7712b355d6569522ca80a6dfd70a40b82e6aa0a9364513cf04916dbb"
+ "sha256": "70b9327067cc5200330e04e70b22a41db5aa3b78f978060f61f49bd3a45d125e"
}
},
{
- "@id": "urn:d3ee1eb9-ba34-4c1b-be52-8fb9737bcae5",
+ "@id": "urn:uuid:747672f0-0684-4712-88d7-7caece60c42c",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "GeneratedBy": "urn:d867fd7f-631d-420b-900e-78f8937f4436"
+ "GeneratedBy": "urn:movefile-gzlPmudm"
},
{
- "@id": "urn:f6388f61-a430-4ddb-8dc8-558e2ef8b0ac",
+ "@id": "urn:uuid:36203fcb-8c36-4398-8626-9fb725695b3a",
"Label": "anat_sub-01_T1w.nii.gz",
- "GeneratedBy": "urn:10f8b075-1fca-472e-b140-189ba027fbad"
+ "GeneratedBy": "urn:movefile-ybi7EcAT"
},
{
- "@id": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
+ "@id": "urn:uuid:dda513d4-ddb2-4de3-8f87-fb8621f2b48e",
"Label": "func_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:4f8e64ff-f2e7-4b80-b21d-aab197e3b643"
+ "GeneratedBy": "urn:gunzip3-yNT9tbr5"
},
{
- "@id": "urn:717e6e9d-b97e-467c-aab3-ae4f15459b31",
+ "@id": "urn:uuid:c410a960-d03c-4151-87b8-f58dab758b29",
"Label": "meanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:29e1c19f-538c-4342-9e76-a6866ccd580f"
+ "GeneratedBy": "urn:realign5-mYV2jEjf"
},
{
- "@id": "urn:d27d94c1-784a-4d97-94ff-b674103f64e8",
+ "@id": "urn:uuid:00b87638-397e-4a77-9523-896dc7559560",
"Label": "anat_sub-01_T1w.nii",
- "GeneratedBy": "urn:c612758d-292e-4c5c-9f22-09f64fa14d84"
+ "GeneratedBy": "urn:gunzip4-YMI34NTy"
},
{
- "@id": "urn:2fc6ed9f-b90f-4833-a80d-770788678427",
+ "@id": "bids::c1anat_sub-01_T1w.nii",
"Label": "segment1",
- "Atlocation": "c1xxx.nii.gz",
- "GeneratedBy": "urn:e255be3b-54f2-4438-a0c3-73a0866a113e",
"AtLocation": "c1anat_sub-01_T1w.nii",
+ "GeneratedBy": "urn:segment7-cEoNDdlV",
"digest": {
"sha256": "61ca923955d0a5c9088df9e258f41644067ec964e1c9a83284ba03b0515079b0"
}
},
{
- "@id": "urn:51597196-e9da-4265-8d9f-85e8e2c7d6cb",
+ "@id": "bids::c2anat_sub-01_T1w.nii",
"Label": "segment2",
- "Atlocation": "c2xxx.nii.gz",
- "GeneratedBy": "urn:e255be3b-54f2-4438-a0c3-73a0866a113e",
"AtLocation": "c2anat_sub-01_T1w.nii",
+ "GeneratedBy": "urn:segment7-cEoNDdlV",
"digest": {
"sha256": "10ad88ebeebebd0bd03ccbdd4df92d500d28d14715fa5375fd35589caddf49a6"
}
},
{
- "@id": "urn:aaa99efc-93c1-456f-a46e-49bb69396a9d",
+ "@id": "urn:uuid:037e6a92-83f4-4faa-992b-6e18e31af216",
"Label": "wsegment1",
- "GeneratedBy": "urn:92706503-83a5-42fd-b68e-7dba8a30c693"
+ "GeneratedBy": "urn:normaliz-ZR78Z1Z8"
},
{
- "@id": "urn:73ab640b-ef65-4907-abc4-6d68bf3b2bf8",
+ "@id": "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"Label": "ONSETS_sub-01-MultiCond.mat",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+ "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"digest": {
- "sha256": "be4671d4f9dc480dd3e5be19aeeab2756f7afdc3b32d81e071685d7a4eafcfed"
+ "sha256": "5599e80629bb4d66cdbfb357511c04060bd3d37cdbfe2a4cd701a2979e9f6610"
}
},
{
- "@id": "urn:1abedd81-306e-4748-aebb-1f5e42437347",
+ "@id": "urn:uuid:f8863426-2990-49f3-8228-7c70ae2e41fb",
"Label": "swsegment1",
- "GeneratedBy": "urn:39992d62-da1f-4153-b77c-a96fe95f8555"
+ "GeneratedBy": "urn:smooth10-IadoLaCi"
},
{
- "@id": "urn:e9ee1116-9225-47b0-8405-d050722eeb4e",
+ "@id": "urn:uuid:acced37c-e797-480a-bb60-90518dd89a5a",
"Label": "SPM.mat",
- "GeneratedBy": "urn:eefd5f21-3c8d-40a0-bac6-7edd58d696ea"
+ "GeneratedBy": "urn:statdesi-myWd5TJA"
},
{
- "@id": "urn:839c0971-255e-4c75-9e1a-542046cca671",
+ "@id": "urn:uuid:99fb6d5b-1d5e-4460-9a59-b669a7b1f326",
"Label": "SPM.mat",
- "GeneratedBy": "urn:eca62f47-2d02-415d-bf7d-769f76277959"
+ "GeneratedBy": "urn:estimate-ToFAvQwO"
},
{
- "@id": "urn:b10473eb-5f57-4126-b12a-75a8302c7d6c",
+ "@id": "urn:uuid:9585246b-56b1-478a-84ba-6cf5cb399a11",
"Label": "SPM.mat",
- "GeneratedBy": "urn:9b7413de-84c5-4192-89bf-80266e1ab5ee"
+ "GeneratedBy": "urn:estimate-E0P2nF9m"
}
]
}
diff --git a/examples/from_parsers/spm/spm_HRF_informed_basis_batch.m b/examples/from_parsers/spm/spm_HRF_informed_basis_batch.m
index 5e07b34e7..ed15d49b8 100644
--- a/examples/from_parsers/spm/spm_HRF_informed_basis_batch.m
+++ b/examples/from_parsers/spm/spm_HRF_informed_basis_batch.m
@@ -3,10 +3,10 @@
% spm SPM - SPM12 (12.1)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------
-matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};
-matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};
-matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};
-matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};
+matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};
+matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};
+matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};
+matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};
matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));
@@ -90,7 +90,7 @@
matlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;
matlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});
-matlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};
+matlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};
matlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});
matlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};
matlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;
diff --git a/examples/from_parsers/spm/spm_HRF_informed_basis_batch.png b/examples/from_parsers/spm/spm_HRF_informed_basis_batch.png
index f188ae93d..04e45ab3a 100644
Binary files a/examples/from_parsers/spm/spm_HRF_informed_basis_batch.png and b/examples/from_parsers/spm/spm_HRF_informed_basis_batch.png differ
diff --git a/examples/from_parsers/spm/spm_con_f_batch.jsonld b/examples/from_parsers/spm/spm_con_f_batch.jsonld
index 2778e5461..61a3f6b4f 100644
--- a/examples/from_parsers/spm/spm_con_f_batch.jsonld
+++ b/examples/from_parsers/spm/spm_con_f_batch.jsonld
@@ -4,63 +4,63 @@
"Records": {
"Software": [
{
- "@id": "urn:6cdc1962-95fb-4726-8f99-e6a217f57a15",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:spm-LIc1sKxA",
"@type": "prov:SoftwareAgent",
"Label": "SPM",
- "Version": "SPM12r7224"
+ "Version": "SPM12r7224",
+ "AltIdentifier": "RRID:SCR_007037"
}
],
"Activities": [
{
- "@id": "urn:4126e001-b2b1-4b12-a084-2ed8afbd3271",
+ "@id": "urn:movefile-l6on4kPt",
"Label": "Move file",
"Used": [
- "urn:48b63383-ce45-404f-bda1-96168e337b80"
+ "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
],
- "AssociatedWith": "urn:6cdc1962-95fb-4726-8f99-e6a217f57a15",
- "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
+ "AssociatedWith": "urn:spm-LIc1sKxA",
+ "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};",
"Parameters": {
- "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
+ "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'}"
}
},
{
- "@id": "urn:0af45bce-46c7-418d-90aa-c60de084ad56",
+ "@id": "urn:movefile-gCawKlZC",
"Label": "Move file",
"Used": [
- "urn:d2ef3f1c-c063-440e-b174-047af4076a07"
+ "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz"
],
- "AssociatedWith": "urn:6cdc1962-95fb-4726-8f99-e6a217f57a15",
- "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
+ "AssociatedWith": "urn:spm-LIc1sKxA",
+ "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};",
"Parameters": {
- "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
+ "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'}"
}
},
{
- "@id": "urn:70f2b950-1da8-47bd-9a74-7baa69660fbe",
+ "@id": "urn:gunzip3-fn7Nh8iV",
"Label": "Gunzip",
"Used": [
- "urn:23a1709c-98bd-4406-a568-7599a5950947"
+ "urn:uuid:f924aef0-c377-4618-90cd-49b9737ac11b"
],
- "AssociatedWith": "urn:6cdc1962-95fb-4726-8f99-e6a217f57a15",
+ "AssociatedWith": "urn:spm-LIc1sKxA",
"Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:c4baf3df-0ef1-46a1-837c-11aa62fc7a4e",
+ "@id": "urn:gunzip4-c5kwgRLI",
"Label": "Gunzip",
"Used": [
- "urn:5cef23cf-7cd9-4210-990e-6e91f48dbd73"
+ "urn:uuid:dcbe17a9-4395-42db-81ad-f008aba1aa73"
],
- "AssociatedWith": "urn:6cdc1962-95fb-4726-8f99-e6a217f57a15",
+ "AssociatedWith": "urn:spm-LIc1sKxA",
"Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:34578183-176c-415f-b749-50fa24842adb",
+ "@id": "urn:realign5-26LxLepY",
"Label": "Realign",
"Used": [
- "urn:ed9cf935-b21a-42ec-a454-ee7dd58818f4"
+ "urn:uuid:d7fe707e-3f18-495a-9770-0880b857106a"
],
- "AssociatedWith": "urn:6cdc1962-95fb-4726-8f99-e6a217f57a15",
+ "AssociatedWith": "urn:spm-LIc1sKxA",
"Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
"Parameters": {
"eoptions.quality": "0.9",
@@ -78,13 +78,13 @@
}
},
{
- "@id": "urn:ba3146d8-e52f-45f1-a1a4-a2af80050930",
+ "@id": "urn:coregist-aXbBMiz5",
"Label": "Coregister",
"Used": [
- "urn:1807e023-7810-4c8a-ba7e-62ac784fe919",
- "urn:98e35494-b413-4218-b09a-4736ca2f5580"
+ "urn:uuid:7dee6d95-ad21-48fd-82b3-94b72841daa9",
+ "urn:uuid:f513ed91-4479-4983-a375-948d936720b2"
],
- "AssociatedWith": "urn:6cdc1962-95fb-4726-8f99-e6a217f57a15",
+ "AssociatedWith": "urn:spm-LIc1sKxA",
"Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
"Parameters": {
"other": "{''}",
@@ -95,12 +95,12 @@
}
},
{
- "@id": "urn:ab106e53-c496-4951-ad6d-145f6d4d938a",
+ "@id": "urn:segment7-1il83Pxd",
"Label": "Segment",
"Used": [
- "urn:1807e023-7810-4c8a-ba7e-62ac784fe919"
+ "urn:uuid:f513ed91-4479-4983-a375-948d936720b2"
],
- "AssociatedWith": "urn:6cdc1962-95fb-4726-8f99-e6a217f57a15",
+ "AssociatedWith": "urn:spm-LIc1sKxA",
"Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
"Parameters": {
"channel.biasreg": "0.001",
@@ -140,13 +140,13 @@
}
},
{
- "@id": "urn:312d6e00-b598-48e6-a211-aa787cc0f427",
+ "@id": "urn:normaliz-sQlDnSmF",
"Label": "Normalize",
"Used": [
- "urn:98e35494-b413-4218-b09a-4736ca2f5580",
- "urn:b87ce270-a7b7-4db0-b9ea-1be043aad9f5"
+ "bids::c1anat_sub-01_T1w.nii",
+ "urn:uuid:7dee6d95-ad21-48fd-82b3-94b72841daa9"
],
- "AssociatedWith": "urn:6cdc1962-95fb-4726-8f99-e6a217f57a15",
+ "AssociatedWith": "urn:spm-LIc1sKxA",
"Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -156,12 +156,12 @@
}
},
{
- "@id": "urn:7acc757f-48c5-4675-a39b-3733beca8099",
+ "@id": "urn:normaliz-NtUekQwA",
"Label": "Normalize",
"Used": [
- "urn:b87ce270-a7b7-4db0-b9ea-1be043aad9f5"
+ "bids::c1anat_sub-01_T1w.nii"
],
- "AssociatedWith": "urn:6cdc1962-95fb-4726-8f99-e6a217f57a15",
+ "AssociatedWith": "urn:spm-LIc1sKxA",
"Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -171,12 +171,12 @@
}
},
{
- "@id": "urn:d6a584e7-0498-400e-8978-13fa03639d6d",
+ "@id": "urn:smooth10-R7RN1eYI",
"Label": "Smooth",
"Used": [
- "urn:91024a06-af86-4fb0-afa9-ebe7bfd999e1"
+ "urn:uuid:69bc2ab3-775e-48d7-adf5-f26c27756556"
],
- "AssociatedWith": "urn:6cdc1962-95fb-4726-8f99-e6a217f57a15",
+ "AssociatedWith": "urn:spm-LIc1sKxA",
"Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
"Parameters": {
"fwhm": "[6, 6, 6]",
@@ -186,14 +186,14 @@
}
},
{
- "@id": "urn:52c1a8e5-c14b-48df-8a80-29367b081e4e",
+ "@id": "urn:statdesi-aEQJ1q4W",
"Label": "Stat Design",
"Used": [
- "urn:3b4e7ef1-b31c-4fb3-ae81-90f628678f4b",
- "urn:28a1f753-74e8-465e-9ba7-0723531947f6"
+ "urn:uuid:6c3ee28c-e553-4883-87e8-be4bcf1ef14e",
+ "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
],
- "AssociatedWith": "urn:6cdc1962-95fb-4726-8f99-e6a217f57a15",
- "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_f_test'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
+ "AssociatedWith": "urn:spm-LIc1sKxA",
+ "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_f_test'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
"Parameters": {
"dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_f_test'}",
"timing.units": "'secs'",
@@ -214,12 +214,12 @@
}
},
{
- "@id": "urn:aab7e482-df3a-4613-8609-1527e33b0cfa",
+ "@id": "urn:estimate-gMGJL5Sw",
"Label": "Estimate stat.",
"Used": [
- "urn:46c30a98-36d1-480e-b0a6-e9e7d245f814"
+ "urn:uuid:6d42344f-9f8a-49f4-9e32-812a3fa10f4f"
],
- "AssociatedWith": "urn:6cdc1962-95fb-4726-8f99-e6a217f57a15",
+ "AssociatedWith": "urn:spm-LIc1sKxA",
"Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
"Parameters": {
"write_residuals": "0",
@@ -227,12 +227,12 @@
}
},
{
- "@id": "urn:012ee049-f81b-45de-a81a-ef7462289b29",
+ "@id": "urn:estimate-G7N1nN5n",
"Label": "Estimate contrast",
"Used": [
- "urn:ceae3128-1252-410b-ae1e-bdbdf0bfc9db"
+ "urn:uuid:d85f47b5-55f9-4f28-ba22-d59267366a84"
],
- "AssociatedWith": "urn:6cdc1962-95fb-4726-8f99-e6a217f57a15",
+ "AssociatedWith": "urn:spm-LIc1sKxA",
"Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.fcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.fcon.weights = [1 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.fcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
"Parameters": {
"consess{1}.fcon.name": "'tone counting vs baseline'",
@@ -242,12 +242,12 @@
}
},
{
- "@id": "urn:f86f58b5-74cf-4907-8b88-34d086b658e3",
+ "@id": "urn:threshol-z8JRdihh",
"Label": "Threshold",
"Used": [
- "urn:5daaf5df-9d7a-4299-bb24-1a91eecda1ef"
+ "urn:uuid:c0af5110-55f0-4492-847d-c70be4c4b90b"
],
- "AssociatedWith": "urn:6cdc1962-95fb-4726-8f99-e6a217f57a15",
+ "AssociatedWith": "urn:spm-LIc1sKxA",
"Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.tspm.basename = 'thresh';",
"Parameters": {
"conspec.titlestr": "''",
@@ -265,98 +265,96 @@
],
"Entities": [
{
- "@id": "urn:48b63383-ce45-404f-bda1-96168e337b80",
+ "@id": "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+ "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"digest": {
- "sha256": "52cc2a3822512db5be3accc8263f2ac1338f32fad8af63cc81fb5af2f335c509"
+ "sha256": "b3d8382360fbbc58cbd8c9e654ddda30b9f0318cf04ebd7539ec75bd724041d2"
}
},
{
- "@id": "urn:d2ef3f1c-c063-440e-b174-047af4076a07",
+ "@id": "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz",
"Label": "anat_sub-01_T1w.nii.gz",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+ "AtLocation": "ds011/sub-01/anat/sub-01_T1w.nii.gz",
"digest": {
- "sha256": "3d9457fa7712b355d6569522ca80a6dfd70a40b82e6aa0a9364513cf04916dbb"
+ "sha256": "70b9327067cc5200330e04e70b22a41db5aa3b78f978060f61f49bd3a45d125e"
}
},
{
- "@id": "urn:23a1709c-98bd-4406-a568-7599a5950947",
+ "@id": "urn:uuid:f924aef0-c377-4618-90cd-49b9737ac11b",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "GeneratedBy": "urn:4126e001-b2b1-4b12-a084-2ed8afbd3271"
+ "GeneratedBy": "urn:movefile-l6on4kPt"
},
{
- "@id": "urn:5cef23cf-7cd9-4210-990e-6e91f48dbd73",
+ "@id": "urn:uuid:dcbe17a9-4395-42db-81ad-f008aba1aa73",
"Label": "anat_sub-01_T1w.nii.gz",
- "GeneratedBy": "urn:0af45bce-46c7-418d-90aa-c60de084ad56"
+ "GeneratedBy": "urn:movefile-gCawKlZC"
},
{
- "@id": "urn:ed9cf935-b21a-42ec-a454-ee7dd58818f4",
+ "@id": "urn:uuid:d7fe707e-3f18-495a-9770-0880b857106a",
"Label": "func_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:70f2b950-1da8-47bd-9a74-7baa69660fbe"
+ "GeneratedBy": "urn:gunzip3-fn7Nh8iV"
},
{
- "@id": "urn:98e35494-b413-4218-b09a-4736ca2f5580",
+ "@id": "urn:uuid:7dee6d95-ad21-48fd-82b3-94b72841daa9",
"Label": "meanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:34578183-176c-415f-b749-50fa24842adb"
+ "GeneratedBy": "urn:realign5-26LxLepY"
},
{
- "@id": "urn:1807e023-7810-4c8a-ba7e-62ac784fe919",
+ "@id": "urn:uuid:f513ed91-4479-4983-a375-948d936720b2",
"Label": "anat_sub-01_T1w.nii",
- "GeneratedBy": "urn:c4baf3df-0ef1-46a1-837c-11aa62fc7a4e"
+ "GeneratedBy": "urn:gunzip4-c5kwgRLI"
},
{
- "@id": "urn:b87ce270-a7b7-4db0-b9ea-1be043aad9f5",
+ "@id": "bids::c1anat_sub-01_T1w.nii",
"Label": "segment1",
- "Atlocation": "c1xxx.nii.gz",
- "GeneratedBy": "urn:ab106e53-c496-4951-ad6d-145f6d4d938a",
"AtLocation": "c1anat_sub-01_T1w.nii",
+ "GeneratedBy": "urn:segment7-1il83Pxd",
"digest": {
"sha256": "61ca923955d0a5c9088df9e258f41644067ec964e1c9a83284ba03b0515079b0"
}
},
{
- "@id": "urn:aca5ea51-558c-4d26-b3e4-687a77410260",
+ "@id": "bids::c2anat_sub-01_T1w.nii",
"Label": "segment2",
- "Atlocation": "c2xxx.nii.gz",
- "GeneratedBy": "urn:ab106e53-c496-4951-ad6d-145f6d4d938a",
"AtLocation": "c2anat_sub-01_T1w.nii",
+ "GeneratedBy": "urn:segment7-1il83Pxd",
"digest": {
"sha256": "10ad88ebeebebd0bd03ccbdd4df92d500d28d14715fa5375fd35589caddf49a6"
}
},
{
- "@id": "urn:91024a06-af86-4fb0-afa9-ebe7bfd999e1",
- "Label": "wmeanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:312d6e00-b598-48e6-a211-aa787cc0f427"
+ "@id": "urn:uuid:69bc2ab3-775e-48d7-adf5-f26c27756556",
+ "Label": "wsegment1",
+ "GeneratedBy": "urn:normaliz-sQlDnSmF"
},
{
- "@id": "urn:28a1f753-74e8-465e-9ba7-0723531947f6",
+ "@id": "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"Label": "ONSETS_sub-01-MultiCond.mat",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+ "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"digest": {
- "sha256": "be4671d4f9dc480dd3e5be19aeeab2756f7afdc3b32d81e071685d7a4eafcfed"
+ "sha256": "5599e80629bb4d66cdbfb357511c04060bd3d37cdbfe2a4cd701a2979e9f6610"
}
},
{
- "@id": "urn:3b4e7ef1-b31c-4fb3-ae81-90f628678f4b",
- "Label": "swmeanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:d6a584e7-0498-400e-8978-13fa03639d6d"
+ "@id": "urn:uuid:6c3ee28c-e553-4883-87e8-be4bcf1ef14e",
+ "Label": "swsegment1",
+ "GeneratedBy": "urn:smooth10-R7RN1eYI"
},
{
- "@id": "urn:46c30a98-36d1-480e-b0a6-e9e7d245f814",
+ "@id": "urn:uuid:6d42344f-9f8a-49f4-9e32-812a3fa10f4f",
"Label": "SPM.mat",
- "GeneratedBy": "urn:52c1a8e5-c14b-48df-8a80-29367b081e4e"
+ "GeneratedBy": "urn:statdesi-aEQJ1q4W"
},
{
- "@id": "urn:ceae3128-1252-410b-ae1e-bdbdf0bfc9db",
+ "@id": "urn:uuid:d85f47b5-55f9-4f28-ba22-d59267366a84",
"Label": "SPM.mat",
- "GeneratedBy": "urn:aab7e482-df3a-4613-8609-1527e33b0cfa"
+ "GeneratedBy": "urn:estimate-gMGJL5Sw"
},
{
- "@id": "urn:5daaf5df-9d7a-4299-bb24-1a91eecda1ef",
+ "@id": "urn:uuid:c0af5110-55f0-4492-847d-c70be4c4b90b",
"Label": "SPM.mat",
- "GeneratedBy": "urn:012ee049-f81b-45de-a81a-ef7462289b29"
+ "GeneratedBy": "urn:estimate-G7N1nN5n"
}
]
}
diff --git a/examples/from_parsers/spm/spm_con_f_batch.m b/examples/from_parsers/spm/spm_con_f_batch.m
index 73253e0b3..dacffb182 100644
--- a/examples/from_parsers/spm/spm_con_f_batch.m
+++ b/examples/from_parsers/spm/spm_con_f_batch.m
@@ -3,10 +3,10 @@
% spm SPM - SPM12 (12.1)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------
-matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};
-matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};
-matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};
-matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};
+matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};
+matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};
+matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};
+matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};
matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));
@@ -90,7 +90,7 @@
matlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;
matlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});
-matlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};
+matlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};
matlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});
matlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};
matlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;
diff --git a/examples/from_parsers/spm/spm_con_f_batch.png b/examples/from_parsers/spm/spm_con_f_batch.png
index 94b4f106a..1f04e078c 100644
Binary files a/examples/from_parsers/spm/spm_con_f_batch.png and b/examples/from_parsers/spm/spm_con_f_batch.png differ
diff --git a/examples/from_parsers/spm/spm_conjunction_batch.jsonld b/examples/from_parsers/spm/spm_conjunction_batch.jsonld
index 45868b72b..eeb1d1cdf 100644
--- a/examples/from_parsers/spm/spm_conjunction_batch.jsonld
+++ b/examples/from_parsers/spm/spm_conjunction_batch.jsonld
@@ -4,63 +4,63 @@
"Records": {
"Software": [
{
- "@id": "urn:226860d4-b23a-417b-83a2-cc885187a875",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:spm-VrPimuXr",
"@type": "prov:SoftwareAgent",
"Label": "SPM",
- "Version": "SPM12r7224"
+ "Version": "SPM12r7224",
+ "AltIdentifier": "RRID:SCR_007037"
}
],
"Activities": [
{
- "@id": "urn:8ec92f01-2cee-4390-89c0-c709c8eb4d3a",
+ "@id": "urn:movefile-tGqsV6q1",
"Label": "Move file",
"Used": [
- "urn:54127544-1b9f-4572-8ddf-9901871049e4"
+ "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
],
- "AssociatedWith": "urn:226860d4-b23a-417b-83a2-cc885187a875",
- "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
+ "AssociatedWith": "urn:spm-VrPimuXr",
+ "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};",
"Parameters": {
- "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
+ "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'}"
}
},
{
- "@id": "urn:bd299897-9eaf-4062-a392-2c4c2e29f7a9",
+ "@id": "urn:movefile-fPTQrpaA",
"Label": "Move file",
"Used": [
- "urn:d501296e-75d6-46af-a589-879fb0c19e1f"
+ "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz"
],
- "AssociatedWith": "urn:226860d4-b23a-417b-83a2-cc885187a875",
- "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
+ "AssociatedWith": "urn:spm-VrPimuXr",
+ "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};",
"Parameters": {
- "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
+ "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'}"
}
},
{
- "@id": "urn:10527ace-1989-4ac8-a63c-3916f35095af",
+ "@id": "urn:gunzip3-tqBGQt7R",
"Label": "Gunzip",
"Used": [
- "urn:4b4de4da-5b6f-47a9-8120-8c797e7906a4"
+ "urn:uuid:2c041aaf-c929-4e12-90b5-cdf5a6ade028"
],
- "AssociatedWith": "urn:226860d4-b23a-417b-83a2-cc885187a875",
+ "AssociatedWith": "urn:spm-VrPimuXr",
"Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:04f39fbd-de85-4f4f-8356-f1af9a58cf82",
+ "@id": "urn:gunzip4-WwCnI7oL",
"Label": "Gunzip",
"Used": [
- "urn:bb94fee4-f2af-4aa5-9265-91d90e21a9ac"
+ "urn:uuid:473debad-a73f-48c7-b52d-5fe5822d3c13"
],
- "AssociatedWith": "urn:226860d4-b23a-417b-83a2-cc885187a875",
+ "AssociatedWith": "urn:spm-VrPimuXr",
"Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:806d8de7-23c7-46e1-b393-3d7fa8d97c2e",
+ "@id": "urn:realign5-T7rMJOC4",
"Label": "Realign",
"Used": [
- "urn:17690087-d2ed-4f96-80fe-672428147074"
+ "urn:uuid:3a64eb02-6ded-4241-aff4-cd111dc36067"
],
- "AssociatedWith": "urn:226860d4-b23a-417b-83a2-cc885187a875",
+ "AssociatedWith": "urn:spm-VrPimuXr",
"Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
"Parameters": {
"eoptions.quality": "0.9",
@@ -78,13 +78,13 @@
}
},
{
- "@id": "urn:57b7a47a-a8bd-4f4f-afe5-7d15cdba2f76",
+ "@id": "urn:coregist-VpPO008W",
"Label": "Coregister",
"Used": [
- "urn:400dfff1-82aa-4fc8-9730-33f12fb8c935",
- "urn:e7a980b9-8ba5-46e3-bbde-f90aa33389b6"
+ "urn:uuid:14f4afb9-bb97-4388-ab12-b659b98d6623",
+ "urn:uuid:dbbfa8c4-6083-4348-b3ea-83228889aec2"
],
- "AssociatedWith": "urn:226860d4-b23a-417b-83a2-cc885187a875",
+ "AssociatedWith": "urn:spm-VrPimuXr",
"Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
"Parameters": {
"other": "{''}",
@@ -95,12 +95,12 @@
}
},
{
- "@id": "urn:af065d62-f7ad-401d-8556-3779423d515c",
+ "@id": "urn:segment7-b7l5mBx1",
"Label": "Segment",
"Used": [
- "urn:400dfff1-82aa-4fc8-9730-33f12fb8c935"
+ "urn:uuid:14f4afb9-bb97-4388-ab12-b659b98d6623"
],
- "AssociatedWith": "urn:226860d4-b23a-417b-83a2-cc885187a875",
+ "AssociatedWith": "urn:spm-VrPimuXr",
"Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
"Parameters": {
"channel.biasreg": "0.001",
@@ -140,13 +140,13 @@
}
},
{
- "@id": "urn:9eed3a2e-d164-447c-b3bc-d21d5bef7b7e",
+ "@id": "urn:normaliz-DWfjdY79",
"Label": "Normalize",
"Used": [
- "urn:4b894bf9-bd29-4196-ae70-53367dfdf420",
- "urn:e7a980b9-8ba5-46e3-bbde-f90aa33389b6"
+ "bids::c1anat_sub-01_T1w.nii",
+ "urn:uuid:dbbfa8c4-6083-4348-b3ea-83228889aec2"
],
- "AssociatedWith": "urn:226860d4-b23a-417b-83a2-cc885187a875",
+ "AssociatedWith": "urn:spm-VrPimuXr",
"Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -156,12 +156,12 @@
}
},
{
- "@id": "urn:869adb8d-9320-4314-abe1-6b6d044a5c59",
+ "@id": "urn:normaliz-R5mjdY3T",
"Label": "Normalize",
"Used": [
- "urn:4b894bf9-bd29-4196-ae70-53367dfdf420"
+ "bids::c1anat_sub-01_T1w.nii"
],
- "AssociatedWith": "urn:226860d4-b23a-417b-83a2-cc885187a875",
+ "AssociatedWith": "urn:spm-VrPimuXr",
"Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -171,12 +171,12 @@
}
},
{
- "@id": "urn:bca7fdff-cf83-4ed5-86ca-ce6de993d731",
+ "@id": "urn:smooth10-eLkTnsVV",
"Label": "Smooth",
"Used": [
- "urn:0b7aab45-33e6-4933-87bf-1f8f951f1bb1"
+ "urn:uuid:24e209e7-b6d1-4657-9d88-3a95ac5cbb5f"
],
- "AssociatedWith": "urn:226860d4-b23a-417b-83a2-cc885187a875",
+ "AssociatedWith": "urn:spm-VrPimuXr",
"Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
"Parameters": {
"fwhm": "[6, 6, 6]",
@@ -186,14 +186,14 @@
}
},
{
- "@id": "urn:1eef669f-661f-4568-8142-004f40d9ce57",
+ "@id": "urn:statdesi-S9xhLPeN",
"Label": "Stat Design",
"Used": [
- "urn:9f28f0a1-da7e-4f27-9c55-3e2ac9572dc0",
- "urn:f6e52004-da13-4dda-b778-6622f666c503"
+ "urn:uuid:aea8ebea-ec5f-4039-bd16-b99011d66766",
+ "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
],
- "AssociatedWith": "urn:226860d4-b23a-417b-83a2-cc885187a875",
- "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_partial_conjunction'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
+ "AssociatedWith": "urn:spm-VrPimuXr",
+ "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_partial_conjunction'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
"Parameters": {
"dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_partial_conjunction'}",
"timing.units": "'secs'",
@@ -214,12 +214,12 @@
}
},
{
- "@id": "urn:46658bb2-25a3-4c69-a644-fecd3b60b9ca",
+ "@id": "urn:estimate-YyEuxb85",
"Label": "Estimate stat.",
"Used": [
- "urn:f23e0548-8b55-4fc9-ada0-c820cb55401c"
+ "urn:uuid:1228ef88-6dd1-4270-866b-396a614e9ae5"
],
- "AssociatedWith": "urn:226860d4-b23a-417b-83a2-cc885187a875",
+ "AssociatedWith": "urn:spm-VrPimuXr",
"Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
"Parameters": {
"write_residuals": "0",
@@ -227,12 +227,12 @@
}
},
{
- "@id": "urn:6d3d46ee-7e37-43d2-8ba4-a2bb416a4b5f",
+ "@id": "urn:estimate-wz8gGYn4",
"Label": "Estimate contrast",
"Used": [
- "urn:703a7425-757e-41ca-ac83-9c8446eab8eb"
+ "urn:uuid:b9686194-6f64-439f-90d7-badf8f509837"
],
- "AssociatedWith": "urn:226860d4-b23a-417b-83a2-cc885187a875",
+ "AssociatedWith": "urn:spm-VrPimuXr",
"Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.name = 'tone counting probe vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.weights = [0 1];\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
"Parameters": {
"consess{1}.tcon.name": "'tone counting vs baseline'",
@@ -245,12 +245,12 @@
}
},
{
- "@id": "urn:8b71facf-7122-43cf-b438-a8fe71f1eb30",
+ "@id": "urn:threshol-rDqjdjVE",
"Label": "Threshold",
"Used": [
- "urn:6845abf4-4f03-4e1e-9fb4-e47350f39fe1"
+ "urn:uuid:b84b03c2-3796-4f03-8a8a-0929d5dbf8bf"
],
- "AssociatedWith": "urn:226860d4-b23a-417b-83a2-cc885187a875",
+ "AssociatedWith": "urn:spm-VrPimuXr",
"Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = [1 2];\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.none = 1;",
"Parameters": {
"conspec.titlestr": "''",
@@ -268,98 +268,96 @@
],
"Entities": [
{
- "@id": "urn:54127544-1b9f-4572-8ddf-9901871049e4",
+ "@id": "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+ "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"digest": {
- "sha256": "52cc2a3822512db5be3accc8263f2ac1338f32fad8af63cc81fb5af2f335c509"
+ "sha256": "b3d8382360fbbc58cbd8c9e654ddda30b9f0318cf04ebd7539ec75bd724041d2"
}
},
{
- "@id": "urn:d501296e-75d6-46af-a589-879fb0c19e1f",
+ "@id": "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz",
"Label": "anat_sub-01_T1w.nii.gz",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+ "AtLocation": "ds011/sub-01/anat/sub-01_T1w.nii.gz",
"digest": {
- "sha256": "3d9457fa7712b355d6569522ca80a6dfd70a40b82e6aa0a9364513cf04916dbb"
+ "sha256": "70b9327067cc5200330e04e70b22a41db5aa3b78f978060f61f49bd3a45d125e"
}
},
{
- "@id": "urn:4b4de4da-5b6f-47a9-8120-8c797e7906a4",
+ "@id": "urn:uuid:2c041aaf-c929-4e12-90b5-cdf5a6ade028",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "GeneratedBy": "urn:8ec92f01-2cee-4390-89c0-c709c8eb4d3a"
+ "GeneratedBy": "urn:movefile-tGqsV6q1"
},
{
- "@id": "urn:bb94fee4-f2af-4aa5-9265-91d90e21a9ac",
+ "@id": "urn:uuid:473debad-a73f-48c7-b52d-5fe5822d3c13",
"Label": "anat_sub-01_T1w.nii.gz",
- "GeneratedBy": "urn:bd299897-9eaf-4062-a392-2c4c2e29f7a9"
+ "GeneratedBy": "urn:movefile-fPTQrpaA"
},
{
- "@id": "urn:17690087-d2ed-4f96-80fe-672428147074",
+ "@id": "urn:uuid:3a64eb02-6ded-4241-aff4-cd111dc36067",
"Label": "func_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:10527ace-1989-4ac8-a63c-3916f35095af"
+ "GeneratedBy": "urn:gunzip3-tqBGQt7R"
},
{
- "@id": "urn:e7a980b9-8ba5-46e3-bbde-f90aa33389b6",
+ "@id": "urn:uuid:dbbfa8c4-6083-4348-b3ea-83228889aec2",
"Label": "meanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:806d8de7-23c7-46e1-b393-3d7fa8d97c2e"
+ "GeneratedBy": "urn:realign5-T7rMJOC4"
},
{
- "@id": "urn:400dfff1-82aa-4fc8-9730-33f12fb8c935",
+ "@id": "urn:uuid:14f4afb9-bb97-4388-ab12-b659b98d6623",
"Label": "anat_sub-01_T1w.nii",
- "GeneratedBy": "urn:04f39fbd-de85-4f4f-8356-f1af9a58cf82"
+ "GeneratedBy": "urn:gunzip4-WwCnI7oL"
},
{
- "@id": "urn:4b894bf9-bd29-4196-ae70-53367dfdf420",
+ "@id": "bids::c1anat_sub-01_T1w.nii",
"Label": "segment1",
- "Atlocation": "c1xxx.nii.gz",
- "GeneratedBy": "urn:af065d62-f7ad-401d-8556-3779423d515c",
"AtLocation": "c1anat_sub-01_T1w.nii",
+ "GeneratedBy": "urn:segment7-b7l5mBx1",
"digest": {
"sha256": "61ca923955d0a5c9088df9e258f41644067ec964e1c9a83284ba03b0515079b0"
}
},
{
- "@id": "urn:aab53304-9b12-437b-806d-49e31efb24d7",
+ "@id": "bids::c2anat_sub-01_T1w.nii",
"Label": "segment2",
- "Atlocation": "c2xxx.nii.gz",
- "GeneratedBy": "urn:af065d62-f7ad-401d-8556-3779423d515c",
"AtLocation": "c2anat_sub-01_T1w.nii",
+ "GeneratedBy": "urn:segment7-b7l5mBx1",
"digest": {
"sha256": "10ad88ebeebebd0bd03ccbdd4df92d500d28d14715fa5375fd35589caddf49a6"
}
},
{
- "@id": "urn:0b7aab45-33e6-4933-87bf-1f8f951f1bb1",
+ "@id": "urn:uuid:24e209e7-b6d1-4657-9d88-3a95ac5cbb5f",
"Label": "wsegment1",
- "GeneratedBy": "urn:9eed3a2e-d164-447c-b3bc-d21d5bef7b7e"
+ "GeneratedBy": "urn:normaliz-DWfjdY79"
},
{
- "@id": "urn:f6e52004-da13-4dda-b778-6622f666c503",
+ "@id": "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"Label": "ONSETS_sub-01-MultiCond.mat",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+ "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"digest": {
- "sha256": "be4671d4f9dc480dd3e5be19aeeab2756f7afdc3b32d81e071685d7a4eafcfed"
+ "sha256": "5599e80629bb4d66cdbfb357511c04060bd3d37cdbfe2a4cd701a2979e9f6610"
}
},
{
- "@id": "urn:9f28f0a1-da7e-4f27-9c55-3e2ac9572dc0",
+ "@id": "urn:uuid:aea8ebea-ec5f-4039-bd16-b99011d66766",
"Label": "swsegment1",
- "GeneratedBy": "urn:bca7fdff-cf83-4ed5-86ca-ce6de993d731"
+ "GeneratedBy": "urn:smooth10-eLkTnsVV"
},
{
- "@id": "urn:f23e0548-8b55-4fc9-ada0-c820cb55401c",
+ "@id": "urn:uuid:1228ef88-6dd1-4270-866b-396a614e9ae5",
"Label": "SPM.mat",
- "GeneratedBy": "urn:1eef669f-661f-4568-8142-004f40d9ce57"
+ "GeneratedBy": "urn:statdesi-S9xhLPeN"
},
{
- "@id": "urn:703a7425-757e-41ca-ac83-9c8446eab8eb",
+ "@id": "urn:uuid:b9686194-6f64-439f-90d7-badf8f509837",
"Label": "SPM.mat",
- "GeneratedBy": "urn:46658bb2-25a3-4c69-a644-fecd3b60b9ca"
+ "GeneratedBy": "urn:estimate-YyEuxb85"
},
{
- "@id": "urn:6845abf4-4f03-4e1e-9fb4-e47350f39fe1",
+ "@id": "urn:uuid:b84b03c2-3796-4f03-8a8a-0929d5dbf8bf",
"Label": "SPM.mat",
- "GeneratedBy": "urn:6d3d46ee-7e37-43d2-8ba4-a2bb416a4b5f"
+ "GeneratedBy": "urn:estimate-wz8gGYn4"
}
]
}
diff --git a/examples/from_parsers/spm/spm_conjunction_batch.m b/examples/from_parsers/spm/spm_conjunction_batch.m
index 1e586c9cc..9b032b1de 100644
--- a/examples/from_parsers/spm/spm_conjunction_batch.m
+++ b/examples/from_parsers/spm/spm_conjunction_batch.m
@@ -3,10 +3,10 @@
% spm SPM - SPM12 (12.1)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------
-matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};
-matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};
-matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};
-matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};
+matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};
+matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};
+matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};
+matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};
matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));
@@ -90,7 +90,7 @@
matlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;
matlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});
-matlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};
+matlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};
matlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});
matlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};
matlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;
diff --git a/examples/from_parsers/spm/spm_conjunction_batch.png b/examples/from_parsers/spm/spm_conjunction_batch.png
index 754061507..d191651e9 100644
Binary files a/examples/from_parsers/spm/spm_conjunction_batch.png and b/examples/from_parsers/spm/spm_conjunction_batch.png differ
diff --git a/examples/from_parsers/spm/spm_contrast_mask_batch.jsonld b/examples/from_parsers/spm/spm_contrast_mask_batch.jsonld
index f7a49a089..9a85cb125 100644
--- a/examples/from_parsers/spm/spm_contrast_mask_batch.jsonld
+++ b/examples/from_parsers/spm/spm_contrast_mask_batch.jsonld
@@ -4,63 +4,63 @@
"Records": {
"Software": [
{
- "@id": "urn:a1419230-2b3e-4817-b640-05d85bd9dcd1",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:spm-9BNLPRS1",
"@type": "prov:SoftwareAgent",
"Label": "SPM",
- "Version": "SPM12r7224"
+ "Version": "SPM12r7224",
+ "AltIdentifier": "RRID:SCR_007037"
}
],
"Activities": [
{
- "@id": "urn:74ad9995-210a-4a09-96c1-021ac291fc78",
+ "@id": "urn:movefile-yUJIwuSB",
"Label": "Move file",
"Used": [
- "urn:881e6701-d5f6-4e1d-8b08-b0f422bfc7f7"
+ "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
],
- "AssociatedWith": "urn:a1419230-2b3e-4817-b640-05d85bd9dcd1",
- "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
+ "AssociatedWith": "urn:spm-9BNLPRS1",
+ "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};",
"Parameters": {
- "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
+ "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'}"
}
},
{
- "@id": "urn:2753b48f-12fa-40fc-a095-c4707b8dd571",
+ "@id": "urn:movefile-fRoKDI2e",
"Label": "Move file",
"Used": [
- "urn:c0771e58-a6ad-4067-a247-994db5d57566"
+ "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz"
],
- "AssociatedWith": "urn:a1419230-2b3e-4817-b640-05d85bd9dcd1",
- "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
+ "AssociatedWith": "urn:spm-9BNLPRS1",
+ "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};",
"Parameters": {
- "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
+ "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'}"
}
},
{
- "@id": "urn:d751aff5-d3ee-485c-be17-647730723212",
+ "@id": "urn:gunzip3-ZF0NbJuD",
"Label": "Gunzip",
"Used": [
- "urn:0708ea50-1d83-48c9-be2e-3871dfeb2b0a"
+ "urn:uuid:357f205f-1573-4bc1-8f0e-d94d48788a5d"
],
- "AssociatedWith": "urn:a1419230-2b3e-4817-b640-05d85bd9dcd1",
+ "AssociatedWith": "urn:spm-9BNLPRS1",
"Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:c3f9594d-ed7f-4c6d-b18c-c38b41dafd7f",
+ "@id": "urn:gunzip4-7VNZFWp2",
"Label": "Gunzip",
"Used": [
- "urn:eb38131d-32b2-4cbf-9b65-bb40b299df05"
+ "urn:uuid:6a87cd1a-ea9a-4d7d-b8d4-8dddc1bf2340"
],
- "AssociatedWith": "urn:a1419230-2b3e-4817-b640-05d85bd9dcd1",
+ "AssociatedWith": "urn:spm-9BNLPRS1",
"Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:842c7ba0-0064-4d8d-8f99-6361ff2599d4",
+ "@id": "urn:realign5-ud5VE1Gu",
"Label": "Realign",
"Used": [
- "urn:52511106-bdb5-436c-8f3f-0c0d2edaa139"
+ "urn:uuid:9941a786-0a67-439d-8bca-bafc3b34cbc2"
],
- "AssociatedWith": "urn:a1419230-2b3e-4817-b640-05d85bd9dcd1",
+ "AssociatedWith": "urn:spm-9BNLPRS1",
"Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
"Parameters": {
"eoptions.quality": "0.9",
@@ -78,13 +78,13 @@
}
},
{
- "@id": "urn:7977ef19-0ce9-4505-9a7b-b235b81e2024",
+ "@id": "urn:coregist-oPzLgR5z",
"Label": "Coregister",
"Used": [
- "urn:930d09a1-32c6-4f83-97de-52e2b4e5dd1e",
- "urn:c2684b63-598f-4f5e-b259-31d0868f9fbd"
+ "urn:uuid:07dfde62-9084-4f4d-b991-e3c8be405785",
+ "urn:uuid:78b1081a-34a1-4dce-96f0-89a9f7c53801"
],
- "AssociatedWith": "urn:a1419230-2b3e-4817-b640-05d85bd9dcd1",
+ "AssociatedWith": "urn:spm-9BNLPRS1",
"Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
"Parameters": {
"other": "{''}",
@@ -95,12 +95,12 @@
}
},
{
- "@id": "urn:5c7cbc9b-48c8-44b8-8f20-4487d457e76b",
+ "@id": "urn:segment7-8MUq9DK6",
"Label": "Segment",
"Used": [
- "urn:c2684b63-598f-4f5e-b259-31d0868f9fbd"
+ "urn:uuid:07dfde62-9084-4f4d-b991-e3c8be405785"
],
- "AssociatedWith": "urn:a1419230-2b3e-4817-b640-05d85bd9dcd1",
+ "AssociatedWith": "urn:spm-9BNLPRS1",
"Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
"Parameters": {
"channel.biasreg": "0.001",
@@ -140,13 +140,13 @@
}
},
{
- "@id": "urn:ffee68b2-1ae4-4e18-b7c4-8b3ea7e3669d",
+ "@id": "urn:normaliz-Rt8gp4xI",
"Label": "Normalize",
"Used": [
- "urn:930d09a1-32c6-4f83-97de-52e2b4e5dd1e",
- "urn:9c0f5dac-fd86-459b-b326-320b070d354c"
+ "bids::c1anat_sub-01_T1w.nii",
+ "urn:uuid:78b1081a-34a1-4dce-96f0-89a9f7c53801"
],
- "AssociatedWith": "urn:a1419230-2b3e-4817-b640-05d85bd9dcd1",
+ "AssociatedWith": "urn:spm-9BNLPRS1",
"Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -156,12 +156,12 @@
}
},
{
- "@id": "urn:6aaedc63-f21c-4f7b-81ae-55afae124789",
+ "@id": "urn:normaliz-tmfheJ0r",
"Label": "Normalize",
"Used": [
- "urn:9c0f5dac-fd86-459b-b326-320b070d354c"
+ "bids::c1anat_sub-01_T1w.nii"
],
- "AssociatedWith": "urn:a1419230-2b3e-4817-b640-05d85bd9dcd1",
+ "AssociatedWith": "urn:spm-9BNLPRS1",
"Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -171,12 +171,12 @@
}
},
{
- "@id": "urn:3ebb9f9c-0f46-4208-9d6b-8e296d89ad87",
+ "@id": "urn:smooth10-XN1Ey3dn",
"Label": "Smooth",
"Used": [
- "urn:768bdff7-fc79-48ed-b4be-76ffa67c22a7"
+ "urn:uuid:5d723e97-e2b2-4a28-9d61-3d89050ad61f"
],
- "AssociatedWith": "urn:a1419230-2b3e-4817-b640-05d85bd9dcd1",
+ "AssociatedWith": "urn:spm-9BNLPRS1",
"Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
"Parameters": {
"fwhm": "[6, 6, 6]",
@@ -186,14 +186,14 @@
}
},
{
- "@id": "urn:bfcf713f-14cd-4468-8f5c-7cf48df3c5b4",
+ "@id": "urn:statdesi-0RyEu7cy",
"Label": "Stat Design",
"Used": [
- "urn:03dc0426-616f-474d-baa7-d076a27da8f9",
- "urn:0a875af3-87ed-447a-b565-fb7896612717"
+ "urn:uuid:85cbe84d-fbf4-4366-825d-54931c139b4d",
+ "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
],
- "AssociatedWith": "urn:a1419230-2b3e-4817-b640-05d85bd9dcd1",
- "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_contrast_mask'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
+ "AssociatedWith": "urn:spm-9BNLPRS1",
+ "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_contrast_mask'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
"Parameters": {
"dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_contrast_mask'}",
"timing.units": "'secs'",
@@ -214,12 +214,12 @@
}
},
{
- "@id": "urn:682174ce-71d8-497c-a179-f0b800788bb7",
+ "@id": "urn:estimate-oi0j6pNf",
"Label": "Estimate stat.",
"Used": [
- "urn:efedbec8-04bc-46cb-b396-0ba5ad3d910a"
+ "urn:uuid:abafb5fa-fa32-4591-9115-a717462f2ce5"
],
- "AssociatedWith": "urn:a1419230-2b3e-4817-b640-05d85bd9dcd1",
+ "AssociatedWith": "urn:spm-9BNLPRS1",
"Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
"Parameters": {
"write_residuals": "0",
@@ -227,12 +227,12 @@
}
},
{
- "@id": "urn:0a6fbff3-07bf-42fa-a99d-6fafd73ac089",
+ "@id": "urn:estimate-ir88jhgN",
"Label": "Estimate contrast",
"Used": [
- "urn:5fc905ed-edca-44b6-ae43-65c143fb6ce5"
+ "urn:uuid:ca9dcba3-debf-4891-b190-d312089278da"
],
- "AssociatedWith": "urn:a1419230-2b3e-4817-b640-05d85bd9dcd1",
+ "AssociatedWith": "urn:spm-9BNLPRS1",
"Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.name = 'tone counting probe vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.weights = [0 1];\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
"Parameters": {
"consess{1}.tcon.name": "'tone counting vs baseline'",
@@ -245,12 +245,12 @@
}
},
{
- "@id": "urn:fb106cb1-fa61-4956-bd0a-3929d8b94354",
+ "@id": "urn:threshol-L2zqpDyV",
"Label": "Threshold",
"Used": [
- "urn:ca497e60-981f-473b-acd0-38e3b7c2067a"
+ "urn:uuid:fd8fe8cb-966a-49ab-b146-36373fe5be5a"
],
- "AssociatedWith": "urn:a1419230-2b3e-4817-b640-05d85bd9dcd1",
+ "AssociatedWith": "urn:spm-9BNLPRS1",
"Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = 1;\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.contrast.contrasts = 2;\nmatlabbatch{14}.spm.stats.results.conspec.mask.contrast.thresh = 0.05;\nmatlabbatch{14}.spm.stats.results.conspec.mask.contrast.mtype = 0;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.none = 1;",
"Parameters": {
"conspec.titlestr": "''",
@@ -270,98 +270,96 @@
],
"Entities": [
{
- "@id": "urn:881e6701-d5f6-4e1d-8b08-b0f422bfc7f7",
+ "@id": "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+ "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"digest": {
- "sha256": "52cc2a3822512db5be3accc8263f2ac1338f32fad8af63cc81fb5af2f335c509"
+ "sha256": "b3d8382360fbbc58cbd8c9e654ddda30b9f0318cf04ebd7539ec75bd724041d2"
}
},
{
- "@id": "urn:c0771e58-a6ad-4067-a247-994db5d57566",
+ "@id": "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz",
"Label": "anat_sub-01_T1w.nii.gz",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+ "AtLocation": "ds011/sub-01/anat/sub-01_T1w.nii.gz",
"digest": {
- "sha256": "3d9457fa7712b355d6569522ca80a6dfd70a40b82e6aa0a9364513cf04916dbb"
+ "sha256": "70b9327067cc5200330e04e70b22a41db5aa3b78f978060f61f49bd3a45d125e"
}
},
{
- "@id": "urn:0708ea50-1d83-48c9-be2e-3871dfeb2b0a",
+ "@id": "urn:uuid:357f205f-1573-4bc1-8f0e-d94d48788a5d",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "GeneratedBy": "urn:74ad9995-210a-4a09-96c1-021ac291fc78"
+ "GeneratedBy": "urn:movefile-yUJIwuSB"
},
{
- "@id": "urn:eb38131d-32b2-4cbf-9b65-bb40b299df05",
+ "@id": "urn:uuid:6a87cd1a-ea9a-4d7d-b8d4-8dddc1bf2340",
"Label": "anat_sub-01_T1w.nii.gz",
- "GeneratedBy": "urn:2753b48f-12fa-40fc-a095-c4707b8dd571"
+ "GeneratedBy": "urn:movefile-fRoKDI2e"
},
{
- "@id": "urn:52511106-bdb5-436c-8f3f-0c0d2edaa139",
+ "@id": "urn:uuid:9941a786-0a67-439d-8bca-bafc3b34cbc2",
"Label": "func_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:d751aff5-d3ee-485c-be17-647730723212"
+ "GeneratedBy": "urn:gunzip3-ZF0NbJuD"
},
{
- "@id": "urn:930d09a1-32c6-4f83-97de-52e2b4e5dd1e",
+ "@id": "urn:uuid:78b1081a-34a1-4dce-96f0-89a9f7c53801",
"Label": "meanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:842c7ba0-0064-4d8d-8f99-6361ff2599d4"
+ "GeneratedBy": "urn:realign5-ud5VE1Gu"
},
{
- "@id": "urn:c2684b63-598f-4f5e-b259-31d0868f9fbd",
+ "@id": "urn:uuid:07dfde62-9084-4f4d-b991-e3c8be405785",
"Label": "anat_sub-01_T1w.nii",
- "GeneratedBy": "urn:c3f9594d-ed7f-4c6d-b18c-c38b41dafd7f"
+ "GeneratedBy": "urn:gunzip4-7VNZFWp2"
},
{
- "@id": "urn:9c0f5dac-fd86-459b-b326-320b070d354c",
+ "@id": "bids::c1anat_sub-01_T1w.nii",
"Label": "segment1",
- "Atlocation": "c1xxx.nii.gz",
- "GeneratedBy": "urn:5c7cbc9b-48c8-44b8-8f20-4487d457e76b",
"AtLocation": "c1anat_sub-01_T1w.nii",
+ "GeneratedBy": "urn:segment7-8MUq9DK6",
"digest": {
"sha256": "61ca923955d0a5c9088df9e258f41644067ec964e1c9a83284ba03b0515079b0"
}
},
{
- "@id": "urn:ac43406f-3117-41a6-b7af-c087a2a0ab63",
+ "@id": "bids::c2anat_sub-01_T1w.nii",
"Label": "segment2",
- "Atlocation": "c2xxx.nii.gz",
- "GeneratedBy": "urn:5c7cbc9b-48c8-44b8-8f20-4487d457e76b",
"AtLocation": "c2anat_sub-01_T1w.nii",
+ "GeneratedBy": "urn:segment7-8MUq9DK6",
"digest": {
"sha256": "10ad88ebeebebd0bd03ccbdd4df92d500d28d14715fa5375fd35589caddf49a6"
}
},
{
- "@id": "urn:768bdff7-fc79-48ed-b4be-76ffa67c22a7",
- "Label": "wmeanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:ffee68b2-1ae4-4e18-b7c4-8b3ea7e3669d"
+ "@id": "urn:uuid:5d723e97-e2b2-4a28-9d61-3d89050ad61f",
+ "Label": "wsegment1",
+ "GeneratedBy": "urn:normaliz-Rt8gp4xI"
},
{
- "@id": "urn:0a875af3-87ed-447a-b565-fb7896612717",
+ "@id": "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"Label": "ONSETS_sub-01-MultiCond.mat",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+ "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"digest": {
- "sha256": "be4671d4f9dc480dd3e5be19aeeab2756f7afdc3b32d81e071685d7a4eafcfed"
+ "sha256": "5599e80629bb4d66cdbfb357511c04060bd3d37cdbfe2a4cd701a2979e9f6610"
}
},
{
- "@id": "urn:03dc0426-616f-474d-baa7-d076a27da8f9",
- "Label": "swmeanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:3ebb9f9c-0f46-4208-9d6b-8e296d89ad87"
+ "@id": "urn:uuid:85cbe84d-fbf4-4366-825d-54931c139b4d",
+ "Label": "swsegment1",
+ "GeneratedBy": "urn:smooth10-XN1Ey3dn"
},
{
- "@id": "urn:efedbec8-04bc-46cb-b396-0ba5ad3d910a",
+ "@id": "urn:uuid:abafb5fa-fa32-4591-9115-a717462f2ce5",
"Label": "SPM.mat",
- "GeneratedBy": "urn:bfcf713f-14cd-4468-8f5c-7cf48df3c5b4"
+ "GeneratedBy": "urn:statdesi-0RyEu7cy"
},
{
- "@id": "urn:5fc905ed-edca-44b6-ae43-65c143fb6ce5",
+ "@id": "urn:uuid:ca9dcba3-debf-4891-b190-d312089278da",
"Label": "SPM.mat",
- "GeneratedBy": "urn:682174ce-71d8-497c-a179-f0b800788bb7"
+ "GeneratedBy": "urn:estimate-oi0j6pNf"
},
{
- "@id": "urn:ca497e60-981f-473b-acd0-38e3b7c2067a",
+ "@id": "urn:uuid:fd8fe8cb-966a-49ab-b146-36373fe5be5a",
"Label": "SPM.mat",
- "GeneratedBy": "urn:0a6fbff3-07bf-42fa-a99d-6fafd73ac089"
+ "GeneratedBy": "urn:estimate-ir88jhgN"
}
]
}
diff --git a/examples/from_parsers/spm/spm_contrast_mask_batch.m b/examples/from_parsers/spm/spm_contrast_mask_batch.m
index 3fe9d515a..e8c932ad7 100644
--- a/examples/from_parsers/spm/spm_contrast_mask_batch.m
+++ b/examples/from_parsers/spm/spm_contrast_mask_batch.m
@@ -3,10 +3,10 @@
% spm SPM - SPM12 (12.1)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------
-matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};
-matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};
-matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};
-matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};
+matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};
+matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};
+matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};
+matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};
matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));
@@ -90,7 +90,7 @@
matlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;
matlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});
-matlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};
+matlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};
matlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});
matlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};
matlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;
diff --git a/examples/from_parsers/spm/spm_contrast_mask_batch.png b/examples/from_parsers/spm/spm_contrast_mask_batch.png
index 719de5523..0827c6b24 100644
Binary files a/examples/from_parsers/spm/spm_contrast_mask_batch.png and b/examples/from_parsers/spm/spm_contrast_mask_batch.png differ
diff --git a/examples/from_parsers/spm/spm_covariate_batch.jsonld b/examples/from_parsers/spm/spm_covariate_batch.jsonld
index 55a06b84a..498a9d62f 100644
--- a/examples/from_parsers/spm/spm_covariate_batch.jsonld
+++ b/examples/from_parsers/spm/spm_covariate_batch.jsonld
@@ -4,34 +4,34 @@
"Records": {
"Software": [
{
- "@id": "urn:77da241f-f67f-473f-b2ba-3e092fcb2693",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:spm-ILFsPa9q",
"@type": "prov:SoftwareAgent",
"Label": "SPM",
- "Version": "SPM12r7224"
+ "Version": "SPM12r7224",
+ "AltIdentifier": "RRID:SCR_007037"
}
],
"Activities": [
{
- "@id": "urn:38ea2ea2-f085-4e72-9a11-8b81a426d4da",
+ "@id": "urn:statsfac-klpMDd74",
"Label": "stats.factorial_design",
"Used": [
- "urn:b7b049f4-fa84-443d-bd23-cd4cbc67b736",
- "urn:69ff2bf5-eb0b-4ec3-b409-c7915a8763fd",
- "urn:e4fff7da-26ea-4221-bc58-8c8d6b7ca84f",
- "urn:1dbc03de-284a-4cbb-834e-9ec6a25791a0",
- "urn:57727fd5-7503-4003-9938-26f02c545627",
- "urn:88774907-0d85-47ff-a700-e37b59c8ffcb",
- "urn:835ac5af-9eea-4ef7-9bdc-ea0fa543a819",
- "urn:ea284690-ee72-45dd-9e8d-4c28ba50d808",
- "urn:9c3526b4-b784-4300-968c-fc5b10e380a8",
- "urn:c4311fc9-ed5b-4d31-b220-b221fcc84cbf",
- "urn:d5916783-9b2c-4299-b00f-0c402f2b5de0",
- "urn:3171bb22-275c-48a9-b96d-e7300d4c194a",
- "urn:d130b0aa-0565-4af9-9055-3f6733ece33d"
+ "bids:ds000052:/derivatives/RESULTS/Sub01/con_0001.nii",
+ "bids:ds000052:/derivatives/RESULTS/Sub02/con_0001.nii",
+ "bids:ds000052:/derivatives/RESULTS/Sub03/con_0001.nii",
+ "bids:ds000052:/derivatives/RESULTS/Sub04/con_0001.nii",
+ "bids:ds000052:/derivatives/RESULTS/Sub05/con_0001.nii",
+ "bids:ds000052:/derivatives/RESULTS/Sub06/con_0001.nii",
+ "bids:ds000052:/derivatives/RESULTS/Sub07/con_0001.nii",
+ "bids:ds000052:/derivatives/RESULTS/Sub08/con_0001.nii",
+ "bids:ds000052:/derivatives/RESULTS/Sub09/con_0001.nii",
+ "bids:ds000052:/derivatives/RESULTS/Sub10/con_0001.nii",
+ "bids:ds000052:/derivatives/RESULTS/Sub11/con_0001.nii",
+ "bids:ds000052:/derivatives/RESULTS/Sub12/con_0001.nii",
+ "bids:ds000052:/derivatives/RESULTS/Sub13/con_0001.nii"
],
- "AssociatedWith": "urn:77da241f-f67f-473f-b2ba-3e092fcb2693",
- "Command": "matlabbatch{1}.spm.stats.factorial_design.dir = {'/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Group/Con1/Covariate'};\nmatlabbatch{1}.spm.stats.factorial_design.des.t1.scans = {'/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub01/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub02/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub03/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub04/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub05/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub06/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub07/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub08/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub09/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub10/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub11/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub12/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub13/con_0001.nii,1',};\nmatlabbatch{1}.spm.stats.factorial_design.cov.c = [1 2 3 4 5 6 7 8 9 10 11 12 13];\nmatlabbatch{1}.spm.stats.factorial_design.cov.cname = 'Subject ID Covariate';\nmatlabbatch{1}.spm.stats.factorial_design.cov.iCFI = 1;\nmatlabbatch{1}.spm.stats.factorial_design.cov.iCC = 1;\nmatlabbatch{1}.spm.stats.factorial_design.multi_cov = struct('files', {}, 'iCFI', {}, 'iCC', {});\nmatlabbatch{1}.spm.stats.factorial_design.masking.tm.tm_none = 1;\nmatlabbatch{1}.spm.stats.factorial_design.masking.im = 1;\nmatlabbatch{1}.spm.stats.factorial_design.masking.em = {''};\nmatlabbatch{1}.spm.stats.factorial_design.globalc.g_omit = 1;\nmatlabbatch{1}.spm.stats.factorial_design.globalm.gmsca.gmsca_no = 1;\nmatlabbatch{1}.spm.stats.factorial_design.globalm.glonorm = 1;",
+ "AssociatedWith": "urn:spm-ILFsPa9q",
+ "Command": "matlabbatch{1}.spm.stats.factorial_design.dir = {'/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Group/Con1/Covariate'};\nmatlabbatch{1}.spm.stats.factorial_design.des.t1.scans = {'ds000052/derivatives/RESULTS/Sub01/con_0001.nii,1','ds000052/derivatives/RESULTS/Sub02/con_0001.nii,1','ds000052/derivatives/RESULTS/Sub03/con_0001.nii,1','ds000052/derivatives/RESULTS/Sub04/con_0001.nii,1','ds000052/derivatives/RESULTS/Sub05/con_0001.nii,1','ds000052/derivatives/RESULTS/Sub06/con_0001.nii,1','ds000052/derivatives/RESULTS/Sub07/con_0001.nii,1','ds000052/derivatives/RESULTS/Sub08/con_0001.nii,1','ds000052/derivatives/RESULTS/Sub09/con_0001.nii,1','ds000052/derivatives/RESULTS/Sub10/con_0001.nii,1','ds000052/derivatives/RESULTS/Sub11/con_0001.nii,1','ds000052/derivatives/RESULTS/Sub12/con_0001.nii,1','ds000052/derivatives/RESULTS/Sub13/con_0001.nii,1',};\nmatlabbatch{1}.spm.stats.factorial_design.cov.c = [1 2 3 4 5 6 7 8 9 10 11 12 13];\nmatlabbatch{1}.spm.stats.factorial_design.cov.cname = 'Subject ID Covariate';\nmatlabbatch{1}.spm.stats.factorial_design.cov.iCFI = 1;\nmatlabbatch{1}.spm.stats.factorial_design.cov.iCC = 1;\nmatlabbatch{1}.spm.stats.factorial_design.multi_cov = struct('files', {}, 'iCFI', {}, 'iCC', {});\nmatlabbatch{1}.spm.stats.factorial_design.masking.tm.tm_none = 1;\nmatlabbatch{1}.spm.stats.factorial_design.masking.im = 1;\nmatlabbatch{1}.spm.stats.factorial_design.masking.em = {''};\nmatlabbatch{1}.spm.stats.factorial_design.globalc.g_omit = 1;\nmatlabbatch{1}.spm.stats.factorial_design.globalm.gmsca.gmsca_no = 1;\nmatlabbatch{1}.spm.stats.factorial_design.globalm.glonorm = 1;",
"Parameters": {
"dir": "{'/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Group/Con1/Covariate'}",
"cov.c": "[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13]",
@@ -48,12 +48,12 @@
}
},
{
- "@id": "urn:9365d298-c58e-4d85-89eb-b035a0a2db37",
+ "@id": "urn:estimate-1w72t2Pw",
"Label": "Estimate stat.",
"Used": [
- "urn:c00db8db-eb32-474f-9295-5d4577ab7c7d"
+ "urn:uuid:cfc80838-d9ff-4793-ac2c-e0a0851ad593"
],
- "AssociatedWith": "urn:77da241f-f67f-473f-b2ba-3e092fcb2693",
+ "AssociatedWith": "urn:spm-ILFsPa9q",
"Command": "matlabbatch{2}.spm.stats.fmri_est.spmmat(1) = cfg_dep('Factorial design specification: SPM.mat File', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{2}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{2}.spm.stats.fmri_est.method.Classical = 1;",
"Parameters": {
"write_residuals": "0",
@@ -61,12 +61,12 @@
}
},
{
- "@id": "urn:2be6debc-12a1-4190-9b50-9aa4d972bc30",
+ "@id": "urn:estimate-oPD2ORTX",
"Label": "Estimate contrast",
"Used": [
- "urn:b1993396-80d7-421e-9034-9c4e853fc3af"
+ "urn:uuid:9e95a934-5b6d-4d9c-a449-95270860b977"
],
- "AssociatedWith": "urn:77da241f-f67f-473f-b2ba-3e092fcb2693",
+ "AssociatedWith": "urn:spm-ILFsPa9q",
"Command": "matlabbatch{3}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{3}.spm.stats.con.consess{1}.tcon.name = 'mr vs plain covariate';\nmatlabbatch{3}.spm.stats.con.consess{1}.tcon.weights = 1;\nmatlabbatch{3}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{3}.spm.stats.con.delete = 0;",
"Parameters": {
"consess{1}.tcon.name": "'mr vs plain covariate'",
@@ -76,12 +76,12 @@
}
},
{
- "@id": "urn:e3c78c58-4927-4458-b6a5-a0f7b70e3051",
+ "@id": "urn:threshol-tg0hxfC6",
"Label": "Threshold",
"Used": [
- "urn:64aaaf3b-4f76-4f27-a079-b66006c759b1"
+ "urn:uuid:5e027a17-5b75-42a3-b146-0daadab5e6fe"
],
- "AssociatedWith": "urn:77da241f-f67f-473f-b2ba-3e092fcb2693",
+ "AssociatedWith": "urn:spm-ILFsPa9q",
"Command": "matlabbatch{4}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{4}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{4}.spm.stats.results.conspec.contrasts = 1;\nmatlabbatch{4}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{4}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{4}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{4}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{4}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{4}.spm.stats.results.units = 1;\nmatlabbatch{4}.spm.stats.results.print = 'pdf';\nmatlabbatch{4}.spm.stats.results.write.none = 1;",
"Parameters": {
"conspec.titlestr": "''",
@@ -99,123 +99,123 @@
],
"Entities": [
{
- "@id": "urn:b7b049f4-fa84-443d-bd23-cd4cbc67b736",
+ "@id": "bids:ds000052:/derivatives/RESULTS/Sub01/con_0001.nii",
"Label": "Sub01_con_0001.nii",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub01/con_0001.nii",
+ "AtLocation": "ds000052/derivatives/RESULTS/Sub01/con_0001.nii",
"digest": {
- "sha256": "704577900564ed2e3e736d470b01bad03b83022cf231d8378a167ec7348905f1"
+ "sha256": "c14419840edfdea555406b52849de36be2f7230b0877b056b9101011cbf1fd7d"
}
},
{
- "@id": "urn:69ff2bf5-eb0b-4ec3-b409-c7915a8763fd",
+ "@id": "bids:ds000052:/derivatives/RESULTS/Sub02/con_0001.nii",
"Label": "Sub02_con_0001.nii",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub02/con_0001.nii",
+ "AtLocation": "ds000052/derivatives/RESULTS/Sub02/con_0001.nii",
"digest": {
- "sha256": "14babae7ee4ec3b0900aba762fbacb79528cfa00d1a7bcd26b71136e15ddbb61"
+ "sha256": "741bcd68a30e79ea65ea38035ab841c67bc108e65ffc4c3b93ac9d8d1363e8d3"
}
},
{
- "@id": "urn:e4fff7da-26ea-4221-bc58-8c8d6b7ca84f",
+ "@id": "bids:ds000052:/derivatives/RESULTS/Sub03/con_0001.nii",
"Label": "Sub03_con_0001.nii",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub03/con_0001.nii",
+ "AtLocation": "ds000052/derivatives/RESULTS/Sub03/con_0001.nii",
"digest": {
- "sha256": "714d199baaa9dfa41cf5c4ca0f9a776f3267ae67035bb2ce47280233c4f27605"
+ "sha256": "25040c6d252b447614a368ac2af1ac90abd612f050039700d7aa9a7dff0794e3"
}
},
{
- "@id": "urn:1dbc03de-284a-4cbb-834e-9ec6a25791a0",
+ "@id": "bids:ds000052:/derivatives/RESULTS/Sub04/con_0001.nii",
"Label": "Sub04_con_0001.nii",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub04/con_0001.nii",
+ "AtLocation": "ds000052/derivatives/RESULTS/Sub04/con_0001.nii",
"digest": {
- "sha256": "40d17679357316a794c6022e01bb3961d089c91ef7d3bc1758e36dad76d3d8ca"
+ "sha256": "21d270ed11f33895cc0aa0181f443872c11d8c2cc336386c6bcc35c6eadf3c21"
}
},
{
- "@id": "urn:57727fd5-7503-4003-9938-26f02c545627",
+ "@id": "bids:ds000052:/derivatives/RESULTS/Sub05/con_0001.nii",
"Label": "Sub05_con_0001.nii",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub05/con_0001.nii",
+ "AtLocation": "ds000052/derivatives/RESULTS/Sub05/con_0001.nii",
"digest": {
- "sha256": "e19f465c6715be288733d5a058f5d77ddf860988c4ddc0fbe4ca8e1b998c367e"
+ "sha256": "95a6e92d930cd24b203e3923df7413f928bc6036d1c1ecffca52c879de159a65"
}
},
{
- "@id": "urn:88774907-0d85-47ff-a700-e37b59c8ffcb",
+ "@id": "bids:ds000052:/derivatives/RESULTS/Sub06/con_0001.nii",
"Label": "Sub06_con_0001.nii",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub06/con_0001.nii",
+ "AtLocation": "ds000052/derivatives/RESULTS/Sub06/con_0001.nii",
"digest": {
- "sha256": "8871fd17416dd4fa6d4fc1eaec9f9de8ecc4881ab3a717248bdcbeab339f62ea"
+ "sha256": "d624963f2c71c041a275bc88536e89234ddbe0becba129fedc32e3256abab7bd"
}
},
{
- "@id": "urn:835ac5af-9eea-4ef7-9bdc-ea0fa543a819",
+ "@id": "bids:ds000052:/derivatives/RESULTS/Sub07/con_0001.nii",
"Label": "Sub07_con_0001.nii",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub07/con_0001.nii",
+ "AtLocation": "ds000052/derivatives/RESULTS/Sub07/con_0001.nii",
"digest": {
- "sha256": "26bea69994f70bb534f943c181a9e29285a4847588c3b37b078390c517148ce7"
+ "sha256": "369e1c91a65a2b54ed8bc6285d2473e56b490cb5595022ac9a221882b2167ee2"
}
},
{
- "@id": "urn:ea284690-ee72-45dd-9e8d-4c28ba50d808",
+ "@id": "bids:ds000052:/derivatives/RESULTS/Sub08/con_0001.nii",
"Label": "Sub08_con_0001.nii",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub08/con_0001.nii",
+ "AtLocation": "ds000052/derivatives/RESULTS/Sub08/con_0001.nii",
"digest": {
- "sha256": "607ec837ad2ac763888312643b9a26dac34935f3877640166953d1d39b11f7d4"
+ "sha256": "6c196ea2d482a350cb343d20e601fc50fb8d153e11d970bbb242aa13c39e7cce"
}
},
{
- "@id": "urn:9c3526b4-b784-4300-968c-fc5b10e380a8",
+ "@id": "bids:ds000052:/derivatives/RESULTS/Sub09/con_0001.nii",
"Label": "Sub09_con_0001.nii",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub09/con_0001.nii",
+ "AtLocation": "ds000052/derivatives/RESULTS/Sub09/con_0001.nii",
"digest": {
- "sha256": "1dfee1d8dd34377d9c9647574c17ca67f958dab99ddbee7c2fda1ad8514f135f"
+ "sha256": "6a93a12c6d89080af5ea69ec7a3078e843def7269ed4d4cf776ccc7d080f8cfe"
}
},
{
- "@id": "urn:c4311fc9-ed5b-4d31-b220-b221fcc84cbf",
+ "@id": "bids:ds000052:/derivatives/RESULTS/Sub10/con_0001.nii",
"Label": "Sub10_con_0001.nii",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub10/con_0001.nii",
+ "AtLocation": "ds000052/derivatives/RESULTS/Sub10/con_0001.nii",
"digest": {
- "sha256": "93177653f7acb26a20a92f6df631b9ffdc119e8e40ecc9247e276439e27574b2"
+ "sha256": "f923f8151fdf7119e5cb426a935cae7f1aa1582822fb07a865364c3bba02e3c9"
}
},
{
- "@id": "urn:d5916783-9b2c-4299-b00f-0c402f2b5de0",
+ "@id": "bids:ds000052:/derivatives/RESULTS/Sub11/con_0001.nii",
"Label": "Sub11_con_0001.nii",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub11/con_0001.nii",
+ "AtLocation": "ds000052/derivatives/RESULTS/Sub11/con_0001.nii",
"digest": {
- "sha256": "e2431595e2d7c4cf169ad2f2c4af36e864cbf4ff096cea38de561563e18d54f6"
+ "sha256": "e076877ebd2146a298d0380ddbe45580171fc71cfa94eb8ac337118ccef3bbff"
}
},
{
- "@id": "urn:3171bb22-275c-48a9-b96d-e7300d4c194a",
+ "@id": "bids:ds000052:/derivatives/RESULTS/Sub12/con_0001.nii",
"Label": "Sub12_con_0001.nii",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub12/con_0001.nii",
+ "AtLocation": "ds000052/derivatives/RESULTS/Sub12/con_0001.nii",
"digest": {
- "sha256": "fb18a6c85cf95c02a096c6c5f6d2711e9615b62f181ca3a8d166ccf2712a9d62"
+ "sha256": "cc40406387b7b11378733abac384fbfc2193ba48f8bab85290cc1cbb3aabfd27"
}
},
{
- "@id": "urn:d130b0aa-0565-4af9-9055-3f6733ece33d",
+ "@id": "bids:ds000052:/derivatives/RESULTS/Sub13/con_0001.nii",
"Label": "Sub13_con_0001.nii",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub13/con_0001.nii",
+ "AtLocation": "ds000052/derivatives/RESULTS/Sub13/con_0001.nii",
"digest": {
- "sha256": "cc87406762aa344c9da8d218226464f61a05c1486aa7b9ad0708de27a8ee879d"
+ "sha256": "16c2d63a3e674532436f5e263ee7da006d79483fa114a4a6f1cfc31c56d8cda9"
}
},
{
- "@id": "urn:c00db8db-eb32-474f-9295-5d4577ab7c7d",
+ "@id": "urn:uuid:cfc80838-d9ff-4793-ac2c-e0a0851ad593",
"Label": "SPM.mat",
- "GeneratedBy": "urn:38ea2ea2-f085-4e72-9a11-8b81a426d4da"
+ "GeneratedBy": "urn:statsfac-klpMDd74"
},
{
- "@id": "urn:b1993396-80d7-421e-9034-9c4e853fc3af",
+ "@id": "urn:uuid:9e95a934-5b6d-4d9c-a449-95270860b977",
"Label": "SPM.mat",
- "GeneratedBy": "urn:9365d298-c58e-4d85-89eb-b035a0a2db37"
+ "GeneratedBy": "urn:estimate-1w72t2Pw"
},
{
- "@id": "urn:64aaaf3b-4f76-4f27-a079-b66006c759b1",
+ "@id": "urn:uuid:5e027a17-5b75-42a3-b146-0daadab5e6fe",
"Label": "SPM.mat",
- "GeneratedBy": "urn:2be6debc-12a1-4190-9b50-9aa4d972bc30"
+ "GeneratedBy": "urn:estimate-oPD2ORTX"
}
]
}
diff --git a/examples/from_parsers/spm/spm_covariate_batch.m b/examples/from_parsers/spm/spm_covariate_batch.m
index 6e9afdf66..931871f93 100644
--- a/examples/from_parsers/spm/spm_covariate_batch.m
+++ b/examples/from_parsers/spm/spm_covariate_batch.m
@@ -6,19 +6,19 @@
matlabbatch{1}.spm.stats.factorial_design.dir = {'/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Group/Con1/Covariate'};
%%
matlabbatch{1}.spm.stats.factorial_design.des.t1.scans = {
- '/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub01/con_0001.nii,1'
- '/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub02/con_0001.nii,1'
- '/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub03/con_0001.nii,1'
- '/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub04/con_0001.nii,1'
- '/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub05/con_0001.nii,1'
- '/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub06/con_0001.nii,1'
- '/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub07/con_0001.nii,1'
- '/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub08/con_0001.nii,1'
- '/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub09/con_0001.nii,1'
- '/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub10/con_0001.nii,1'
- '/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub11/con_0001.nii,1'
- '/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub12/con_0001.nii,1'
- '/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub13/con_0001.nii,1'
+ 'ds000052/derivatives/RESULTS/Sub01/con_0001.nii,1'
+ 'ds000052/derivatives/RESULTS/Sub02/con_0001.nii,1'
+ 'ds000052/derivatives/RESULTS/Sub03/con_0001.nii,1'
+ 'ds000052/derivatives/RESULTS/Sub04/con_0001.nii,1'
+ 'ds000052/derivatives/RESULTS/Sub05/con_0001.nii,1'
+ 'ds000052/derivatives/RESULTS/Sub06/con_0001.nii,1'
+ 'ds000052/derivatives/RESULTS/Sub07/con_0001.nii,1'
+ 'ds000052/derivatives/RESULTS/Sub08/con_0001.nii,1'
+ 'ds000052/derivatives/RESULTS/Sub09/con_0001.nii,1'
+ 'ds000052/derivatives/RESULTS/Sub10/con_0001.nii,1'
+ 'ds000052/derivatives/RESULTS/Sub11/con_0001.nii,1'
+ 'ds000052/derivatives/RESULTS/Sub12/con_0001.nii,1'
+ 'ds000052/derivatives/RESULTS/Sub13/con_0001.nii,1'
};
%%
%%
diff --git a/examples/from_parsers/spm/spm_covariate_batch.png b/examples/from_parsers/spm/spm_covariate_batch.png
index d83cf39c5..401717dc0 100644
Binary files a/examples/from_parsers/spm/spm_covariate_batch.png and b/examples/from_parsers/spm/spm_covariate_batch.png differ
diff --git a/examples/from_parsers/spm/spm_default_batch.jsonld b/examples/from_parsers/spm/spm_default_batch.jsonld
index abb8c71fc..05ae3dd7b 100644
--- a/examples/from_parsers/spm/spm_default_batch.jsonld
+++ b/examples/from_parsers/spm/spm_default_batch.jsonld
@@ -4,63 +4,63 @@
"Records": {
"Software": [
{
- "@id": "urn:73c58698-91b1-4c9c-acbe-4e8dfa0baf93",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:spm-gmrVZH0W",
"@type": "prov:SoftwareAgent",
"Label": "SPM",
- "Version": "SPM12r7224"
+ "Version": "SPM12r7224",
+ "AltIdentifier": "RRID:SCR_007037"
}
],
"Activities": [
{
- "@id": "urn:deaf5c0e-1599-499f-bb03-f61d26803be5",
+ "@id": "urn:movefile-R2ejLXJG",
"Label": "Move file",
"Used": [
- "urn:9c0f6952-8770-4a4e-b180-052debb7b271"
+ "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
],
- "AssociatedWith": "urn:73c58698-91b1-4c9c-acbe-4e8dfa0baf93",
- "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
+ "AssociatedWith": "urn:spm-gmrVZH0W",
+ "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};",
"Parameters": {
- "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
+ "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'}"
}
},
{
- "@id": "urn:e87352cf-8f22-4cbb-8087-9676bac3f385",
+ "@id": "urn:movefile-hivUZu8r",
"Label": "Move file",
"Used": [
- "urn:f2a0c67e-543e-4a43-b76e-6537953e1d33"
+ "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz"
],
- "AssociatedWith": "urn:73c58698-91b1-4c9c-acbe-4e8dfa0baf93",
- "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
+ "AssociatedWith": "urn:spm-gmrVZH0W",
+ "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};",
"Parameters": {
- "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
+ "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'}"
}
},
{
- "@id": "urn:c3352e3a-ea37-483e-b2b1-280dca36a952",
+ "@id": "urn:gunzip3-g2tm7TGy",
"Label": "Gunzip",
"Used": [
- "urn:2eab2af1-766c-40ab-bc73-07fe63cd5afa"
+ "urn:uuid:8bc92dcc-ff1e-49c3-9d0f-0ca7a0978c4c"
],
- "AssociatedWith": "urn:73c58698-91b1-4c9c-acbe-4e8dfa0baf93",
+ "AssociatedWith": "urn:spm-gmrVZH0W",
"Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:d6280dcc-b014-4407-947d-5ba6e9264918",
+ "@id": "urn:gunzip4-CspxFW4L",
"Label": "Gunzip",
"Used": [
- "urn:4c2f5457-5e29-4350-a2e1-dac8ecfa35c9"
+ "urn:uuid:2022f810-7796-4926-b5ef-b6351613bf09"
],
- "AssociatedWith": "urn:73c58698-91b1-4c9c-acbe-4e8dfa0baf93",
+ "AssociatedWith": "urn:spm-gmrVZH0W",
"Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:91fa6de6-3f29-454c-844f-7ac0acea8093",
+ "@id": "urn:realign5-0lmvZ8J2",
"Label": "Realign",
"Used": [
- "urn:eea4fd33-05eb-45c5-b022-11c629c9ab6f"
+ "urn:uuid:833d4a70-af77-4275-9995-28633331ce6f"
],
- "AssociatedWith": "urn:73c58698-91b1-4c9c-acbe-4e8dfa0baf93",
+ "AssociatedWith": "urn:spm-gmrVZH0W",
"Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
"Parameters": {
"eoptions.quality": "0.9",
@@ -78,13 +78,13 @@
}
},
{
- "@id": "urn:01ea16dd-67a3-468a-a252-b8a86d38be4a",
+ "@id": "urn:coregist-uVmVbkCL",
"Label": "Coregister",
"Used": [
- "urn:3dea5b32-a6d3-4561-93c2-9c2bd9440596",
- "urn:f5ed89fb-1c45-403f-bc50-15b764964175"
+ "urn:uuid:98ed04e6-b64d-4072-ac94-72573b9239f7",
+ "urn:uuid:ffaf2426-c9c9-461a-8c0b-e7090b56835b"
],
- "AssociatedWith": "urn:73c58698-91b1-4c9c-acbe-4e8dfa0baf93",
+ "AssociatedWith": "urn:spm-gmrVZH0W",
"Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
"Parameters": {
"other": "{''}",
@@ -95,12 +95,12 @@
}
},
{
- "@id": "urn:7bcd13f8-15cf-4d96-ad31-3adc7d5d4ac5",
+ "@id": "urn:segment7-OSxYXQ3N",
"Label": "Segment",
"Used": [
- "urn:f5ed89fb-1c45-403f-bc50-15b764964175"
+ "urn:uuid:98ed04e6-b64d-4072-ac94-72573b9239f7"
],
- "AssociatedWith": "urn:73c58698-91b1-4c9c-acbe-4e8dfa0baf93",
+ "AssociatedWith": "urn:spm-gmrVZH0W",
"Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
"Parameters": {
"channel.biasreg": "0.001",
@@ -140,13 +140,13 @@
}
},
{
- "@id": "urn:7fe0ba44-96f1-4d1e-8b14-7bb758f60575",
+ "@id": "urn:normaliz-UQldWGr6",
"Label": "Normalize",
"Used": [
- "urn:3dea5b32-a6d3-4561-93c2-9c2bd9440596",
- "urn:c942e5a2-3cba-4471-9a8d-83cfb7806b93"
+ "bids::c1anat_sub-01_T1w.nii",
+ "urn:uuid:ffaf2426-c9c9-461a-8c0b-e7090b56835b"
],
- "AssociatedWith": "urn:73c58698-91b1-4c9c-acbe-4e8dfa0baf93",
+ "AssociatedWith": "urn:spm-gmrVZH0W",
"Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -156,12 +156,12 @@
}
},
{
- "@id": "urn:46953106-4e01-4407-a4a6-3f757a89965b",
+ "@id": "urn:normaliz-cSR3dWyW",
"Label": "Normalize",
"Used": [
- "urn:c942e5a2-3cba-4471-9a8d-83cfb7806b93"
+ "bids::c1anat_sub-01_T1w.nii"
],
- "AssociatedWith": "urn:73c58698-91b1-4c9c-acbe-4e8dfa0baf93",
+ "AssociatedWith": "urn:spm-gmrVZH0W",
"Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -171,12 +171,12 @@
}
},
{
- "@id": "urn:42fd9295-622f-45a3-989a-5d0236370afe",
+ "@id": "urn:smooth10-64HVOnIl",
"Label": "Smooth",
"Used": [
- "urn:fb54cd87-4126-4543-872f-309d9543ac84"
+ "urn:uuid:c664b813-5420-42eb-a5a5-9c05ab5f4e95"
],
- "AssociatedWith": "urn:73c58698-91b1-4c9c-acbe-4e8dfa0baf93",
+ "AssociatedWith": "urn:spm-gmrVZH0W",
"Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
"Parameters": {
"fwhm": "[6, 6, 6]",
@@ -186,14 +186,14 @@
}
},
{
- "@id": "urn:a7f4c949-e33a-47c0-936e-17a33bbe797b",
+ "@id": "urn:statdesi-5uR8fASG",
"Label": "Stat Design",
"Used": [
- "urn:0ff95592-e05d-4465-84d2-4755ce6e3121",
- "urn:c0f665e7-d7b3-4212-9491-a22e6c058bb0"
+ "urn:uuid:6749b2cb-16d7-4e8d-a0e9-5e7af5c41a66",
+ "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
],
- "AssociatedWith": "urn:73c58698-91b1-4c9c-acbe-4e8dfa0baf93",
- "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_voxelwise_p0001'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
+ "AssociatedWith": "urn:spm-gmrVZH0W",
+ "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_voxelwise_p0001'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
"Parameters": {
"dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_voxelwise_p0001'}",
"timing.units": "'secs'",
@@ -214,12 +214,12 @@
}
},
{
- "@id": "urn:3db3351e-810d-4ab8-beca-d7de5a696f13",
+ "@id": "urn:estimate-Cd8b72px",
"Label": "Estimate stat.",
"Used": [
- "urn:8c8d4609-f20f-49da-ac41-b1fdfab6067c"
+ "urn:uuid:8d6e09be-e06d-49d2-9490-3303a4ae36e9"
],
- "AssociatedWith": "urn:73c58698-91b1-4c9c-acbe-4e8dfa0baf93",
+ "AssociatedWith": "urn:spm-gmrVZH0W",
"Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
"Parameters": {
"write_residuals": "0",
@@ -227,12 +227,12 @@
}
},
{
- "@id": "urn:1b733724-c865-41c8-a4b3-89ec4e7bf1b6",
+ "@id": "urn:estimate-8yANFDZg",
"Label": "Estimate contrast",
"Used": [
- "urn:af9b0233-5698-428b-ae17-9346c8c597a3"
+ "urn:uuid:2f3e3ace-ed36-41c6-98e3-ac229e6cece4"
],
- "AssociatedWith": "urn:73c58698-91b1-4c9c-acbe-4e8dfa0baf93",
+ "AssociatedWith": "urn:spm-gmrVZH0W",
"Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
"Parameters": {
"consess{1}.tcon.name": "'tone counting vs baseline'",
@@ -242,12 +242,12 @@
}
},
{
- "@id": "urn:5bed2526-c418-4531-8f5c-210a4c2044b2",
+ "@id": "urn:threshol-JsBJDZmD",
"Label": "Threshold",
"Used": [
- "urn:223988f1-fdfc-4dfa-b192-f52e6e3df12f"
+ "urn:uuid:d3038c12-9d83-4af2-a740-7c83b7ec0161"
],
- "AssociatedWith": "urn:73c58698-91b1-4c9c-acbe-4e8dfa0baf93",
+ "AssociatedWith": "urn:spm-gmrVZH0W",
"Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.tspm.basename = 'thresh';",
"Parameters": {
"conspec.titlestr": "''",
@@ -265,98 +265,96 @@
],
"Entities": [
{
- "@id": "urn:9c0f6952-8770-4a4e-b180-052debb7b271",
+ "@id": "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+ "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"digest": {
- "sha256": "52cc2a3822512db5be3accc8263f2ac1338f32fad8af63cc81fb5af2f335c509"
+ "sha256": "b3d8382360fbbc58cbd8c9e654ddda30b9f0318cf04ebd7539ec75bd724041d2"
}
},
{
- "@id": "urn:f2a0c67e-543e-4a43-b76e-6537953e1d33",
+ "@id": "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz",
"Label": "anat_sub-01_T1w.nii.gz",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+ "AtLocation": "ds011/sub-01/anat/sub-01_T1w.nii.gz",
"digest": {
- "sha256": "3d9457fa7712b355d6569522ca80a6dfd70a40b82e6aa0a9364513cf04916dbb"
+ "sha256": "70b9327067cc5200330e04e70b22a41db5aa3b78f978060f61f49bd3a45d125e"
}
},
{
- "@id": "urn:2eab2af1-766c-40ab-bc73-07fe63cd5afa",
+ "@id": "urn:uuid:8bc92dcc-ff1e-49c3-9d0f-0ca7a0978c4c",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "GeneratedBy": "urn:deaf5c0e-1599-499f-bb03-f61d26803be5"
+ "GeneratedBy": "urn:movefile-R2ejLXJG"
},
{
- "@id": "urn:4c2f5457-5e29-4350-a2e1-dac8ecfa35c9",
+ "@id": "urn:uuid:2022f810-7796-4926-b5ef-b6351613bf09",
"Label": "anat_sub-01_T1w.nii.gz",
- "GeneratedBy": "urn:e87352cf-8f22-4cbb-8087-9676bac3f385"
+ "GeneratedBy": "urn:movefile-hivUZu8r"
},
{
- "@id": "urn:eea4fd33-05eb-45c5-b022-11c629c9ab6f",
+ "@id": "urn:uuid:833d4a70-af77-4275-9995-28633331ce6f",
"Label": "func_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:c3352e3a-ea37-483e-b2b1-280dca36a952"
+ "GeneratedBy": "urn:gunzip3-g2tm7TGy"
},
{
- "@id": "urn:3dea5b32-a6d3-4561-93c2-9c2bd9440596",
+ "@id": "urn:uuid:ffaf2426-c9c9-461a-8c0b-e7090b56835b",
"Label": "meanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:91fa6de6-3f29-454c-844f-7ac0acea8093"
+ "GeneratedBy": "urn:realign5-0lmvZ8J2"
},
{
- "@id": "urn:f5ed89fb-1c45-403f-bc50-15b764964175",
+ "@id": "urn:uuid:98ed04e6-b64d-4072-ac94-72573b9239f7",
"Label": "anat_sub-01_T1w.nii",
- "GeneratedBy": "urn:d6280dcc-b014-4407-947d-5ba6e9264918"
+ "GeneratedBy": "urn:gunzip4-CspxFW4L"
},
{
- "@id": "urn:c942e5a2-3cba-4471-9a8d-83cfb7806b93",
+ "@id": "bids::c1anat_sub-01_T1w.nii",
"Label": "segment1",
- "Atlocation": "c1xxx.nii.gz",
- "GeneratedBy": "urn:7bcd13f8-15cf-4d96-ad31-3adc7d5d4ac5",
"AtLocation": "c1anat_sub-01_T1w.nii",
+ "GeneratedBy": "urn:segment7-OSxYXQ3N",
"digest": {
"sha256": "61ca923955d0a5c9088df9e258f41644067ec964e1c9a83284ba03b0515079b0"
}
},
{
- "@id": "urn:c1ce2e28-1499-4c87-8b18-6aa1b859c620",
+ "@id": "bids::c2anat_sub-01_T1w.nii",
"Label": "segment2",
- "Atlocation": "c2xxx.nii.gz",
- "GeneratedBy": "urn:7bcd13f8-15cf-4d96-ad31-3adc7d5d4ac5",
"AtLocation": "c2anat_sub-01_T1w.nii",
+ "GeneratedBy": "urn:segment7-OSxYXQ3N",
"digest": {
"sha256": "10ad88ebeebebd0bd03ccbdd4df92d500d28d14715fa5375fd35589caddf49a6"
}
},
{
- "@id": "urn:fb54cd87-4126-4543-872f-309d9543ac84",
- "Label": "wmeanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:7fe0ba44-96f1-4d1e-8b14-7bb758f60575"
+ "@id": "urn:uuid:c664b813-5420-42eb-a5a5-9c05ab5f4e95",
+ "Label": "wsegment1",
+ "GeneratedBy": "urn:normaliz-UQldWGr6"
},
{
- "@id": "urn:c0f665e7-d7b3-4212-9491-a22e6c058bb0",
+ "@id": "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"Label": "ONSETS_sub-01-MultiCond.mat",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+ "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"digest": {
- "sha256": "be4671d4f9dc480dd3e5be19aeeab2756f7afdc3b32d81e071685d7a4eafcfed"
+ "sha256": "5599e80629bb4d66cdbfb357511c04060bd3d37cdbfe2a4cd701a2979e9f6610"
}
},
{
- "@id": "urn:0ff95592-e05d-4465-84d2-4755ce6e3121",
- "Label": "swmeanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:42fd9295-622f-45a3-989a-5d0236370afe"
+ "@id": "urn:uuid:6749b2cb-16d7-4e8d-a0e9-5e7af5c41a66",
+ "Label": "swsegment1",
+ "GeneratedBy": "urn:smooth10-64HVOnIl"
},
{
- "@id": "urn:8c8d4609-f20f-49da-ac41-b1fdfab6067c",
+ "@id": "urn:uuid:8d6e09be-e06d-49d2-9490-3303a4ae36e9",
"Label": "SPM.mat",
- "GeneratedBy": "urn:a7f4c949-e33a-47c0-936e-17a33bbe797b"
+ "GeneratedBy": "urn:statdesi-5uR8fASG"
},
{
- "@id": "urn:af9b0233-5698-428b-ae17-9346c8c597a3",
+ "@id": "urn:uuid:2f3e3ace-ed36-41c6-98e3-ac229e6cece4",
"Label": "SPM.mat",
- "GeneratedBy": "urn:3db3351e-810d-4ab8-beca-d7de5a696f13"
+ "GeneratedBy": "urn:estimate-Cd8b72px"
},
{
- "@id": "urn:223988f1-fdfc-4dfa-b192-f52e6e3df12f",
+ "@id": "urn:uuid:d3038c12-9d83-4af2-a740-7c83b7ec0161",
"Label": "SPM.mat",
- "GeneratedBy": "urn:1b733724-c865-41c8-a4b3-89ec4e7bf1b6"
+ "GeneratedBy": "urn:estimate-8yANFDZg"
}
]
}
diff --git a/examples/from_parsers/spm/spm_default_batch.m b/examples/from_parsers/spm/spm_default_batch.m
index 4b22e99f4..7bb8f7aa8 100644
--- a/examples/from_parsers/spm/spm_default_batch.m
+++ b/examples/from_parsers/spm/spm_default_batch.m
@@ -3,10 +3,10 @@
% spm SPM - SPM12 (12.1)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------
-matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};
-matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};
-matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};
-matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};
+matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};
+matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};
+matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};
+matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};
matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));
@@ -90,7 +90,7 @@
matlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;
matlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});
-matlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};
+matlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};
matlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});
matlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};
matlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;
diff --git a/examples/from_parsers/spm/spm_default_batch.png b/examples/from_parsers/spm/spm_default_batch.png
index e79399e66..89b3288d3 100644
Binary files a/examples/from_parsers/spm/spm_default_batch.png and b/examples/from_parsers/spm/spm_default_batch.png differ
diff --git a/examples/from_parsers/spm/spm_explicit_mask_batch.jsonld b/examples/from_parsers/spm/spm_explicit_mask_batch.jsonld
index 5fd2759e9..2dea16b0a 100644
--- a/examples/from_parsers/spm/spm_explicit_mask_batch.jsonld
+++ b/examples/from_parsers/spm/spm_explicit_mask_batch.jsonld
@@ -4,63 +4,63 @@
"Records": {
"Software": [
{
- "@id": "urn:59a04790-c3a4-41d1-b2eb-268899fbfc53",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:spm-BV9bpoY8",
"@type": "prov:SoftwareAgent",
"Label": "SPM",
- "Version": "SPM12r7224"
+ "Version": "SPM12r7224",
+ "AltIdentifier": "RRID:SCR_007037"
}
],
"Activities": [
{
- "@id": "urn:b7d85a37-7161-4b8b-8d00-a9248190fda3",
+ "@id": "urn:movefile-jGxWpvIe",
"Label": "Move file",
"Used": [
- "urn:2b0afdd2-8abd-4f81-8748-cecd12c9987f"
+ "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
],
- "AssociatedWith": "urn:59a04790-c3a4-41d1-b2eb-268899fbfc53",
- "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
+ "AssociatedWith": "urn:spm-BV9bpoY8",
+ "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};",
"Parameters": {
- "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
+ "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'}"
}
},
{
- "@id": "urn:90f4ce46-a2df-4096-90c7-3df6f3bed73f",
+ "@id": "urn:movefile-YafG4xzl",
"Label": "Move file",
"Used": [
- "urn:c122b76b-49dd-4080-9464-c17425a84159"
+ "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz"
],
- "AssociatedWith": "urn:59a04790-c3a4-41d1-b2eb-268899fbfc53",
- "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
+ "AssociatedWith": "urn:spm-BV9bpoY8",
+ "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};",
"Parameters": {
- "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
+ "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'}"
}
},
{
- "@id": "urn:b3fa8179-1978-4507-901d-c57dcd4f10d4",
+ "@id": "urn:gunzip3-zT2qlwaP",
"Label": "Gunzip",
"Used": [
- "urn:cd65ffe8-9cc1-4916-a8ec-12d359d7c0ad"
+ "urn:uuid:8ba73954-26e1-4ff7-9d9b-66dfabc07097"
],
- "AssociatedWith": "urn:59a04790-c3a4-41d1-b2eb-268899fbfc53",
+ "AssociatedWith": "urn:spm-BV9bpoY8",
"Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:a53f3efb-78d9-4ff0-b2c3-4ac3e36ff6ef",
+ "@id": "urn:gunzip4-bRqp0Ozl",
"Label": "Gunzip",
"Used": [
- "urn:18a72054-7748-48b3-915b-e2258a624a59"
+ "urn:uuid:e7f95829-5ab9-44a6-8ba3-f137c1611a61"
],
- "AssociatedWith": "urn:59a04790-c3a4-41d1-b2eb-268899fbfc53",
+ "AssociatedWith": "urn:spm-BV9bpoY8",
"Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:33f294ce-d765-47e4-b535-f1020bad14d8",
+ "@id": "urn:realign5-mqbIZ2Tp",
"Label": "Realign",
"Used": [
- "urn:ab6f0993-5b04-419b-b373-e7d235e9e740"
+ "urn:uuid:c50bff1d-2d38-4a41-aa74-bfc2d7e430c7"
],
- "AssociatedWith": "urn:59a04790-c3a4-41d1-b2eb-268899fbfc53",
+ "AssociatedWith": "urn:spm-BV9bpoY8",
"Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
"Parameters": {
"eoptions.quality": "0.9",
@@ -78,13 +78,13 @@
}
},
{
- "@id": "urn:2a627ccb-2b5e-4427-8fef-388a1db6a555",
+ "@id": "urn:coregist-kAY0Uc7I",
"Label": "Coregister",
"Used": [
- "urn:487c72a9-6acb-41f0-b6c3-b7ab2043a5b4",
- "urn:f0832953-3f73-48a7-8fe2-1b48270b2cd4"
+ "urn:uuid:52afae0b-ad7e-4658-b27c-4905e2de3984",
+ "urn:uuid:f2617557-abba-4df6-874a-3c010e8fd72a"
],
- "AssociatedWith": "urn:59a04790-c3a4-41d1-b2eb-268899fbfc53",
+ "AssociatedWith": "urn:spm-BV9bpoY8",
"Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
"Parameters": {
"other": "{''}",
@@ -95,12 +95,12 @@
}
},
{
- "@id": "urn:7a17faa4-3ab2-4c80-9222-973582ab9023",
+ "@id": "urn:segment7-ucSpHhHm",
"Label": "Segment",
"Used": [
- "urn:f0832953-3f73-48a7-8fe2-1b48270b2cd4"
+ "urn:uuid:52afae0b-ad7e-4658-b27c-4905e2de3984"
],
- "AssociatedWith": "urn:59a04790-c3a4-41d1-b2eb-268899fbfc53",
+ "AssociatedWith": "urn:spm-BV9bpoY8",
"Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
"Parameters": {
"channel.biasreg": "0.001",
@@ -140,13 +140,13 @@
}
},
{
- "@id": "urn:ce8b87ba-2004-4ada-a824-b801b408e7dd",
+ "@id": "urn:normaliz-C3cRQGpI",
"Label": "Normalize",
"Used": [
- "urn:487c72a9-6acb-41f0-b6c3-b7ab2043a5b4",
- "urn:744a70cd-015b-4826-9ba4-98cdeb78c2f7"
+ "bids::c1anat_sub-01_T1w.nii",
+ "urn:uuid:f2617557-abba-4df6-874a-3c010e8fd72a"
],
- "AssociatedWith": "urn:59a04790-c3a4-41d1-b2eb-268899fbfc53",
+ "AssociatedWith": "urn:spm-BV9bpoY8",
"Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -156,12 +156,12 @@
}
},
{
- "@id": "urn:c096c03f-c432-46db-905d-5012d624a850",
+ "@id": "urn:normaliz-PQInmCre",
"Label": "Normalize",
"Used": [
- "urn:744a70cd-015b-4826-9ba4-98cdeb78c2f7"
+ "bids::c1anat_sub-01_T1w.nii"
],
- "AssociatedWith": "urn:59a04790-c3a4-41d1-b2eb-268899fbfc53",
+ "AssociatedWith": "urn:spm-BV9bpoY8",
"Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -171,12 +171,12 @@
}
},
{
- "@id": "urn:14296cb6-f8ed-4556-a51f-d2fbc11b01b7",
+ "@id": "urn:smooth10-ae0MM1Bg",
"Label": "Smooth",
"Used": [
- "urn:f92855c4-a077-4204-9bfc-18f441b7ad0d"
+ "urn:uuid:74b85b8d-dabe-461a-8437-f651eeb688f1"
],
- "AssociatedWith": "urn:59a04790-c3a4-41d1-b2eb-268899fbfc53",
+ "AssociatedWith": "urn:spm-BV9bpoY8",
"Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
"Parameters": {
"fwhm": "[6, 6, 6]",
@@ -186,15 +186,15 @@
}
},
{
- "@id": "urn:6f7e8239-6b3d-48fd-a94f-62a8a825aee7",
+ "@id": "urn:statdesi-0irxle1q",
"Label": "Stat Design",
"Used": [
- "urn:ee1865c2-68cc-4fd3-8767-5b9488363617",
- "urn:1d965db1-c424-4236-9d86-cd4a7939aad7",
- "urn:e4b557f4-93fa-4d8c-8650-78fd658a67b5"
+ "urn:uuid:bc9496f8-bcf3-4739-b090-4cdefbb34658",
+ "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+ "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_contrast_mask/mask.nii"
],
- "AssociatedWith": "urn:59a04790-c3a4-41d1-b2eb-268899fbfc53",
- "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_explicit_mask'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_contrast_mask/mask.nii,1'};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
+ "AssociatedWith": "urn:spm-BV9bpoY8",
+ "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_explicit_mask'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_contrast_mask/mask.nii,1'};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
"Parameters": {
"dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_explicit_mask'}",
"timing.units": "'secs'",
@@ -214,12 +214,12 @@
}
},
{
- "@id": "urn:2ed3ab6c-8c7d-421f-b06f-a8f6fc205cab",
+ "@id": "urn:estimate-A3hfenJb",
"Label": "Estimate stat.",
"Used": [
- "urn:9f4bb0cf-d032-467e-ba07-b8a64af8e023"
+ "urn:uuid:722ca52b-0e63-4bf3-bf23-c30162249c80"
],
- "AssociatedWith": "urn:59a04790-c3a4-41d1-b2eb-268899fbfc53",
+ "AssociatedWith": "urn:spm-BV9bpoY8",
"Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
"Parameters": {
"write_residuals": "0",
@@ -227,12 +227,12 @@
}
},
{
- "@id": "urn:ccc86f3b-621d-42b8-9fa0-b8df15f2fc1f",
+ "@id": "urn:estimate-tetu1egn",
"Label": "Estimate contrast",
"Used": [
- "urn:d01f6cb7-895c-4263-9c4f-66641a6521d4"
+ "urn:uuid:254a2df1-3258-4823-9d72-9c544501cb45"
],
- "AssociatedWith": "urn:59a04790-c3a4-41d1-b2eb-268899fbfc53",
+ "AssociatedWith": "urn:spm-BV9bpoY8",
"Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
"Parameters": {
"consess{1}.tcon.name": "'tone counting vs baseline'",
@@ -242,12 +242,12 @@
}
},
{
- "@id": "urn:6bf1c686-4bf2-4b26-8333-472d5735d202",
+ "@id": "urn:threshol-CsNtOug2",
"Label": "Threshold",
"Used": [
- "urn:33370220-43b1-4281-b4eb-e06e198ee679"
+ "urn:uuid:a1ee1a5b-4890-4153-b8ca-892a637471e1"
],
- "AssociatedWith": "urn:59a04790-c3a4-41d1-b2eb-268899fbfc53",
+ "AssociatedWith": "urn:spm-BV9bpoY8",
"Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.none = 1;",
"Parameters": {
"conspec.titlestr": "''",
@@ -265,81 +265,79 @@
],
"Entities": [
{
- "@id": "urn:2b0afdd2-8abd-4f81-8748-cecd12c9987f",
+ "@id": "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+ "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"digest": {
- "sha256": "52cc2a3822512db5be3accc8263f2ac1338f32fad8af63cc81fb5af2f335c509"
+ "sha256": "b3d8382360fbbc58cbd8c9e654ddda30b9f0318cf04ebd7539ec75bd724041d2"
}
},
{
- "@id": "urn:c122b76b-49dd-4080-9464-c17425a84159",
+ "@id": "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz",
"Label": "anat_sub-01_T1w.nii.gz",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+ "AtLocation": "ds011/sub-01/anat/sub-01_T1w.nii.gz",
"digest": {
- "sha256": "3d9457fa7712b355d6569522ca80a6dfd70a40b82e6aa0a9364513cf04916dbb"
+ "sha256": "70b9327067cc5200330e04e70b22a41db5aa3b78f978060f61f49bd3a45d125e"
}
},
{
- "@id": "urn:cd65ffe8-9cc1-4916-a8ec-12d359d7c0ad",
+ "@id": "urn:uuid:8ba73954-26e1-4ff7-9d9b-66dfabc07097",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "GeneratedBy": "urn:b7d85a37-7161-4b8b-8d00-a9248190fda3"
+ "GeneratedBy": "urn:movefile-jGxWpvIe"
},
{
- "@id": "urn:18a72054-7748-48b3-915b-e2258a624a59",
+ "@id": "urn:uuid:e7f95829-5ab9-44a6-8ba3-f137c1611a61",
"Label": "anat_sub-01_T1w.nii.gz",
- "GeneratedBy": "urn:90f4ce46-a2df-4096-90c7-3df6f3bed73f"
+ "GeneratedBy": "urn:movefile-YafG4xzl"
},
{
- "@id": "urn:ab6f0993-5b04-419b-b373-e7d235e9e740",
+ "@id": "urn:uuid:c50bff1d-2d38-4a41-aa74-bfc2d7e430c7",
"Label": "func_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:b3fa8179-1978-4507-901d-c57dcd4f10d4"
+ "GeneratedBy": "urn:gunzip3-zT2qlwaP"
},
{
- "@id": "urn:487c72a9-6acb-41f0-b6c3-b7ab2043a5b4",
+ "@id": "urn:uuid:f2617557-abba-4df6-874a-3c010e8fd72a",
"Label": "meanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:33f294ce-d765-47e4-b535-f1020bad14d8"
+ "GeneratedBy": "urn:realign5-mqbIZ2Tp"
},
{
- "@id": "urn:f0832953-3f73-48a7-8fe2-1b48270b2cd4",
+ "@id": "urn:uuid:52afae0b-ad7e-4658-b27c-4905e2de3984",
"Label": "anat_sub-01_T1w.nii",
- "GeneratedBy": "urn:a53f3efb-78d9-4ff0-b2c3-4ac3e36ff6ef"
+ "GeneratedBy": "urn:gunzip4-bRqp0Ozl"
},
{
- "@id": "urn:744a70cd-015b-4826-9ba4-98cdeb78c2f7",
+ "@id": "bids::c1anat_sub-01_T1w.nii",
"Label": "segment1",
- "Atlocation": "c1xxx.nii.gz",
- "GeneratedBy": "urn:7a17faa4-3ab2-4c80-9222-973582ab9023",
"AtLocation": "c1anat_sub-01_T1w.nii",
+ "GeneratedBy": "urn:segment7-ucSpHhHm",
"digest": {
"sha256": "61ca923955d0a5c9088df9e258f41644067ec964e1c9a83284ba03b0515079b0"
}
},
{
- "@id": "urn:d7d53e37-2e1e-421a-bf26-c23e78eac0fe",
+ "@id": "bids::c2anat_sub-01_T1w.nii",
"Label": "segment2",
- "Atlocation": "c2xxx.nii.gz",
- "GeneratedBy": "urn:7a17faa4-3ab2-4c80-9222-973582ab9023",
"AtLocation": "c2anat_sub-01_T1w.nii",
+ "GeneratedBy": "urn:segment7-ucSpHhHm",
"digest": {
"sha256": "10ad88ebeebebd0bd03ccbdd4df92d500d28d14715fa5375fd35589caddf49a6"
}
},
{
- "@id": "urn:f92855c4-a077-4204-9bfc-18f441b7ad0d",
- "Label": "wmeanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:ce8b87ba-2004-4ada-a824-b801b408e7dd"
+ "@id": "urn:uuid:74b85b8d-dabe-461a-8437-f651eeb688f1",
+ "Label": "wsegment1",
+ "GeneratedBy": "urn:normaliz-C3cRQGpI"
},
{
- "@id": "urn:1d965db1-c424-4236-9d86-cd4a7939aad7",
+ "@id": "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"Label": "ONSETS_sub-01-MultiCond.mat",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+ "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"digest": {
- "sha256": "be4671d4f9dc480dd3e5be19aeeab2756f7afdc3b32d81e071685d7a4eafcfed"
+ "sha256": "5599e80629bb4d66cdbfb357511c04060bd3d37cdbfe2a4cd701a2979e9f6610"
}
},
{
- "@id": "urn:e4b557f4-93fa-4d8c-8650-78fd658a67b5",
+ "@id": "bids:storage:/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_contrast_mask/mask.nii",
"Label": "spm_contrast_mask_mask.nii",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_contrast_mask/mask.nii",
"digest": {
@@ -347,24 +345,24 @@
}
},
{
- "@id": "urn:ee1865c2-68cc-4fd3-8767-5b9488363617",
- "Label": "swmeanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:14296cb6-f8ed-4556-a51f-d2fbc11b01b7"
+ "@id": "urn:uuid:bc9496f8-bcf3-4739-b090-4cdefbb34658",
+ "Label": "swsegment1",
+ "GeneratedBy": "urn:smooth10-ae0MM1Bg"
},
{
- "@id": "urn:9f4bb0cf-d032-467e-ba07-b8a64af8e023",
+ "@id": "urn:uuid:722ca52b-0e63-4bf3-bf23-c30162249c80",
"Label": "SPM.mat",
- "GeneratedBy": "urn:6f7e8239-6b3d-48fd-a94f-62a8a825aee7"
+ "GeneratedBy": "urn:statdesi-0irxle1q"
},
{
- "@id": "urn:d01f6cb7-895c-4263-9c4f-66641a6521d4",
+ "@id": "urn:uuid:254a2df1-3258-4823-9d72-9c544501cb45",
"Label": "SPM.mat",
- "GeneratedBy": "urn:2ed3ab6c-8c7d-421f-b06f-a8f6fc205cab"
+ "GeneratedBy": "urn:estimate-A3hfenJb"
},
{
- "@id": "urn:33370220-43b1-4281-b4eb-e06e198ee679",
+ "@id": "urn:uuid:a1ee1a5b-4890-4153-b8ca-892a637471e1",
"Label": "SPM.mat",
- "GeneratedBy": "urn:ccc86f3b-621d-42b8-9fa0-b8df15f2fc1f"
+ "GeneratedBy": "urn:estimate-tetu1egn"
}
]
}
diff --git a/examples/from_parsers/spm/spm_explicit_mask_batch.m b/examples/from_parsers/spm/spm_explicit_mask_batch.m
index a851678c0..ecf703063 100644
--- a/examples/from_parsers/spm/spm_explicit_mask_batch.m
+++ b/examples/from_parsers/spm/spm_explicit_mask_batch.m
@@ -3,10 +3,10 @@
% spm SPM - SPM12 (12.1)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------
-matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};
-matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};
-matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};
-matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};
+matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};
+matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};
+matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};
+matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};
matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));
@@ -90,7 +90,7 @@
matlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;
matlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});
-matlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};
+matlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};
matlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});
matlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};
matlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;
diff --git a/examples/from_parsers/spm/spm_explicit_mask_batch.png b/examples/from_parsers/spm/spm_explicit_mask_batch.png
index 5607fa96b..26559d3e7 100644
Binary files a/examples/from_parsers/spm/spm_explicit_mask_batch.png and b/examples/from_parsers/spm/spm_explicit_mask_batch.png differ
diff --git a/examples/from_parsers/spm/spm_group_ols_batch.jsonld b/examples/from_parsers/spm/spm_group_ols_batch.jsonld
index e04290c78..0ffa21d6f 100644
--- a/examples/from_parsers/spm/spm_group_ols_batch.jsonld
+++ b/examples/from_parsers/spm/spm_group_ols_batch.jsonld
@@ -4,35 +4,35 @@
"Records": {
"Software": [
{
- "@id": "urn:a1ae76b6-98c6-405b-aadb-5898c973ad78",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:spm-tmzVSYkl",
"@type": "prov:SoftwareAgent",
"Label": "SPM",
- "Version": "SPM12r7224"
+ "Version": "SPM12r7224",
+ "AltIdentifier": "RRID:SCR_007037"
}
],
"Activities": [
{
- "@id": "urn:7ec5b7a4-7374-4686-b27c-81a58c3b3e98",
+ "@id": "urn:statsfac-txmFBMTH",
"Label": "stats.factorial_design",
"Used": [
- "urn:8f10d30f-de71-4768-a788-1ab96c863c20",
- "urn:696bea66-9b1b-47a7-9d50-4fc276f012d7",
- "urn:38c05196-6be2-4e4e-a4f1-0ec7328be2dd",
- "urn:b889cc5f-d33a-4375-9707-5241f6701604",
- "urn:b4a86db6-024c-43d1-a350-f0d1da9a6e0a",
- "urn:e4549dc8-e7dc-4d2d-a4fc-5aef29e6af69",
- "urn:dda7883b-7b5a-4449-bac3-ffcbe0ef3bf2",
- "urn:b8097281-e20e-4997-a059-1965f255d018",
- "urn:94c531f1-e0a2-45a2-955c-3c5e0fc00c59",
- "urn:b64e7dcb-f9fd-480c-b8d1-f72de36ef22a",
- "urn:70bfd749-6110-4cc8-8de4-e88be8987dd8",
- "urn:64729fa6-5fa8-4e4c-9622-e340d68a72fc",
- "urn:3fd0f707-15fa-407a-9224-edfda6528cb1",
- "urn:f7465d5c-46f7-490e-a5a2-08d59b567b0d"
+ "bids:ds011:/derivatives/SPM/LEVEL1/sub-01/con_0001.nii",
+ "bids:ds011:/derivatives/SPM/LEVEL1/sub-02/con_0001.nii",
+ "bids:ds011:/derivatives/SPM/LEVEL1/sub-03/con_0001.nii",
+ "bids:ds011:/derivatives/SPM/LEVEL1/sub-04/con_0001.nii",
+ "bids:ds011:/derivatives/SPM/LEVEL1/sub-05/con_0001.nii",
+ "bids:ds011:/derivatives/SPM/LEVEL1/sub-06/con_0001.nii",
+ "bids:ds011:/derivatives/SPM/LEVEL1/sub-07/con_0001.nii",
+ "bids:ds011:/derivatives/SPM/LEVEL1/sub-08/con_0001.nii",
+ "bids:ds011:/derivatives/SPM/LEVEL1/sub-09/con_0001.nii",
+ "bids:ds011:/derivatives/SPM/LEVEL1/sub-10/con_0001.nii",
+ "bids:ds011:/derivatives/SPM/LEVEL1/sub-11/con_0001.nii",
+ "bids:ds011:/derivatives/SPM/LEVEL1/sub-12/con_0001.nii",
+ "bids:ds011:/derivatives/SPM/LEVEL1/sub-13/con_0001.nii",
+ "bids:ds011:/derivatives/SPM/LEVEL1/sub-14/con_0001.nii"
],
- "AssociatedWith": "urn:a1ae76b6-98c6-405b-aadb-5898c973ad78",
- "Command": "matlabbatch{1}.spm.stats.factorial_design.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_t_test'};\nmatlabbatch{1}.spm.stats.factorial_design.des.t1.scans = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-01/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-02/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-03/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-04/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-05/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-06/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-07/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-08/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-09/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-10/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-11/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-12/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-13/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-14/con_0001.nii,1',};\nmatlabbatch{1}.spm.stats.factorial_design.cov = struct('c', {}, 'cname', {}, 'iCFI', {}, 'iCC', {});\nmatlabbatch{1}.spm.stats.factorial_design.multi_cov = struct('files', {}, 'iCFI', {}, 'iCC', {});\nmatlabbatch{1}.spm.stats.factorial_design.masking.tm.tm_none = 1;\nmatlabbatch{1}.spm.stats.factorial_design.masking.im = 1;\nmatlabbatch{1}.spm.stats.factorial_design.masking.em = {''};\nmatlabbatch{1}.spm.stats.factorial_design.globalc.g_omit = 1;\nmatlabbatch{1}.spm.stats.factorial_design.globalm.gmsca.gmsca_no = 1;\nmatlabbatch{1}.spm.stats.factorial_design.globalm.glonorm = 1;",
+ "AssociatedWith": "urn:spm-tmzVSYkl",
+ "Command": "matlabbatch{1}.spm.stats.factorial_design.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_t_test'};\nmatlabbatch{1}.spm.stats.factorial_design.des.t1.scans = {'ds011/derivatives/SPM/LEVEL1/sub-01/con_0001.nii,1','ds011/derivatives/SPM/LEVEL1/sub-02/con_0001.nii,1','ds011/derivatives/SPM/LEVEL1/sub-03/con_0001.nii,1','ds011/derivatives/SPM/LEVEL1/sub-04/con_0001.nii,1','ds011/derivatives/SPM/LEVEL1/sub-05/con_0001.nii,1','ds011/derivatives/SPM/LEVEL1/sub-06/con_0001.nii,1','ds011/derivatives/SPM/LEVEL1/sub-07/con_0001.nii,1','ds011/derivatives/SPM/LEVEL1/sub-08/con_0001.nii,1','ds011/derivatives/SPM/LEVEL1/sub-09/con_0001.nii,1','ds011/derivatives/SPM/LEVEL1/sub-10/con_0001.nii,1','ds011/derivatives/SPM/LEVEL1/sub-11/con_0001.nii,1','ds011/derivatives/SPM/LEVEL1/sub-12/con_0001.nii,1','ds011/derivatives/SPM/LEVEL1/sub-13/con_0001.nii,1','ds011/derivatives/SPM/LEVEL1/sub-14/con_0001.nii,1',};\nmatlabbatch{1}.spm.stats.factorial_design.cov = struct('c', {}, 'cname', {}, 'iCFI', {}, 'iCC', {});\nmatlabbatch{1}.spm.stats.factorial_design.multi_cov = struct('files', {}, 'iCFI', {}, 'iCC', {});\nmatlabbatch{1}.spm.stats.factorial_design.masking.tm.tm_none = 1;\nmatlabbatch{1}.spm.stats.factorial_design.masking.im = 1;\nmatlabbatch{1}.spm.stats.factorial_design.masking.em = {''};\nmatlabbatch{1}.spm.stats.factorial_design.globalc.g_omit = 1;\nmatlabbatch{1}.spm.stats.factorial_design.globalm.gmsca.gmsca_no = 1;\nmatlabbatch{1}.spm.stats.factorial_design.globalm.glonorm = 1;",
"Parameters": {
"dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_t_test'}",
"cov": "struct('c', {}, 'cname', {}, 'iCFI', {}, 'iCC', {})",
@@ -46,12 +46,12 @@
}
},
{
- "@id": "urn:33c0adb5-01c5-4303-a15c-09d7f72fe426",
+ "@id": "urn:estimate-6XE9snDm",
"Label": "Estimate stat.",
"Used": [
- "urn:4f7fe1b2-ce65-4d83-98cd-a2992b80e685"
+ "urn:uuid:992d5295-4683-4a9d-adac-ba9e417e892d"
],
- "AssociatedWith": "urn:a1ae76b6-98c6-405b-aadb-5898c973ad78",
+ "AssociatedWith": "urn:spm-tmzVSYkl",
"Command": "matlabbatch{2}.spm.stats.fmri_est.spmmat(1) = cfg_dep('Factorial design specification: SPM.mat File', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{2}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{2}.spm.stats.fmri_est.method.Classical = 1;",
"Parameters": {
"write_residuals": "0",
@@ -59,12 +59,12 @@
}
},
{
- "@id": "urn:1f446a54-dba5-425b-95ef-552dba8677b7",
+ "@id": "urn:estimate-MhmHP2O9",
"Label": "Estimate contrast",
"Used": [
- "urn:951b9cd2-26a6-42d7-8125-f162f3a38fee"
+ "urn:uuid:3f7c5997-5086-4784-8228-73b2631c18f5"
],
- "AssociatedWith": "urn:a1ae76b6-98c6-405b-aadb-5898c973ad78",
+ "AssociatedWith": "urn:spm-tmzVSYkl",
"Command": "matlabbatch{3}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{3}.spm.stats.con.consess{1}.tcon.name = 'con-01';\nmatlabbatch{3}.spm.stats.con.consess{1}.tcon.weights = 1;\nmatlabbatch{3}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{3}.spm.stats.con.delete = 0;",
"Parameters": {
"consess{1}.tcon.name": "'con-01'",
@@ -74,12 +74,12 @@
}
},
{
- "@id": "urn:9aad2ff0-103d-4539-a7e1-72733b6c8cef",
+ "@id": "urn:threshol-BeAdFDGg",
"Label": "Threshold",
"Used": [
- "urn:b8d7c546-8d76-4977-902e-54a5f98165f9"
+ "urn:uuid:94a73b31-ec31-4e8a-bf32-3f67f1e4d027"
],
- "AssociatedWith": "urn:a1ae76b6-98c6-405b-aadb-5898c973ad78",
+ "AssociatedWith": "urn:spm-tmzVSYkl",
"Command": "matlabbatch{4}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{4}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{4}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{4}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{4}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{4}.spm.stats.results.conspec.extent = 120;\nmatlabbatch{4}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{4}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{4}.spm.stats.results.units = 1;\nmatlabbatch{4}.spm.stats.results.print = 'pdf';\nmatlabbatch{4}.spm.stats.results.write.tspm.basename = 'thresh';",
"Parameters": {
"conspec.titlestr": "''",
@@ -97,131 +97,131 @@
],
"Entities": [
{
- "@id": "urn:8f10d30f-de71-4768-a788-1ab96c863c20",
+ "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-01/con_0001.nii",
"Label": "sub-01_con_0001.nii",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-01/con_0001.nii",
+ "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-01/con_0001.nii",
"digest": {
- "sha256": "6ed900b612440819b1ee78120c31845727d5efd253ec5a4ecd854a089df24632"
+ "sha256": "ae87ebacacac9fa044115eb7f72f465ed7df0cd564afeea1b21c31a53eb5a5d9"
}
},
{
- "@id": "urn:696bea66-9b1b-47a7-9d50-4fc276f012d7",
+ "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-02/con_0001.nii",
"Label": "sub-02_con_0001.nii",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-02/con_0001.nii",
+ "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-02/con_0001.nii",
"digest": {
- "sha256": "29fa8570577a60a7e696ec351bd5691ac56363eead45a356c62955cde829bf2f"
+ "sha256": "7b39fed4ec7aa41bc936735eb90614f2999338b8ebc323d522ff78cae3e9f771"
}
},
{
- "@id": "urn:38c05196-6be2-4e4e-a4f1-0ec7328be2dd",
+ "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-03/con_0001.nii",
"Label": "sub-03_con_0001.nii",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-03/con_0001.nii",
+ "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-03/con_0001.nii",
"digest": {
- "sha256": "ef3b712491acc95eeb160602a3c00225d383fba86e6f9c10bb8c8d1f0e1856e0"
+ "sha256": "248d7d970e5382f37be821713be2a94b495c2a0cb374cd12843f7b11b7b15357"
}
},
{
- "@id": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-04/con_0001.nii",
"Label": "sub-04_con_0001.nii",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-04/con_0001.nii",
+ "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-04/con_0001.nii",
"digest": {
- "sha256": "c7abe341e414634bb339e95b796e6852069d462b43d175926b35390b1dda3822"
+ "sha256": "26db772214370fd1b0d1593312940d717d1d013dc52b5645a2d3f3b93c606ab9"
}
},
{
- "@id": "urn:b4a86db6-024c-43d1-a350-f0d1da9a6e0a",
+ "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-05/con_0001.nii",
"Label": "sub-05_con_0001.nii",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-05/con_0001.nii",
+ "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-05/con_0001.nii",
"digest": {
- "sha256": "9fd384b58154c0d76897084a262de2a59850e86aebf25175d425cab5c64c0c8f"
+ "sha256": "5c2373d05b955686e92b1143f623fd2a203810da7f079f85ba60f0605925b6e3"
}
},
{
- "@id": "urn:e4549dc8-e7dc-4d2d-a4fc-5aef29e6af69",
+ "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-06/con_0001.nii",
"Label": "sub-06_con_0001.nii",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-06/con_0001.nii",
+ "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-06/con_0001.nii",
"digest": {
- "sha256": "7d4a384efbb99af0e4dbfa333193c6c47cf315ad112f7e13fa7c34a280708097"
+ "sha256": "39c6029429ff0b8b7739ba5cf49ec609d39b87ac1f4f6eb500d1537aefaec3df"
}
},
{
- "@id": "urn:dda7883b-7b5a-4449-bac3-ffcbe0ef3bf2",
+ "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-07/con_0001.nii",
"Label": "sub-07_con_0001.nii",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-07/con_0001.nii",
+ "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-07/con_0001.nii",
"digest": {
- "sha256": "695d8ce6fee350c4f1f75a38a1913959e363f3ae96c224e30703d564d6635fd0"
+ "sha256": "61b19b16193c7c29b36e99ed192fe08fdc465b887fe68d6f42a2c5856d48fce1"
}
},
{
- "@id": "urn:b8097281-e20e-4997-a059-1965f255d018",
+ "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-08/con_0001.nii",
"Label": "sub-08_con_0001.nii",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-08/con_0001.nii",
+ "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-08/con_0001.nii",
"digest": {
- "sha256": "31118b396b250e757aa372893cdbce86ceab283c2e51dc21501c68b6c6048318"
+ "sha256": "74f3311a2884e50ebe2d8ac35d656f25e2e866674dcc82e39a7220a711138a7b"
}
},
{
- "@id": "urn:94c531f1-e0a2-45a2-955c-3c5e0fc00c59",
+ "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-09/con_0001.nii",
"Label": "sub-09_con_0001.nii",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-09/con_0001.nii",
+ "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-09/con_0001.nii",
"digest": {
- "sha256": "23caf9a8e4ce2a1dd1df54197790b512610381fd5ca30650e2c370bcc1446f50"
+ "sha256": "6488f9d23381e94eb7820fe3278be4cbace66cf4fdbcffc670fcce12fb2f7d4c"
}
},
{
- "@id": "urn:b64e7dcb-f9fd-480c-b8d1-f72de36ef22a",
+ "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-10/con_0001.nii",
"Label": "sub-10_con_0001.nii",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-10/con_0001.nii",
+ "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-10/con_0001.nii",
"digest": {
- "sha256": "9e874e772e65c78cfa0b69591841cda01a3db0a953ccb345a4e2d22ecce0d783"
+ "sha256": "5b5de6f711454549d0856063de3516465e8006e8a7c2496e3e7f376f6e95003c"
}
},
{
- "@id": "urn:70bfd749-6110-4cc8-8de4-e88be8987dd8",
+ "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-11/con_0001.nii",
"Label": "sub-11_con_0001.nii",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-11/con_0001.nii",
+ "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-11/con_0001.nii",
"digest": {
- "sha256": "b76148bef6738f69125d542e630dd83c91e65e4bf2122d4e3b7eb4870c503647"
+ "sha256": "1e366bf13ff4d821d33d13776322c280b386ef362af73fa2c3e4379f8b093a46"
}
},
{
- "@id": "urn:64729fa6-5fa8-4e4c-9622-e340d68a72fc",
+ "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-12/con_0001.nii",
"Label": "sub-12_con_0001.nii",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-12/con_0001.nii",
+ "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-12/con_0001.nii",
"digest": {
- "sha256": "efc402e0e889c64156eedefc45aa73baef871f491bb38087ed2ba88333a13c5d"
+ "sha256": "bfd0934a7da341836e1d45d2a1607bc25e3d1963d5f5fdbb3a1b089ac99cb683"
}
},
{
- "@id": "urn:3fd0f707-15fa-407a-9224-edfda6528cb1",
+ "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-13/con_0001.nii",
"Label": "sub-13_con_0001.nii",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-13/con_0001.nii",
+ "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-13/con_0001.nii",
"digest": {
- "sha256": "30d7f60a178fcc805321140edc1223b452640468ce370c845eec552daec178f9"
+ "sha256": "e2ff39848ea765ac4077e8eb0bc9a8cbf68aaf25b03d0eb569294aa64c0a47b8"
}
},
{
- "@id": "urn:f7465d5c-46f7-490e-a5a2-08d59b567b0d",
+ "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-14/con_0001.nii",
"Label": "sub-14_con_0001.nii",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-14/con_0001.nii",
+ "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-14/con_0001.nii",
"digest": {
- "sha256": "645ffc262eccd1ee6318d1b6f73294d9cedd4ea772ccbab0fdd9bc57c5f6e27c"
+ "sha256": "59b92ae61893090c2213e60524a7325bba900871c3b7cddd3ed2839aef67686d"
}
},
{
- "@id": "urn:4f7fe1b2-ce65-4d83-98cd-a2992b80e685",
+ "@id": "urn:uuid:992d5295-4683-4a9d-adac-ba9e417e892d",
"Label": "SPM.mat",
- "GeneratedBy": "urn:7ec5b7a4-7374-4686-b27c-81a58c3b3e98"
+ "GeneratedBy": "urn:statsfac-txmFBMTH"
},
{
- "@id": "urn:951b9cd2-26a6-42d7-8125-f162f3a38fee",
+ "@id": "urn:uuid:3f7c5997-5086-4784-8228-73b2631c18f5",
"Label": "SPM.mat",
- "GeneratedBy": "urn:33c0adb5-01c5-4303-a15c-09d7f72fe426"
+ "GeneratedBy": "urn:estimate-6XE9snDm"
},
{
- "@id": "urn:b8d7c546-8d76-4977-902e-54a5f98165f9",
+ "@id": "urn:uuid:94a73b31-ec31-4e8a-bf32-3f67f1e4d027",
"Label": "SPM.mat",
- "GeneratedBy": "urn:1f446a54-dba5-425b-95ef-552dba8677b7"
+ "GeneratedBy": "urn:estimate-MhmHP2O9"
}
]
}
diff --git a/examples/from_parsers/spm/spm_group_ols_batch.m b/examples/from_parsers/spm/spm_group_ols_batch.m
index def9d7fc5..199a7a32e 100644
--- a/examples/from_parsers/spm/spm_group_ols_batch.m
+++ b/examples/from_parsers/spm/spm_group_ols_batch.m
@@ -6,20 +6,20 @@
matlabbatch{1}.spm.stats.factorial_design.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_t_test'};
%%
matlabbatch{1}.spm.stats.factorial_design.des.t1.scans = {
- '/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-01/con_0001.nii,1'
- '/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-02/con_0001.nii,1'
- '/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-03/con_0001.nii,1'
- '/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-04/con_0001.nii,1'
- '/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-05/con_0001.nii,1'
- '/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-06/con_0001.nii,1'
- '/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-07/con_0001.nii,1'
- '/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-08/con_0001.nii,1'
- '/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-09/con_0001.nii,1'
- '/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-10/con_0001.nii,1'
- '/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-11/con_0001.nii,1'
- '/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-12/con_0001.nii,1'
- '/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-13/con_0001.nii,1'
- '/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-14/con_0001.nii,1'
+ 'ds011/derivatives/SPM/LEVEL1/sub-01/con_0001.nii,1'
+ 'ds011/derivatives/SPM/LEVEL1/sub-02/con_0001.nii,1'
+ 'ds011/derivatives/SPM/LEVEL1/sub-03/con_0001.nii,1'
+ 'ds011/derivatives/SPM/LEVEL1/sub-04/con_0001.nii,1'
+ 'ds011/derivatives/SPM/LEVEL1/sub-05/con_0001.nii,1'
+ 'ds011/derivatives/SPM/LEVEL1/sub-06/con_0001.nii,1'
+ 'ds011/derivatives/SPM/LEVEL1/sub-07/con_0001.nii,1'
+ 'ds011/derivatives/SPM/LEVEL1/sub-08/con_0001.nii,1'
+ 'ds011/derivatives/SPM/LEVEL1/sub-09/con_0001.nii,1'
+ 'ds011/derivatives/SPM/LEVEL1/sub-10/con_0001.nii,1'
+ 'ds011/derivatives/SPM/LEVEL1/sub-11/con_0001.nii,1'
+ 'ds011/derivatives/SPM/LEVEL1/sub-12/con_0001.nii,1'
+ 'ds011/derivatives/SPM/LEVEL1/sub-13/con_0001.nii,1'
+ 'ds011/derivatives/SPM/LEVEL1/sub-14/con_0001.nii,1'
};
%%
matlabbatch{1}.spm.stats.factorial_design.cov = struct('c', {}, 'cname', {}, 'iCFI', {}, 'iCC', {});
diff --git a/examples/from_parsers/spm/spm_group_ols_batch.png b/examples/from_parsers/spm/spm_group_ols_batch.png
index 26783c670..46a3168db 100644
Binary files a/examples/from_parsers/spm/spm_group_ols_batch.png and b/examples/from_parsers/spm/spm_group_ols_batch.png differ
diff --git a/examples/from_parsers/spm/spm_group_wls_batch.jsonld b/examples/from_parsers/spm/spm_group_wls_batch.jsonld
index 7382d8620..ed36754fd 100644
--- a/examples/from_parsers/spm/spm_group_wls_batch.jsonld
+++ b/examples/from_parsers/spm/spm_group_wls_batch.jsonld
@@ -4,46 +4,46 @@
"Records": {
"Software": [
{
- "@id": "urn:e522e69f-2f06-4730-b9db-c7204a36f5a4",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:spm-FjaG6SLD",
"@type": "prov:SoftwareAgent",
"Label": "SPM",
- "Version": "SPM12r7224"
+ "Version": "SPM12r7224",
+ "AltIdentifier": "RRID:SCR_007037"
}
],
"Activities": [
{
- "@id": "urn:0e24554b-322d-4be9-87cd-9dd642325442",
+ "@id": "urn:statsmfx-6NcnuSxV",
"Label": "stats.mfx.ffx",
"Used": [
- "urn:f4f108d9-ad44-4f62-bef2-0214e3e76d69",
- "urn:ed8e6d73-f02f-417f-86a2-619df64156ac",
- "urn:5b10beae-c90a-4bd3-801e-3bba870ee006",
- "urn:deab5f4e-3598-41de-a361-d573731a55b5",
- "urn:d2b88a58-b171-48dd-9b24-909c0df5133d",
- "urn:5b45b716-037e-42e9-a47c-f350030ae099",
- "urn:9a03f285-dfcd-410d-bb99-8b0ebbe3ef20",
- "urn:cda76e9d-1eab-41a7-bee3-e5b36b858062",
- "urn:640954dc-d4ca-4c56-90d3-79b557b615c6",
- "urn:101ace3c-4c3e-4d19-bea7-75b5a7717580",
- "urn:1a741297-35d4-4b05-886b-1d1e8c91bf2e",
- "urn:b5ed0dcb-6f8b-4f0b-972e-0d08e249d112",
- "urn:85d40ec9-6104-4d35-a712-f30b1e91c0bc",
- "urn:bf004824-b637-4840-942f-369d36e3837e"
+ "bids:ds011:/derivatives/SPM/LEVEL1/sub-01/SPM.mat",
+ "bids:ds011:/derivatives/SPM/LEVEL1/sub-02/SPM.mat",
+ "bids:ds011:/derivatives/SPM/LEVEL1/sub-03/SPM.mat",
+ "bids:ds011:/derivatives/SPM/LEVEL1/sub-04/SPM.mat",
+ "bids:ds011:/derivatives/SPM/LEVEL1/sub-06/SPM.mat",
+ "bids:ds011:/derivatives/SPM/LEVEL1/sub-07/SPM.mat",
+ "bids:ds011:/derivatives/SPM/LEVEL1/sub-08/SPM.mat",
+ "bids:ds011:/derivatives/SPM/LEVEL1/sub-09/SPM.mat",
+ "bids:ds011:/derivatives/SPM/LEVEL1/sub-10/SPM.mat",
+ "bids:ds011:/derivatives/SPM/LEVEL1/sub-11/SPM.mat",
+ "bids:ds011:/derivatives/SPM/LEVEL1/sub-12/SPM.mat",
+ "bids:ds011:/derivatives/SPM/LEVEL1/sub-13/SPM.mat",
+ "bids:ds011:/derivatives/SPM/LEVEL1/sub-14/SPM.mat",
+ "bids:ds011:/derivatives/SPM/LEVEL1/sub-05/SPM.mat"
],
- "AssociatedWith": "urn:e522e69f-2f06-4730-b9db-c7204a36f5a4",
- "Command": "matlabbatch{1}.spm.stats.mfx.ffx.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_WLS_t_test'};\nmatlabbatch{1}.spm.stats.mfx.ffx.spmmat = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-01/SPM.mat','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-02/SPM.mat','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-03/SPM.mat','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-04/SPM.mat','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-06/SPM.mat','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-07/SPM.mat','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-08/SPM.mat','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-09/SPM.mat','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-10/SPM.mat','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-11/SPM.mat','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-12/SPM.mat','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-13/SPM.mat','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-14/SPM.mat','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-05/SPM.mat',};",
+ "AssociatedWith": "urn:spm-FjaG6SLD",
+ "Command": "matlabbatch{1}.spm.stats.mfx.ffx.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_WLS_t_test'};\nmatlabbatch{1}.spm.stats.mfx.ffx.spmmat = {'ds011/derivatives/SPM/LEVEL1/sub-01/SPM.mat','ds011/derivatives/SPM/LEVEL1/sub-02/SPM.mat','ds011/derivatives/SPM/LEVEL1/sub-03/SPM.mat','ds011/derivatives/SPM/LEVEL1/sub-04/SPM.mat','ds011/derivatives/SPM/LEVEL1/sub-06/SPM.mat','ds011/derivatives/SPM/LEVEL1/sub-07/SPM.mat','ds011/derivatives/SPM/LEVEL1/sub-08/SPM.mat','ds011/derivatives/SPM/LEVEL1/sub-09/SPM.mat','ds011/derivatives/SPM/LEVEL1/sub-10/SPM.mat','ds011/derivatives/SPM/LEVEL1/sub-11/SPM.mat','ds011/derivatives/SPM/LEVEL1/sub-12/SPM.mat','ds011/derivatives/SPM/LEVEL1/sub-13/SPM.mat','ds011/derivatives/SPM/LEVEL1/sub-14/SPM.mat','ds011/derivatives/SPM/LEVEL1/sub-05/SPM.mat',};",
"Parameters": {
"dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_WLS_t_test'}"
}
},
{
- "@id": "urn:2e0e52f8-04a3-4102-b205-304afb4b5f2e",
+ "@id": "urn:estimate-hypn0pbc",
"Label": "Estimate stat.",
"Used": [
- "urn:39022742-83e8-4de3-85de-35824e023294"
+ "urn:uuid:c9346e65-f190-4a60-9a5b-ad26f0c85da3"
],
- "AssociatedWith": "urn:e522e69f-2f06-4730-b9db-c7204a36f5a4",
+ "AssociatedWith": "urn:spm-FjaG6SLD",
"Command": "matlabbatch{2}.spm.stats.fmri_est.spmmat(1) = cfg_dep('FFX Specification: SPM.mat File', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{2}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{2}.spm.stats.fmri_est.method.Classical = 1;",
"Parameters": {
"write_residuals": "0",
@@ -51,24 +51,24 @@
}
},
{
- "@id": "urn:032c0d43-1024-43f1-9646-64523294f3b1",
+ "@id": "urn:statsmfx-Fy5cpUID",
"Label": "stats.mfx.spec",
"Used": [
- "urn:99b48746-909d-452d-bf6b-24a0e1ebf9c5"
+ "urn:uuid:73c5f0c0-cfe5-4458-acfd-50c8bb5815d2"
],
- "AssociatedWith": "urn:e522e69f-2f06-4730-b9db-c7204a36f5a4",
+ "AssociatedWith": "urn:spm-FjaG6SLD",
"Command": "matlabbatch{3}.spm.stats.mfx.spec.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{3}.spm.stats.mfx.spec.contrast = [];",
"Parameters": {
"contrast": "[]"
}
},
{
- "@id": "urn:b2fe76ce-e994-4c27-95fb-efa9e1b13e2a",
+ "@id": "urn:estimate-LzIKLSqR",
"Label": "Estimate stat.",
"Used": [
- "urn:403c944c-e137-48ae-a96a-5bee552c4e45"
+ "urn:uuid:73bd38cc-7a73-483f-9f5e-c83b7013635a"
],
- "AssociatedWith": "urn:e522e69f-2f06-4730-b9db-c7204a36f5a4",
+ "AssociatedWith": "urn:spm-FjaG6SLD",
"Command": "matlabbatch{4}.spm.stats.fmri_est.spmmat(1) = cfg_dep('MFX Specification: SPM.mat File', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{4}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{4}.spm.stats.fmri_est.method.Classical = 1;",
"Parameters": {
"write_residuals": "0",
@@ -76,12 +76,12 @@
}
},
{
- "@id": "urn:2e5ce908-c114-456f-a59e-06957d7f777e",
+ "@id": "urn:estimate-wlbXNqhL",
"Label": "Estimate contrast",
"Used": [
- "urn:53c1cf75-c2b5-4387-8517-de84410720a8"
+ "urn:uuid:63220836-af6f-43c5-b08a-4f738039ab3a"
],
- "AssociatedWith": "urn:e522e69f-2f06-4730-b9db-c7204a36f5a4",
+ "AssociatedWith": "urn:spm-FjaG6SLD",
"Command": "matlabbatch{5}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{5}.spm.stats.con.consess{1}.tcon.name = 'con-01: Tone Counting vs Baseline';\nmatlabbatch{5}.spm.stats.con.consess{1}.tcon.weights = 1;\nmatlabbatch{5}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{5}.spm.stats.con.delete = 0;",
"Parameters": {
"consess{1}.tcon.name": "'con-01: Tone Counting vs Baseline'",
@@ -91,12 +91,12 @@
}
},
{
- "@id": "urn:35a508ce-4afe-4a32-ae36-7424fc154d95",
+ "@id": "urn:threshol-Yhbdm09O",
"Label": "Threshold",
"Used": [
- "urn:6c0d5299-32be-4a6d-8e1f-465d2b2aa15b"
+ "urn:uuid:2502b6a5-f5c5-4310-845e-816607158694"
],
- "AssociatedWith": "urn:e522e69f-2f06-4730-b9db-c7204a36f5a4",
+ "AssociatedWith": "urn:spm-FjaG6SLD",
"Command": "matlabbatch{6}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{6}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{6}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{6}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{6}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{6}.spm.stats.results.conspec.extent = 2;\nmatlabbatch{6}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{6}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{6}.spm.stats.results.units = 1;\nmatlabbatch{6}.spm.stats.results.print = 'pdf';\nmatlabbatch{6}.spm.stats.results.write.tspm.basename = 'thresh';",
"Parameters": {
"conspec.titlestr": "''",
@@ -114,141 +114,141 @@
],
"Entities": [
{
- "@id": "urn:f4f108d9-ad44-4f62-bef2-0214e3e76d69",
+ "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-01/SPM.mat",
"Label": "sub-01_SPM.mat",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-01/SPM.mat",
+ "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-01/SPM.mat",
"digest": {
- "sha256": "441618d2bff3613f944118e5942d8e66b6d9727e997267dcdbcedc9ca924ddcf"
+ "sha256": "7ee54cdfc3a3766d1cd9fc53eb3b080fb8eda5ce92a6be7abd226bb7482e3821"
}
},
{
- "@id": "urn:ed8e6d73-f02f-417f-86a2-619df64156ac",
+ "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-02/SPM.mat",
"Label": "sub-02_SPM.mat",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-02/SPM.mat",
+ "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-02/SPM.mat",
"digest": {
- "sha256": "30fa910dd37ad302a1beef5f9f4a19b92c01222ecb99e685f3127588ce7bfafb"
+ "sha256": "08ac55808031570c33ef9f9348ad3a8bd8a88df6829933f41bda58cd328d20be"
}
},
{
- "@id": "urn:5b10beae-c90a-4bd3-801e-3bba870ee006",
+ "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-03/SPM.mat",
"Label": "sub-03_SPM.mat",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-03/SPM.mat",
+ "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-03/SPM.mat",
"digest": {
- "sha256": "76053c189ea109e3c3bf6271ba440f8d2a234fd9f9dfb19f648624224ba3c67f"
+ "sha256": "48a60737f0c66071641ebbce1169788e79a684b40dedd9130bdf295a304949bf"
}
},
{
- "@id": "urn:deab5f4e-3598-41de-a361-d573731a55b5",
+ "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-04/SPM.mat",
"Label": "sub-04_SPM.mat",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-04/SPM.mat",
+ "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-04/SPM.mat",
"digest": {
- "sha256": "4dc9d4316a1acd3e5b73a80d3d047c78736cdea4b6bbd231b35a863565a6deb0"
+ "sha256": "a4b7bc85e7fe3a8e8bf83a2cd6188ddbdf298b1827d754f6cb170cfb3d6bcdfc"
}
},
{
- "@id": "urn:d2b88a58-b171-48dd-9b24-909c0df5133d",
+ "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-06/SPM.mat",
"Label": "sub-06_SPM.mat",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-06/SPM.mat",
+ "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-06/SPM.mat",
"digest": {
- "sha256": "ec9afe39bb1915d78d656bbf925c8bd91a58e95776e263bcf86aee3051210d3c"
+ "sha256": "fe65b7d9b8836ba80f8c86d90a255773fea0279d4f4546900354b38089a7109f"
}
},
{
- "@id": "urn:5b45b716-037e-42e9-a47c-f350030ae099",
+ "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-07/SPM.mat",
"Label": "sub-07_SPM.mat",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-07/SPM.mat",
+ "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-07/SPM.mat",
"digest": {
- "sha256": "7025698ecf8d02b19ef4d94462beefc902ca603eed07023df5019cfe3e59cf53"
+ "sha256": "12ec99599b441a31ddaf8ec5cf8383ef3e4eb93be1237e0ef31dad36d8c933af"
}
},
{
- "@id": "urn:9a03f285-dfcd-410d-bb99-8b0ebbe3ef20",
+ "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-08/SPM.mat",
"Label": "sub-08_SPM.mat",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-08/SPM.mat",
+ "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-08/SPM.mat",
"digest": {
- "sha256": "72a13f603f81068778e7112453946f9ea13e24771d9f061c0a5ddf0131805bb9"
+ "sha256": "cfc4a42edfa2ce9aaf5b5bbabea235dde525928ac8bb8789dae6000c73a62c00"
}
},
{
- "@id": "urn:cda76e9d-1eab-41a7-bee3-e5b36b858062",
+ "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-09/SPM.mat",
"Label": "sub-09_SPM.mat",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-09/SPM.mat",
+ "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-09/SPM.mat",
"digest": {
- "sha256": "6176e571e96deca6f880327802a63eb19dc038f1922701f4068eaf0ed6414257"
+ "sha256": "f82ba0e7b0812e1e4ca501b3ec9af5da8cc6e59a1d7e8390ae3472441d28192b"
}
},
{
- "@id": "urn:640954dc-d4ca-4c56-90d3-79b557b615c6",
+ "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-10/SPM.mat",
"Label": "sub-10_SPM.mat",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-10/SPM.mat",
+ "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-10/SPM.mat",
"digest": {
- "sha256": "e2a3867b076a8f6aa12d20a95057d38221fd5e0da5175e0b5a33b6661e811897"
+ "sha256": "27c346f569177ac9c93bc84d34c7375a540565d0755e9aae4f6f5153f54aee8e"
}
},
{
- "@id": "urn:101ace3c-4c3e-4d19-bea7-75b5a7717580",
+ "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-11/SPM.mat",
"Label": "sub-11_SPM.mat",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-11/SPM.mat",
+ "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-11/SPM.mat",
"digest": {
- "sha256": "64020b5a770246c406dd26cccf751b053d4ad6179e652f99967a109ea8ce27c0"
+ "sha256": "8937ceea6f689bbe77b9a885e59a035ee8835dd9ed54e72c534015da3f37b9bf"
}
},
{
- "@id": "urn:1a741297-35d4-4b05-886b-1d1e8c91bf2e",
+ "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-12/SPM.mat",
"Label": "sub-12_SPM.mat",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-12/SPM.mat",
+ "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-12/SPM.mat",
"digest": {
- "sha256": "630720d0b74f64a3501da3cbfbc1506affc26df70c85e6ca7f04685f0d6b54cb"
+ "sha256": "5ad1865c53953093b55177487f92e5b9dd8f4f059e2205b28fb8de04a358891a"
}
},
{
- "@id": "urn:b5ed0dcb-6f8b-4f0b-972e-0d08e249d112",
+ "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-13/SPM.mat",
"Label": "sub-13_SPM.mat",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-13/SPM.mat",
+ "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-13/SPM.mat",
"digest": {
- "sha256": "0d7c0e476a420f026c3664b827681e0cdef9b48833db4b2629293b7ee5acdf4d"
+ "sha256": "de8e6fd0ea79aa7bac1f78f13fb97e970fede0c0fe8cad9df8356df2bd27e5c5"
}
},
{
- "@id": "urn:85d40ec9-6104-4d35-a712-f30b1e91c0bc",
+ "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-14/SPM.mat",
"Label": "sub-14_SPM.mat",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-14/SPM.mat",
+ "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-14/SPM.mat",
"digest": {
- "sha256": "91f643585bc990782d2e1890bc60d454647bc6eec0850aa0e529a9378927df4e"
+ "sha256": "74459bee0eb3411118758c85edefbca8b974fe99272839b0586156031306f36f"
}
},
{
- "@id": "urn:bf004824-b637-4840-942f-369d36e3837e",
+ "@id": "bids:ds011:/derivatives/SPM/LEVEL1/sub-05/SPM.mat",
"Label": "sub-05_SPM.mat",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-05/SPM.mat",
+ "AtLocation": "ds011/derivatives/SPM/LEVEL1/sub-05/SPM.mat",
"digest": {
- "sha256": "82553bb332b3133407b1da2fd73527c99691e1fef7445c5ba8c6aa53a97da615"
+ "sha256": "d19456101522384c27a8a89e85edfa0dc62de1a5a69fe52a2a10c13b0a643c10"
}
},
{
- "@id": "urn:39022742-83e8-4de3-85de-35824e023294",
+ "@id": "urn:uuid:c9346e65-f190-4a60-9a5b-ad26f0c85da3",
"Label": "SPM.mat",
- "GeneratedBy": "urn:0e24554b-322d-4be9-87cd-9dd642325442"
+ "GeneratedBy": "urn:statsmfx-6NcnuSxV"
},
{
- "@id": "urn:99b48746-909d-452d-bf6b-24a0e1ebf9c5",
+ "@id": "urn:uuid:73c5f0c0-cfe5-4458-acfd-50c8bb5815d2",
"Label": "SPM.mat",
- "GeneratedBy": "urn:2e0e52f8-04a3-4102-b205-304afb4b5f2e"
+ "GeneratedBy": "urn:estimate-hypn0pbc"
},
{
- "@id": "urn:403c944c-e137-48ae-a96a-5bee552c4e45",
+ "@id": "urn:uuid:73bd38cc-7a73-483f-9f5e-c83b7013635a",
"Label": "SPM.mat",
- "GeneratedBy": "urn:032c0d43-1024-43f1-9646-64523294f3b1"
+ "GeneratedBy": "urn:statsmfx-Fy5cpUID"
},
{
- "@id": "urn:53c1cf75-c2b5-4387-8517-de84410720a8",
+ "@id": "urn:uuid:63220836-af6f-43c5-b08a-4f738039ab3a",
"Label": "SPM.mat",
- "GeneratedBy": "urn:b2fe76ce-e994-4c27-95fb-efa9e1b13e2a"
+ "GeneratedBy": "urn:estimate-LzIKLSqR"
},
{
- "@id": "urn:6c0d5299-32be-4a6d-8e1f-465d2b2aa15b",
+ "@id": "urn:uuid:2502b6a5-f5c5-4310-845e-816607158694",
"Label": "SPM.mat",
- "GeneratedBy": "urn:2e5ce908-c114-456f-a59e-06957d7f777e"
+ "GeneratedBy": "urn:estimate-wlbXNqhL"
}
]
}
diff --git a/examples/from_parsers/spm/spm_group_wls_batch.m b/examples/from_parsers/spm/spm_group_wls_batch.m
index 443b67c21..918737b21 100644
--- a/examples/from_parsers/spm/spm_group_wls_batch.m
+++ b/examples/from_parsers/spm/spm_group_wls_batch.m
@@ -6,20 +6,20 @@
matlabbatch{1}.spm.stats.mfx.ffx.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_WLS_t_test'};
%%
matlabbatch{1}.spm.stats.mfx.ffx.spmmat = {
- '/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-01/SPM.mat'
- '/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-02/SPM.mat'
- '/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-03/SPM.mat'
- '/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-04/SPM.mat'
- '/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-06/SPM.mat'
- '/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-07/SPM.mat'
- '/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-08/SPM.mat'
- '/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-09/SPM.mat'
- '/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-10/SPM.mat'
- '/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-11/SPM.mat'
- '/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-12/SPM.mat'
- '/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-13/SPM.mat'
- '/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-14/SPM.mat'
- '/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-05/SPM.mat'
+ 'ds011/derivatives/SPM/LEVEL1/sub-01/SPM.mat'
+ 'ds011/derivatives/SPM/LEVEL1/sub-02/SPM.mat'
+ 'ds011/derivatives/SPM/LEVEL1/sub-03/SPM.mat'
+ 'ds011/derivatives/SPM/LEVEL1/sub-04/SPM.mat'
+ 'ds011/derivatives/SPM/LEVEL1/sub-06/SPM.mat'
+ 'ds011/derivatives/SPM/LEVEL1/sub-07/SPM.mat'
+ 'ds011/derivatives/SPM/LEVEL1/sub-08/SPM.mat'
+ 'ds011/derivatives/SPM/LEVEL1/sub-09/SPM.mat'
+ 'ds011/derivatives/SPM/LEVEL1/sub-10/SPM.mat'
+ 'ds011/derivatives/SPM/LEVEL1/sub-11/SPM.mat'
+ 'ds011/derivatives/SPM/LEVEL1/sub-12/SPM.mat'
+ 'ds011/derivatives/SPM/LEVEL1/sub-13/SPM.mat'
+ 'ds011/derivatives/SPM/LEVEL1/sub-14/SPM.mat'
+ 'ds011/derivatives/SPM/LEVEL1/sub-05/SPM.mat'
};
%%
matlabbatch{2}.spm.stats.fmri_est.spmmat(1) = cfg_dep('FFX Specification: SPM.mat File', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));
diff --git a/examples/from_parsers/spm/spm_group_wls_batch.png b/examples/from_parsers/spm/spm_group_wls_batch.png
index 17b7cb125..d52267ec5 100644
Binary files a/examples/from_parsers/spm/spm_group_wls_batch.png and b/examples/from_parsers/spm/spm_group_wls_batch.png differ
diff --git a/examples/from_parsers/spm/spm_hrf_fir_batch.jsonld b/examples/from_parsers/spm/spm_hrf_fir_batch.jsonld
index 9a0c669f9..d48e333b4 100644
--- a/examples/from_parsers/spm/spm_hrf_fir_batch.jsonld
+++ b/examples/from_parsers/spm/spm_hrf_fir_batch.jsonld
@@ -4,63 +4,63 @@
"Records": {
"Software": [
{
- "@id": "urn:bbcb84ec-a02f-4564-9cb9-372890d1db97",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:spm-qiv4p9Xd",
"@type": "prov:SoftwareAgent",
"Label": "SPM",
- "Version": "SPM12r7224"
+ "Version": "SPM12r7224",
+ "AltIdentifier": "RRID:SCR_007037"
}
],
"Activities": [
{
- "@id": "urn:795e07b1-1d9b-4dab-a710-0d6826630aca",
+ "@id": "urn:movefile-yFdmdoKh",
"Label": "Move file",
"Used": [
- "urn:08f0a212-4e7f-4c0f-972e-7e64312cdf16"
+ "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
],
- "AssociatedWith": "urn:bbcb84ec-a02f-4564-9cb9-372890d1db97",
- "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
+ "AssociatedWith": "urn:spm-qiv4p9Xd",
+ "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};",
"Parameters": {
- "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
+ "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'}"
}
},
{
- "@id": "urn:fdec7cf7-b051-44d5-a381-e3b0ebab89f3",
+ "@id": "urn:movefile-y7t2Z5pu",
"Label": "Move file",
"Used": [
- "urn:1ac2dcd4-a126-4a34-a538-0abc16b33907"
+ "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz"
],
- "AssociatedWith": "urn:bbcb84ec-a02f-4564-9cb9-372890d1db97",
- "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
+ "AssociatedWith": "urn:spm-qiv4p9Xd",
+ "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};",
"Parameters": {
- "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
+ "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'}"
}
},
{
- "@id": "urn:83cb5338-7333-4019-a2bf-e413de151931",
+ "@id": "urn:gunzip3-ZG5WLt1m",
"Label": "Gunzip",
"Used": [
- "urn:0fe8ebe4-db43-4829-83ac-469fc72abfdc"
+ "urn:uuid:9e0ef7b6-f708-4c54-b7d0-0dda9e7b2dcd"
],
- "AssociatedWith": "urn:bbcb84ec-a02f-4564-9cb9-372890d1db97",
+ "AssociatedWith": "urn:spm-qiv4p9Xd",
"Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:ca9d036e-8e6c-430a-9cdb-c8333b595eeb",
+ "@id": "urn:gunzip4-lqCoqCpN",
"Label": "Gunzip",
"Used": [
- "urn:3f4c9f31-a464-4c8c-8391-72d97a89b53c"
+ "urn:uuid:f10ba202-e81b-4c88-a2e0-da4b10f1081f"
],
- "AssociatedWith": "urn:bbcb84ec-a02f-4564-9cb9-372890d1db97",
+ "AssociatedWith": "urn:spm-qiv4p9Xd",
"Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:127a38fe-34a4-4248-9396-9b5106b4bca0",
+ "@id": "urn:realign5-oU7kyoTI",
"Label": "Realign",
"Used": [
- "urn:b361905e-407f-4981-8e58-3208f23a069a"
+ "urn:uuid:e36fad5d-dcec-40cf-b6ea-df80a876f12d"
],
- "AssociatedWith": "urn:bbcb84ec-a02f-4564-9cb9-372890d1db97",
+ "AssociatedWith": "urn:spm-qiv4p9Xd",
"Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
"Parameters": {
"eoptions.quality": "0.9",
@@ -78,13 +78,13 @@
}
},
{
- "@id": "urn:9ae838f4-3473-4c09-af74-fad420e11482",
+ "@id": "urn:coregist-oH4OCWWT",
"Label": "Coregister",
"Used": [
- "urn:f466d8dd-a512-444e-87cd-fbea05a30301",
- "urn:fdfa03a0-afb7-4faf-ac92-c3820dcd9366"
+ "urn:uuid:b2e934fb-5f1c-40bf-b5b6-51b885d8faff",
+ "urn:uuid:e233cc3f-54dc-4464-8f5a-10bb7b09e039"
],
- "AssociatedWith": "urn:bbcb84ec-a02f-4564-9cb9-372890d1db97",
+ "AssociatedWith": "urn:spm-qiv4p9Xd",
"Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
"Parameters": {
"other": "{''}",
@@ -95,12 +95,12 @@
}
},
{
- "@id": "urn:ba57b40b-bdc1-4b20-baa6-a0a500e6d912",
+ "@id": "urn:segment7-e8tpZVIm",
"Label": "Segment",
"Used": [
- "urn:fdfa03a0-afb7-4faf-ac92-c3820dcd9366"
+ "urn:uuid:b2e934fb-5f1c-40bf-b5b6-51b885d8faff"
],
- "AssociatedWith": "urn:bbcb84ec-a02f-4564-9cb9-372890d1db97",
+ "AssociatedWith": "urn:spm-qiv4p9Xd",
"Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
"Parameters": {
"channel.biasreg": "0.001",
@@ -140,13 +140,13 @@
}
},
{
- "@id": "urn:4495f152-217c-4c22-8568-7fa88bb8598d",
+ "@id": "urn:normaliz-Keen4iD8",
"Label": "Normalize",
"Used": [
- "urn:8ddecffb-ef11-4fc1-87c4-ab560a8c9f96",
- "urn:f466d8dd-a512-444e-87cd-fbea05a30301"
+ "bids::c1anat_sub-01_T1w.nii",
+ "urn:uuid:e233cc3f-54dc-4464-8f5a-10bb7b09e039"
],
- "AssociatedWith": "urn:bbcb84ec-a02f-4564-9cb9-372890d1db97",
+ "AssociatedWith": "urn:spm-qiv4p9Xd",
"Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -156,12 +156,12 @@
}
},
{
- "@id": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
+ "@id": "urn:normaliz-grJqrlDm",
"Label": "Normalize",
"Used": [
- "urn:8ddecffb-ef11-4fc1-87c4-ab560a8c9f96"
+ "bids::c1anat_sub-01_T1w.nii"
],
- "AssociatedWith": "urn:bbcb84ec-a02f-4564-9cb9-372890d1db97",
+ "AssociatedWith": "urn:spm-qiv4p9Xd",
"Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -171,12 +171,12 @@
}
},
{
- "@id": "urn:c358f7b3-73cf-45d3-acf3-497f46cedbea",
+ "@id": "urn:smooth10-hDFOI74w",
"Label": "Smooth",
"Used": [
- "urn:7e3db413-8335-4676-9cf6-1602a3b1f94f"
+ "urn:uuid:cb881a9c-46a8-4c17-a093-4ff7d167e3a6"
],
- "AssociatedWith": "urn:bbcb84ec-a02f-4564-9cb9-372890d1db97",
+ "AssociatedWith": "urn:spm-qiv4p9Xd",
"Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
"Parameters": {
"fwhm": "[6, 6, 6]",
@@ -186,14 +186,14 @@
}
},
{
- "@id": "urn:776184ac-3435-4832-bef8-2c899faf87b9",
+ "@id": "urn:statdesi-X0E1qIrM",
"Label": "Stat Design",
"Used": [
- "urn:b7fec75e-d2e7-44b7-8375-e8f8f053e571",
- "urn:4256ab70-0769-45e6-a40b-c7adda1ca1d2"
+ "urn:uuid:d6abb162-b880-4a28-9176-a59c7e5e4b63",
+ "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
],
- "AssociatedWith": "urn:bbcb84ec-a02f-4564-9cb9-372890d1db97",
- "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_FIR_basis'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.fir.length = 20;\nmatlabbatch{11}.spm.stats.fmri_spec.bases.fir.order = 10;\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
+ "AssociatedWith": "urn:spm-qiv4p9Xd",
+ "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_FIR_basis'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.fir.length = 20;\nmatlabbatch{11}.spm.stats.fmri_spec.bases.fir.order = 10;\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
"Parameters": {
"dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_FIR_basis'}",
"timing.units": "'secs'",
@@ -215,12 +215,12 @@
}
},
{
- "@id": "urn:3aa37749-2a5c-4b29-9c96-95f12460c619",
+ "@id": "urn:estimate-z152r5lq",
"Label": "Estimate stat.",
"Used": [
- "urn:3360db04-b715-4330-b177-7ab1cbce8211"
+ "urn:uuid:0c7b1d5c-c38e-40bd-a371-ee1b23b22d29"
],
- "AssociatedWith": "urn:bbcb84ec-a02f-4564-9cb9-372890d1db97",
+ "AssociatedWith": "urn:spm-qiv4p9Xd",
"Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
"Parameters": {
"write_residuals": "0",
@@ -228,12 +228,12 @@
}
},
{
- "@id": "urn:76dcbbc1-5238-4257-916f-2a589f7983e7",
+ "@id": "urn:estimate-E022Yway",
"Label": "Estimate contrast",
"Used": [
- "urn:02fc8327-ca8d-4b6a-9e0c-339117d4da61"
+ "urn:uuid:75a17631-bcb4-4160-bd04-3eaef4c79383"
],
- "AssociatedWith": "urn:bbcb84ec-a02f-4564-9cb9-372890d1db97",
+ "AssociatedWith": "urn:spm-qiv4p9Xd",
"Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.fcon.name = 'Tone Counting vs Baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.fcon.weights = [1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1];\nmatlabbatch{13}.spm.stats.con.consess{1}.fcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
"Parameters": {
"consess{1}.fcon.name": "'Tone Counting vs Baseline'",
@@ -243,12 +243,12 @@
}
},
{
- "@id": "urn:62ba7534-d1d7-4bed-9ac3-95800b0d03ea",
+ "@id": "urn:threshol-RMzbW9P9",
"Label": "Threshold",
"Used": [
- "urn:032b261b-42a2-41b6-979f-dbd8a82c6d40"
+ "urn:uuid:bd54c40a-bea2-4186-86c3-b863563f214f"
],
- "AssociatedWith": "urn:bbcb84ec-a02f-4564-9cb9-372890d1db97",
+ "AssociatedWith": "urn:spm-qiv4p9Xd",
"Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.tspm.basename = 'thresh';",
"Parameters": {
"conspec.titlestr": "''",
@@ -266,98 +266,96 @@
],
"Entities": [
{
- "@id": "urn:08f0a212-4e7f-4c0f-972e-7e64312cdf16",
+ "@id": "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+ "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"digest": {
- "sha256": "52cc2a3822512db5be3accc8263f2ac1338f32fad8af63cc81fb5af2f335c509"
+ "sha256": "b3d8382360fbbc58cbd8c9e654ddda30b9f0318cf04ebd7539ec75bd724041d2"
}
},
{
- "@id": "urn:1ac2dcd4-a126-4a34-a538-0abc16b33907",
+ "@id": "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz",
"Label": "anat_sub-01_T1w.nii.gz",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+ "AtLocation": "ds011/sub-01/anat/sub-01_T1w.nii.gz",
"digest": {
- "sha256": "3d9457fa7712b355d6569522ca80a6dfd70a40b82e6aa0a9364513cf04916dbb"
+ "sha256": "70b9327067cc5200330e04e70b22a41db5aa3b78f978060f61f49bd3a45d125e"
}
},
{
- "@id": "urn:0fe8ebe4-db43-4829-83ac-469fc72abfdc",
+ "@id": "urn:uuid:9e0ef7b6-f708-4c54-b7d0-0dda9e7b2dcd",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "GeneratedBy": "urn:795e07b1-1d9b-4dab-a710-0d6826630aca"
+ "GeneratedBy": "urn:movefile-yFdmdoKh"
},
{
- "@id": "urn:3f4c9f31-a464-4c8c-8391-72d97a89b53c",
+ "@id": "urn:uuid:f10ba202-e81b-4c88-a2e0-da4b10f1081f",
"Label": "anat_sub-01_T1w.nii.gz",
- "GeneratedBy": "urn:fdec7cf7-b051-44d5-a381-e3b0ebab89f3"
+ "GeneratedBy": "urn:movefile-y7t2Z5pu"
},
{
- "@id": "urn:b361905e-407f-4981-8e58-3208f23a069a",
+ "@id": "urn:uuid:e36fad5d-dcec-40cf-b6ea-df80a876f12d",
"Label": "func_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:83cb5338-7333-4019-a2bf-e413de151931"
+ "GeneratedBy": "urn:gunzip3-ZG5WLt1m"
},
{
- "@id": "urn:f466d8dd-a512-444e-87cd-fbea05a30301",
+ "@id": "urn:uuid:e233cc3f-54dc-4464-8f5a-10bb7b09e039",
"Label": "meanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:127a38fe-34a4-4248-9396-9b5106b4bca0"
+ "GeneratedBy": "urn:realign5-oU7kyoTI"
},
{
- "@id": "urn:fdfa03a0-afb7-4faf-ac92-c3820dcd9366",
+ "@id": "urn:uuid:b2e934fb-5f1c-40bf-b5b6-51b885d8faff",
"Label": "anat_sub-01_T1w.nii",
- "GeneratedBy": "urn:ca9d036e-8e6c-430a-9cdb-c8333b595eeb"
+ "GeneratedBy": "urn:gunzip4-lqCoqCpN"
},
{
- "@id": "urn:8ddecffb-ef11-4fc1-87c4-ab560a8c9f96",
+ "@id": "bids::c1anat_sub-01_T1w.nii",
"Label": "segment1",
- "Atlocation": "c1xxx.nii.gz",
- "GeneratedBy": "urn:ba57b40b-bdc1-4b20-baa6-a0a500e6d912",
"AtLocation": "c1anat_sub-01_T1w.nii",
+ "GeneratedBy": "urn:segment7-e8tpZVIm",
"digest": {
"sha256": "61ca923955d0a5c9088df9e258f41644067ec964e1c9a83284ba03b0515079b0"
}
},
{
- "@id": "urn:b396ec48-bd2b-4ab4-9f0b-81683e0d3dbb",
+ "@id": "bids::c2anat_sub-01_T1w.nii",
"Label": "segment2",
- "Atlocation": "c2xxx.nii.gz",
- "GeneratedBy": "urn:ba57b40b-bdc1-4b20-baa6-a0a500e6d912",
"AtLocation": "c2anat_sub-01_T1w.nii",
+ "GeneratedBy": "urn:segment7-e8tpZVIm",
"digest": {
"sha256": "10ad88ebeebebd0bd03ccbdd4df92d500d28d14715fa5375fd35589caddf49a6"
}
},
{
- "@id": "urn:7e3db413-8335-4676-9cf6-1602a3b1f94f",
+ "@id": "urn:uuid:cb881a9c-46a8-4c17-a093-4ff7d167e3a6",
"Label": "wsegment1",
- "GeneratedBy": "urn:4495f152-217c-4c22-8568-7fa88bb8598d"
+ "GeneratedBy": "urn:normaliz-Keen4iD8"
},
{
- "@id": "urn:4256ab70-0769-45e6-a40b-c7adda1ca1d2",
+ "@id": "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"Label": "ONSETS_sub-01-MultiCond.mat",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+ "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"digest": {
- "sha256": "be4671d4f9dc480dd3e5be19aeeab2756f7afdc3b32d81e071685d7a4eafcfed"
+ "sha256": "5599e80629bb4d66cdbfb357511c04060bd3d37cdbfe2a4cd701a2979e9f6610"
}
},
{
- "@id": "urn:b7fec75e-d2e7-44b7-8375-e8f8f053e571",
+ "@id": "urn:uuid:d6abb162-b880-4a28-9176-a59c7e5e4b63",
"Label": "swsegment1",
- "GeneratedBy": "urn:c358f7b3-73cf-45d3-acf3-497f46cedbea"
+ "GeneratedBy": "urn:smooth10-hDFOI74w"
},
{
- "@id": "urn:3360db04-b715-4330-b177-7ab1cbce8211",
+ "@id": "urn:uuid:0c7b1d5c-c38e-40bd-a371-ee1b23b22d29",
"Label": "SPM.mat",
- "GeneratedBy": "urn:776184ac-3435-4832-bef8-2c899faf87b9"
+ "GeneratedBy": "urn:statdesi-X0E1qIrM"
},
{
- "@id": "urn:02fc8327-ca8d-4b6a-9e0c-339117d4da61",
+ "@id": "urn:uuid:75a17631-bcb4-4160-bd04-3eaef4c79383",
"Label": "SPM.mat",
- "GeneratedBy": "urn:3aa37749-2a5c-4b29-9c96-95f12460c619"
+ "GeneratedBy": "urn:estimate-z152r5lq"
},
{
- "@id": "urn:032b261b-42a2-41b6-979f-dbd8a82c6d40",
+ "@id": "urn:uuid:bd54c40a-bea2-4186-86c3-b863563f214f",
"Label": "SPM.mat",
- "GeneratedBy": "urn:76dcbbc1-5238-4257-916f-2a589f7983e7"
+ "GeneratedBy": "urn:estimate-E022Yway"
}
]
}
diff --git a/examples/from_parsers/spm/spm_hrf_fir_batch.m b/examples/from_parsers/spm/spm_hrf_fir_batch.m
index 21db90a1b..0747f0960 100644
--- a/examples/from_parsers/spm/spm_hrf_fir_batch.m
+++ b/examples/from_parsers/spm/spm_hrf_fir_batch.m
@@ -3,10 +3,10 @@
% spm SPM - SPM12 (12.1)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------
-matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};
-matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};
-matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};
-matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};
+matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};
+matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};
+matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};
+matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};
matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));
@@ -90,7 +90,7 @@
matlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;
matlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});
-matlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};
+matlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};
matlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});
matlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};
matlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;
diff --git a/examples/from_parsers/spm/spm_hrf_fir_batch.png b/examples/from_parsers/spm/spm_hrf_fir_batch.png
index a0ef3c25a..b05a9bf18 100644
Binary files a/examples/from_parsers/spm/spm_hrf_fir_batch.png and b/examples/from_parsers/spm/spm_hrf_fir_batch.png differ
diff --git a/examples/from_parsers/spm/spm_non_sphericity_batch.jsonld b/examples/from_parsers/spm/spm_non_sphericity_batch.jsonld
index ffc0f9e87..24edb106c 100644
--- a/examples/from_parsers/spm/spm_non_sphericity_batch.jsonld
+++ b/examples/from_parsers/spm/spm_non_sphericity_batch.jsonld
@@ -4,19 +4,19 @@
"Records": {
"Software": [
{
- "@id": "urn:1f3d8475-5233-41cd-acd5-a8123bd9a61c",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:spm-VoEw1onB",
"@type": "prov:SoftwareAgent",
"Label": "SPM",
- "Version": "SPM12r7224"
+ "Version": "SPM12r7224",
+ "AltIdentifier": "RRID:SCR_007037"
}
],
"Activities": [
{
- "@id": "urn:b6460b46-78d0-4ffb-881c-50ab145c4342",
+ "@id": "urn:statsfac-cEPGgC8F",
"Label": "stats.factorial_design",
"Used": [],
- "AssociatedWith": "urn:1f3d8475-5233-41cd-acd5-a8123bd9a61c",
+ "AssociatedWith": "urn:spm-VoEw1onB",
"Command": "matlabbatch{1}.spm.stats.factorial_design.dir = {'/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Group/Informed'};\nmatlabbatch{1}.spm.stats.factorial_design.des.fd.fact.name = 'Basis';\nmatlabbatch{1}.spm.stats.factorial_design.des.fd.fact.levels = 3;\nmatlabbatch{1}.spm.stats.factorial_design.des.fd.fact.dept = 1;\nmatlabbatch{1}.spm.stats.factorial_design.des.fd.fact.variance = 1;\nmatlabbatch{1}.spm.stats.factorial_design.des.fd.fact.gmsca = 0;\nmatlabbatch{1}.spm.stats.factorial_design.des.fd.fact.ancova = 0;\nmatlabbatch{1}.spm.stats.factorial_design.des.fd.icell(1).levels = 1;\nmatlabbatch{1}.spm.stats.factorial_design.des.fd.icell(1).scans = {'/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub01/CanonicalHRF/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub02/CanonicalHRF/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub03/CanonicalHRF/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub04/CanonicalHRF/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub05/CanonicalHRF/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub06/CanonicalHRF/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub07/CanonicalHRF/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub08/CanonicalHRF/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub09/CanonicalHRF/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub10/CanonicalHRF/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub11/CanonicalHRF/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub12/CanonicalHRF/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub13/CanonicalHRF/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub14/CanonicalHRF/con_0001.nii,1',};\nmatlabbatch{1}.spm.stats.factorial_design.des.fd.icell(2).levels = 2;\nmatlabbatch{1}.spm.stats.factorial_design.des.fd.icell(2).scans = {'/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub01/CanonicalHRF/con_0005.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub02/CanonicalHRF/con_0005.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub03/CanonicalHRF/con_0005.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub04/CanonicalHRF/con_0005.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub05/CanonicalHRF/con_0005.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub06/CanonicalHRF/con_0005.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub07/CanonicalHRF/con_0005.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub08/CanonicalHRF/con_0005.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub09/CanonicalHRF/con_0005.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub10/CanonicalHRF/con_0005.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub11/CanonicalHRF/con_0005.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub12/CanonicalHRF/con_0005.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub13/CanonicalHRF/con_0005.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub14/CanonicalHRF/con_0005.nii,1',};\nmatlabbatch{1}.spm.stats.factorial_design.des.fd.icell(3).levels = 3;\nmatlabbatch{1}.spm.stats.factorial_design.des.fd.icell(3).scans = {'/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub01/CanonicalHRF/con_0009.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub02/CanonicalHRF/con_0009.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub03/CanonicalHRF/con_0009.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub04/CanonicalHRF/con_0009.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub05/CanonicalHRF/con_0009.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub06/CanonicalHRF/con_0009.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub07/CanonicalHRF/con_0009.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub08/CanonicalHRF/con_0009.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub09/CanonicalHRF/con_0009.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub10/CanonicalHRF/con_0009.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub11/CanonicalHRF/con_0009.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub12/CanonicalHRF/con_0009.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub13/CanonicalHRF/con_0009.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub14/CanonicalHRF/con_0009.nii,1',};\nmatlabbatch{1}.spm.stats.factorial_design.des.fd.contrasts = 1;\nmatlabbatch{1}.spm.stats.factorial_design.cov = struct('c', {}, 'cname', {}, 'iCFI', {}, 'iCC', {});\nmatlabbatch{1}.spm.stats.factorial_design.multi_cov = struct('files', {}, 'iCFI', {}, 'iCC', {});\nmatlabbatch{1}.spm.stats.factorial_design.masking.tm.tm_none = 1;\nmatlabbatch{1}.spm.stats.factorial_design.masking.im = 1;\nmatlabbatch{1}.spm.stats.factorial_design.masking.em = {''};\nmatlabbatch{1}.spm.stats.factorial_design.globalc.g_omit = 1;\nmatlabbatch{1}.spm.stats.factorial_design.globalm.gmsca.gmsca_no = 1;\nmatlabbatch{1}.spm.stats.factorial_design.globalm.glonorm = 1;",
"Parameters": {
"dir": "{'/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Group/Informed'}",
@@ -44,12 +44,12 @@
}
},
{
- "@id": "urn:b11d414b-9380-422f-bf6e-86d8eabb6e1d",
+ "@id": "urn:estimate-qI8NXzKL",
"Label": "Estimate stat.",
"Used": [
- "urn:1d50dc8c-5f1c-432f-816c-beee79b3a710"
+ "urn:uuid:e7a5c2e4-5784-49b4-bc5c-43f34a712c0e"
],
- "AssociatedWith": "urn:1f3d8475-5233-41cd-acd5-a8123bd9a61c",
+ "AssociatedWith": "urn:spm-VoEw1onB",
"Command": "matlabbatch{2}.spm.stats.fmri_est.spmmat(1) = cfg_dep('Factorial design specification: SPM.mat File', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{2}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{2}.spm.stats.fmri_est.method.Classical = 1;",
"Parameters": {
"write_residuals": "0",
@@ -57,12 +57,12 @@
}
},
{
- "@id": "urn:432b8f41-0b8f-4a0f-a96e-ef80c4ddc637",
+ "@id": "urn:estimate-bzJ4hMUW",
"Label": "Estimate contrast",
"Used": [
- "urn:7df7b046-cacd-451d-9d1e-7cfff4b51edc"
+ "urn:uuid:4a2aa5a5-953a-4787-a638-d162b4fce3e0"
],
- "AssociatedWith": "urn:1f3d8475-5233-41cd-acd5-a8123bd9a61c",
+ "AssociatedWith": "urn:spm-VoEw1onB",
"Command": "matlabbatch{3}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{3}.spm.stats.con.consess{1}.tcon.name = 'mr vs plain informed basis';\nmatlabbatch{3}.spm.stats.con.consess{1}.tcon.weights = 1;\nmatlabbatch{3}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{3}.spm.stats.con.delete = 0;",
"Parameters": {
"consess{1}.tcon.name": "'mr vs plain informed basis'",
@@ -72,12 +72,12 @@
}
},
{
- "@id": "urn:7037a182-e09d-4c5f-96d7-6374e329ed9d",
+ "@id": "urn:threshol-mFFNvTJp",
"Label": "Threshold",
"Used": [
- "urn:c34f731d-5f1c-4a5a-9105-7233aca92f22"
+ "urn:uuid:b5676206-f275-4e9c-a547-dfc05f32afdf"
],
- "AssociatedWith": "urn:1f3d8475-5233-41cd-acd5-a8123bd9a61c",
+ "AssociatedWith": "urn:spm-VoEw1onB",
"Command": "matlabbatch{4}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{4}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{4}.spm.stats.results.conspec.contrasts = 1;\nmatlabbatch{4}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{4}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{4}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{4}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{4}.spm.stats.results.units = 1;\nmatlabbatch{4}.spm.stats.results.print = 'pdf';\nmatlabbatch{4}.spm.stats.results.write.none = 1;",
"Parameters": {
"conspec.titlestr": "''",
@@ -94,19 +94,19 @@
],
"Entities": [
{
- "@id": "urn:1d50dc8c-5f1c-432f-816c-beee79b3a710",
+ "@id": "urn:uuid:e7a5c2e4-5784-49b4-bc5c-43f34a712c0e",
"Label": "SPM.mat",
- "GeneratedBy": "urn:b6460b46-78d0-4ffb-881c-50ab145c4342"
+ "GeneratedBy": "urn:statsfac-cEPGgC8F"
},
{
- "@id": "urn:7df7b046-cacd-451d-9d1e-7cfff4b51edc",
+ "@id": "urn:uuid:4a2aa5a5-953a-4787-a638-d162b4fce3e0",
"Label": "SPM.mat",
- "GeneratedBy": "urn:b11d414b-9380-422f-bf6e-86d8eabb6e1d"
+ "GeneratedBy": "urn:estimate-qI8NXzKL"
},
{
- "@id": "urn:c34f731d-5f1c-4a5a-9105-7233aca92f22",
+ "@id": "urn:uuid:b5676206-f275-4e9c-a547-dfc05f32afdf",
"Label": "SPM.mat",
- "GeneratedBy": "urn:432b8f41-0b8f-4a0f-a96e-ef80c4ddc637"
+ "GeneratedBy": "urn:estimate-bzJ4hMUW"
}
]
}
diff --git a/examples/from_parsers/spm/spm_non_sphericity_batch.png b/examples/from_parsers/spm/spm_non_sphericity_batch.png
index d25e8e011..9685b1bce 100644
Binary files a/examples/from_parsers/spm/spm_non_sphericity_batch.png and b/examples/from_parsers/spm/spm_non_sphericity_batch.png differ
diff --git a/examples/from_parsers/spm/spm_partial_conjunction_batch.jsonld b/examples/from_parsers/spm/spm_partial_conjunction_batch.jsonld
index be8976efa..768f2a56d 100644
--- a/examples/from_parsers/spm/spm_partial_conjunction_batch.jsonld
+++ b/examples/from_parsers/spm/spm_partial_conjunction_batch.jsonld
@@ -4,63 +4,63 @@
"Records": {
"Software": [
{
- "@id": "urn:14cc38ee-b9f4-4f09-8da4-2ff6893c9da8",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:spm-kRUWK166",
"@type": "prov:SoftwareAgent",
"Label": "SPM",
- "Version": "SPM12r7224"
+ "Version": "SPM12r7224",
+ "AltIdentifier": "RRID:SCR_007037"
}
],
"Activities": [
{
- "@id": "urn:3aa74700-0b41-45a3-9889-68aad2d2e060",
+ "@id": "urn:movefile-E9SUEKGJ",
"Label": "Move file",
"Used": [
- "urn:c495f808-45f9-4230-9aac-403fe68f2a91"
+ "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
],
- "AssociatedWith": "urn:14cc38ee-b9f4-4f09-8da4-2ff6893c9da8",
- "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
+ "AssociatedWith": "urn:spm-kRUWK166",
+ "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};",
"Parameters": {
- "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
+ "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'}"
}
},
{
- "@id": "urn:7459b441-2e93-4d1a-a6fe-bf28a3d78593",
+ "@id": "urn:movefile-UEkIbFqL",
"Label": "Move file",
"Used": [
- "urn:ba83ee9c-2d02-4116-a2ea-e5e4f1c78a9d"
+ "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz"
],
- "AssociatedWith": "urn:14cc38ee-b9f4-4f09-8da4-2ff6893c9da8",
- "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
+ "AssociatedWith": "urn:spm-kRUWK166",
+ "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};",
"Parameters": {
- "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
+ "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'}"
}
},
{
- "@id": "urn:9bc9d34b-4426-4e61-9d88-ef8ef4e54805",
+ "@id": "urn:gunzip3-qGrj0paZ",
"Label": "Gunzip",
"Used": [
- "urn:b3e881ab-5017-474d-ab20-1ff4734e60f1"
+ "urn:uuid:020b2bdf-e472-42a1-9e43-8c9f9fbeb376"
],
- "AssociatedWith": "urn:14cc38ee-b9f4-4f09-8da4-2ff6893c9da8",
+ "AssociatedWith": "urn:spm-kRUWK166",
"Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:77123f02-8628-496b-ae8c-94d6cbb0a645",
+ "@id": "urn:gunzip4-X87P6yn3",
"Label": "Gunzip",
"Used": [
- "urn:5e650fe4-797e-43ba-a8e5-78407a74f7b4"
+ "urn:uuid:b0e1709d-5501-4e9a-bd09-0f2c82c09610"
],
- "AssociatedWith": "urn:14cc38ee-b9f4-4f09-8da4-2ff6893c9da8",
+ "AssociatedWith": "urn:spm-kRUWK166",
"Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:e5c4e54e-7449-4454-916d-ac095d2d8c98",
+ "@id": "urn:realign5-ZqZuI9nU",
"Label": "Realign",
"Used": [
- "urn:94d83b6c-0071-40c5-b3ad-9687a6570107"
+ "urn:uuid:e7827303-0d45-40a1-a675-c59efc4101fc"
],
- "AssociatedWith": "urn:14cc38ee-b9f4-4f09-8da4-2ff6893c9da8",
+ "AssociatedWith": "urn:spm-kRUWK166",
"Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
"Parameters": {
"eoptions.quality": "0.9",
@@ -78,13 +78,13 @@
}
},
{
- "@id": "urn:65ba8e42-11a5-4a89-805d-2befe29d2c82",
+ "@id": "urn:coregist-U7YxLQ11",
"Label": "Coregister",
"Used": [
- "urn:543ec73e-7a7b-4f1c-b0f2-5e4faa4a024a",
- "urn:736f8ab3-cae1-4022-9c97-ba8843782a36"
+ "urn:uuid:705569ce-f0f4-4551-b596-8e52a4b35e54",
+ "urn:uuid:dad38e4b-0886-4822-ba34-c1bffa39acc8"
],
- "AssociatedWith": "urn:14cc38ee-b9f4-4f09-8da4-2ff6893c9da8",
+ "AssociatedWith": "urn:spm-kRUWK166",
"Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
"Parameters": {
"other": "{''}",
@@ -95,12 +95,12 @@
}
},
{
- "@id": "urn:ce99dac3-455e-42e6-97d0-708e6a12d120",
+ "@id": "urn:segment7-wIsiP0z9",
"Label": "Segment",
"Used": [
- "urn:736f8ab3-cae1-4022-9c97-ba8843782a36"
+ "urn:uuid:705569ce-f0f4-4551-b596-8e52a4b35e54"
],
- "AssociatedWith": "urn:14cc38ee-b9f4-4f09-8da4-2ff6893c9da8",
+ "AssociatedWith": "urn:spm-kRUWK166",
"Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
"Parameters": {
"channel.biasreg": "0.001",
@@ -140,13 +140,13 @@
}
},
{
- "@id": "urn:95dd9372-af2f-48c2-9239-2fa721e54fa1",
+ "@id": "urn:normaliz-prV8DwTN",
"Label": "Normalize",
"Used": [
- "urn:3a8fa6eb-a642-4a2b-983c-79bd02ca66f8",
- "urn:543ec73e-7a7b-4f1c-b0f2-5e4faa4a024a"
+ "bids::c1anat_sub-01_T1w.nii",
+ "urn:uuid:dad38e4b-0886-4822-ba34-c1bffa39acc8"
],
- "AssociatedWith": "urn:14cc38ee-b9f4-4f09-8da4-2ff6893c9da8",
+ "AssociatedWith": "urn:spm-kRUWK166",
"Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -156,12 +156,12 @@
}
},
{
- "@id": "urn:3d08452f-2ec9-47ad-be79-1d9fd0c690c2",
+ "@id": "urn:normaliz-t1VMS4pO",
"Label": "Normalize",
"Used": [
- "urn:3a8fa6eb-a642-4a2b-983c-79bd02ca66f8"
+ "bids::c1anat_sub-01_T1w.nii"
],
- "AssociatedWith": "urn:14cc38ee-b9f4-4f09-8da4-2ff6893c9da8",
+ "AssociatedWith": "urn:spm-kRUWK166",
"Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -171,12 +171,12 @@
}
},
{
- "@id": "urn:3ad61e65-704a-4488-8b98-355fd8537175",
+ "@id": "urn:smooth10-b8F6wlde",
"Label": "Smooth",
"Used": [
- "urn:40705e2b-01dd-4e4b-a30f-4876f90382bb"
+ "urn:uuid:383bcc26-9c00-47ec-8a5b-78af546c286c"
],
- "AssociatedWith": "urn:14cc38ee-b9f4-4f09-8da4-2ff6893c9da8",
+ "AssociatedWith": "urn:spm-kRUWK166",
"Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
"Parameters": {
"fwhm": "[6, 6, 6]",
@@ -186,14 +186,14 @@
}
},
{
- "@id": "urn:bbe97082-e102-4703-8c89-979834092600",
+ "@id": "urn:statdesi-VDl76uNO",
"Label": "Stat Design",
"Used": [
- "urn:9f71d53e-4e02-4a4c-a895-35ba16cbe373",
- "urn:230eecc7-aae1-43d0-af4a-f49dd70b07b1"
+ "urn:uuid:bbcd8fb6-282c-4086-8603-fee526502c2d",
+ "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
],
- "AssociatedWith": "urn:14cc38ee-b9f4-4f09-8da4-2ff6893c9da8",
- "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_conjunction'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
+ "AssociatedWith": "urn:spm-kRUWK166",
+ "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_conjunction'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
"Parameters": {
"dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_conjunction'}",
"timing.units": "'secs'",
@@ -214,12 +214,12 @@
}
},
{
- "@id": "urn:10717391-dda6-43da-8bb9-d65425d0567e",
+ "@id": "urn:estimate-zzN84ivS",
"Label": "Estimate stat.",
"Used": [
- "urn:5335c81d-8e46-452b-9092-fb041b634d5f"
+ "urn:uuid:d6974014-232a-4fc3-93ff-dd5858b45621"
],
- "AssociatedWith": "urn:14cc38ee-b9f4-4f09-8da4-2ff6893c9da8",
+ "AssociatedWith": "urn:spm-kRUWK166",
"Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
"Parameters": {
"write_residuals": "0",
@@ -227,12 +227,12 @@
}
},
{
- "@id": "urn:6354be3e-5870-480b-a4e9-c0337b907c91",
+ "@id": "urn:estimate-kDKaGYJ3",
"Label": "Estimate contrast",
"Used": [
- "urn:4eec8486-836e-48a8-a71d-ee517f4f5bc0"
+ "urn:uuid:eb53674f-1bce-414f-86e0-c3d525f9033d"
],
- "AssociatedWith": "urn:14cc38ee-b9f4-4f09-8da4-2ff6893c9da8",
+ "AssociatedWith": "urn:spm-kRUWK166",
"Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.name = 'tone counting probe vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.weights = [0 1];\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
"Parameters": {
"consess{1}.tcon.name": "'tone counting vs baseline'",
@@ -245,12 +245,12 @@
}
},
{
- "@id": "urn:699344d3-19f3-46c0-98ae-3a9756df0bd8",
+ "@id": "urn:threshol-Ns3QJ9dv",
"Label": "Threshold",
"Used": [
- "urn:ac0cbc3a-d528-41ac-9614-661e260ac537"
+ "urn:uuid:89d4303e-f6be-45e0-a9a9-0e04440761a4"
],
- "AssociatedWith": "urn:14cc38ee-b9f4-4f09-8da4-2ff6893c9da8",
+ "AssociatedWith": "urn:spm-kRUWK166",
"Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = [1 2];\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 2;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.none = 1;",
"Parameters": {
"conspec.titlestr": "''",
@@ -268,98 +268,96 @@
],
"Entities": [
{
- "@id": "urn:c495f808-45f9-4230-9aac-403fe68f2a91",
+ "@id": "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+ "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"digest": {
- "sha256": "52cc2a3822512db5be3accc8263f2ac1338f32fad8af63cc81fb5af2f335c509"
+ "sha256": "b3d8382360fbbc58cbd8c9e654ddda30b9f0318cf04ebd7539ec75bd724041d2"
}
},
{
- "@id": "urn:ba83ee9c-2d02-4116-a2ea-e5e4f1c78a9d",
+ "@id": "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz",
"Label": "anat_sub-01_T1w.nii.gz",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+ "AtLocation": "ds011/sub-01/anat/sub-01_T1w.nii.gz",
"digest": {
- "sha256": "3d9457fa7712b355d6569522ca80a6dfd70a40b82e6aa0a9364513cf04916dbb"
+ "sha256": "70b9327067cc5200330e04e70b22a41db5aa3b78f978060f61f49bd3a45d125e"
}
},
{
- "@id": "urn:b3e881ab-5017-474d-ab20-1ff4734e60f1",
+ "@id": "urn:uuid:020b2bdf-e472-42a1-9e43-8c9f9fbeb376",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "GeneratedBy": "urn:3aa74700-0b41-45a3-9889-68aad2d2e060"
+ "GeneratedBy": "urn:movefile-E9SUEKGJ"
},
{
- "@id": "urn:5e650fe4-797e-43ba-a8e5-78407a74f7b4",
+ "@id": "urn:uuid:b0e1709d-5501-4e9a-bd09-0f2c82c09610",
"Label": "anat_sub-01_T1w.nii.gz",
- "GeneratedBy": "urn:7459b441-2e93-4d1a-a6fe-bf28a3d78593"
+ "GeneratedBy": "urn:movefile-UEkIbFqL"
},
{
- "@id": "urn:94d83b6c-0071-40c5-b3ad-9687a6570107",
+ "@id": "urn:uuid:e7827303-0d45-40a1-a675-c59efc4101fc",
"Label": "func_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:9bc9d34b-4426-4e61-9d88-ef8ef4e54805"
+ "GeneratedBy": "urn:gunzip3-qGrj0paZ"
},
{
- "@id": "urn:543ec73e-7a7b-4f1c-b0f2-5e4faa4a024a",
+ "@id": "urn:uuid:dad38e4b-0886-4822-ba34-c1bffa39acc8",
"Label": "meanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:e5c4e54e-7449-4454-916d-ac095d2d8c98"
+ "GeneratedBy": "urn:realign5-ZqZuI9nU"
},
{
- "@id": "urn:736f8ab3-cae1-4022-9c97-ba8843782a36",
+ "@id": "urn:uuid:705569ce-f0f4-4551-b596-8e52a4b35e54",
"Label": "anat_sub-01_T1w.nii",
- "GeneratedBy": "urn:77123f02-8628-496b-ae8c-94d6cbb0a645"
+ "GeneratedBy": "urn:gunzip4-X87P6yn3"
},
{
- "@id": "urn:3a8fa6eb-a642-4a2b-983c-79bd02ca66f8",
+ "@id": "bids::c1anat_sub-01_T1w.nii",
"Label": "segment1",
- "Atlocation": "c1xxx.nii.gz",
- "GeneratedBy": "urn:ce99dac3-455e-42e6-97d0-708e6a12d120",
"AtLocation": "c1anat_sub-01_T1w.nii",
+ "GeneratedBy": "urn:segment7-wIsiP0z9",
"digest": {
"sha256": "61ca923955d0a5c9088df9e258f41644067ec964e1c9a83284ba03b0515079b0"
}
},
{
- "@id": "urn:458f7948-c301-43af-ae62-817a341f59da",
+ "@id": "bids::c2anat_sub-01_T1w.nii",
"Label": "segment2",
- "Atlocation": "c2xxx.nii.gz",
- "GeneratedBy": "urn:ce99dac3-455e-42e6-97d0-708e6a12d120",
"AtLocation": "c2anat_sub-01_T1w.nii",
+ "GeneratedBy": "urn:segment7-wIsiP0z9",
"digest": {
"sha256": "10ad88ebeebebd0bd03ccbdd4df92d500d28d14715fa5375fd35589caddf49a6"
}
},
{
- "@id": "urn:40705e2b-01dd-4e4b-a30f-4876f90382bb",
+ "@id": "urn:uuid:383bcc26-9c00-47ec-8a5b-78af546c286c",
"Label": "wsegment1",
- "GeneratedBy": "urn:95dd9372-af2f-48c2-9239-2fa721e54fa1"
+ "GeneratedBy": "urn:normaliz-prV8DwTN"
},
{
- "@id": "urn:230eecc7-aae1-43d0-af4a-f49dd70b07b1",
+ "@id": "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"Label": "ONSETS_sub-01-MultiCond.mat",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+ "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"digest": {
- "sha256": "be4671d4f9dc480dd3e5be19aeeab2756f7afdc3b32d81e071685d7a4eafcfed"
+ "sha256": "5599e80629bb4d66cdbfb357511c04060bd3d37cdbfe2a4cd701a2979e9f6610"
}
},
{
- "@id": "urn:9f71d53e-4e02-4a4c-a895-35ba16cbe373",
+ "@id": "urn:uuid:bbcd8fb6-282c-4086-8603-fee526502c2d",
"Label": "swsegment1",
- "GeneratedBy": "urn:3ad61e65-704a-4488-8b98-355fd8537175"
+ "GeneratedBy": "urn:smooth10-b8F6wlde"
},
{
- "@id": "urn:5335c81d-8e46-452b-9092-fb041b634d5f",
+ "@id": "urn:uuid:d6974014-232a-4fc3-93ff-dd5858b45621",
"Label": "SPM.mat",
- "GeneratedBy": "urn:bbe97082-e102-4703-8c89-979834092600"
+ "GeneratedBy": "urn:statdesi-VDl76uNO"
},
{
- "@id": "urn:4eec8486-836e-48a8-a71d-ee517f4f5bc0",
+ "@id": "urn:uuid:eb53674f-1bce-414f-86e0-c3d525f9033d",
"Label": "SPM.mat",
- "GeneratedBy": "urn:10717391-dda6-43da-8bb9-d65425d0567e"
+ "GeneratedBy": "urn:estimate-zzN84ivS"
},
{
- "@id": "urn:ac0cbc3a-d528-41ac-9614-661e260ac537",
+ "@id": "urn:uuid:89d4303e-f6be-45e0-a9a9-0e04440761a4",
"Label": "SPM.mat",
- "GeneratedBy": "urn:6354be3e-5870-480b-a4e9-c0337b907c91"
+ "GeneratedBy": "urn:estimate-kDKaGYJ3"
}
]
}
diff --git a/examples/from_parsers/spm/spm_partial_conjunction_batch.m b/examples/from_parsers/spm/spm_partial_conjunction_batch.m
index 67fad022c..157057f1f 100644
--- a/examples/from_parsers/spm/spm_partial_conjunction_batch.m
+++ b/examples/from_parsers/spm/spm_partial_conjunction_batch.m
@@ -3,10 +3,10 @@
% spm SPM - SPM12 (12.1)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------
-matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};
-matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};
-matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};
-matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};
+matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};
+matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};
+matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};
+matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};
matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));
@@ -90,7 +90,7 @@
matlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;
matlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});
-matlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};
+matlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};
matlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});
matlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};
matlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;
diff --git a/examples/from_parsers/spm/spm_partial_conjunction_batch.png b/examples/from_parsers/spm/spm_partial_conjunction_batch.png
index 002a71f2c..8657c0fed 100644
Binary files a/examples/from_parsers/spm/spm_partial_conjunction_batch.png and b/examples/from_parsers/spm/spm_partial_conjunction_batch.png differ
diff --git a/examples/from_parsers/spm/spm_temporal_derivative_batch.jsonld b/examples/from_parsers/spm/spm_temporal_derivative_batch.jsonld
index a38252ae4..18941ef25 100644
--- a/examples/from_parsers/spm/spm_temporal_derivative_batch.jsonld
+++ b/examples/from_parsers/spm/spm_temporal_derivative_batch.jsonld
@@ -4,63 +4,63 @@
"Records": {
"Software": [
{
- "@id": "urn:646036ac-d41f-4613-83a2-1ab3a0d849ca",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:spm-Iqi6cYes",
"@type": "prov:SoftwareAgent",
"Label": "SPM",
- "Version": "SPM12r7224"
+ "Version": "SPM12r7224",
+ "AltIdentifier": "RRID:SCR_007037"
}
],
"Activities": [
{
- "@id": "urn:68c34e3d-c21c-423c-8152-3fe74f2cf2a2",
+ "@id": "urn:movefile-8gz2vYDp",
"Label": "Move file",
"Used": [
- "urn:d1e011d7-e565-4bea-850c-263729ba79cd"
+ "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
],
- "AssociatedWith": "urn:646036ac-d41f-4613-83a2-1ab3a0d849ca",
- "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
+ "AssociatedWith": "urn:spm-Iqi6cYes",
+ "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};",
"Parameters": {
- "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
+ "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'}"
}
},
{
- "@id": "urn:d9ee762f-9dd7-491b-82a6-000d8178f364",
+ "@id": "urn:movefile-ciNJaxWf",
"Label": "Move file",
"Used": [
- "urn:ae1735e0-33c8-4a6b-9a2d-f92b51e75ae8"
+ "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz"
],
- "AssociatedWith": "urn:646036ac-d41f-4613-83a2-1ab3a0d849ca",
- "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
+ "AssociatedWith": "urn:spm-Iqi6cYes",
+ "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};",
"Parameters": {
- "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
+ "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'}"
}
},
{
- "@id": "urn:008ecd09-9993-4235-84a2-a437a35dab54",
+ "@id": "urn:gunzip3-r9lvn8p1",
"Label": "Gunzip",
"Used": [
- "urn:dfa18369-5868-428e-83a6-730b94365a17"
+ "urn:uuid:d28c66ee-9df4-4f48-bcdb-5cc80f2c82b8"
],
- "AssociatedWith": "urn:646036ac-d41f-4613-83a2-1ab3a0d849ca",
+ "AssociatedWith": "urn:spm-Iqi6cYes",
"Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:bdda387f-4e42-4010-969a-58d6c75a23ae",
+ "@id": "urn:gunzip4-Pq5ZEXnx",
"Label": "Gunzip",
"Used": [
- "urn:1778c562-63a6-473a-baaf-fac05a57a5ba"
+ "urn:uuid:12c70fce-50a2-4587-a377-83845161d6f0"
],
- "AssociatedWith": "urn:646036ac-d41f-4613-83a2-1ab3a0d849ca",
+ "AssociatedWith": "urn:spm-Iqi6cYes",
"Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:0aa34890-8756-4bfc-90db-e611bc459fb7",
+ "@id": "urn:realign5-pT0fpiId",
"Label": "Realign",
"Used": [
- "urn:753c1b0c-e222-4f15-8866-5546c1c4ba3d"
+ "urn:uuid:b9734a59-46f3-4366-aac7-ce4e18652307"
],
- "AssociatedWith": "urn:646036ac-d41f-4613-83a2-1ab3a0d849ca",
+ "AssociatedWith": "urn:spm-Iqi6cYes",
"Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
"Parameters": {
"eoptions.quality": "0.9",
@@ -78,13 +78,13 @@
}
},
{
- "@id": "urn:8745b76c-58c7-4318-8c6d-394b5a2929a9",
+ "@id": "urn:coregist-ooodonch",
"Label": "Coregister",
"Used": [
- "urn:25facea6-f5dd-4a26-a41b-2423688b11ae",
- "urn:7817abad-c255-476c-bb68-b696ba85df03"
+ "urn:uuid:9bfb0b4b-b351-4f87-b425-5ab23b28e8b8",
+ "urn:uuid:bdd303a3-95b8-429d-be7c-5526b3701b1b"
],
- "AssociatedWith": "urn:646036ac-d41f-4613-83a2-1ab3a0d849ca",
+ "AssociatedWith": "urn:spm-Iqi6cYes",
"Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
"Parameters": {
"other": "{''}",
@@ -95,12 +95,12 @@
}
},
{
- "@id": "urn:eb164190-0156-408a-8695-eabc2105da90",
+ "@id": "urn:segment7-TxjeajaC",
"Label": "Segment",
"Used": [
- "urn:7817abad-c255-476c-bb68-b696ba85df03"
+ "urn:uuid:bdd303a3-95b8-429d-be7c-5526b3701b1b"
],
- "AssociatedWith": "urn:646036ac-d41f-4613-83a2-1ab3a0d849ca",
+ "AssociatedWith": "urn:spm-Iqi6cYes",
"Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
"Parameters": {
"channel.biasreg": "0.001",
@@ -140,13 +140,13 @@
}
},
{
- "@id": "urn:12313157-10eb-4297-9463-d87018825ae9",
+ "@id": "urn:normaliz-gxMyUxTC",
"Label": "Normalize",
"Used": [
- "urn:24dc3cb9-8070-4c72-873b-7984f8bce111",
- "urn:25facea6-f5dd-4a26-a41b-2423688b11ae"
+ "bids::c1anat_sub-01_T1w.nii",
+ "urn:uuid:9bfb0b4b-b351-4f87-b425-5ab23b28e8b8"
],
- "AssociatedWith": "urn:646036ac-d41f-4613-83a2-1ab3a0d849ca",
+ "AssociatedWith": "urn:spm-Iqi6cYes",
"Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -156,12 +156,12 @@
}
},
{
- "@id": "urn:6b5b4ba1-493c-4407-b105-4101706e05c3",
+ "@id": "urn:normaliz-HSrOJAko",
"Label": "Normalize",
"Used": [
- "urn:24dc3cb9-8070-4c72-873b-7984f8bce111"
+ "bids::c1anat_sub-01_T1w.nii"
],
- "AssociatedWith": "urn:646036ac-d41f-4613-83a2-1ab3a0d849ca",
+ "AssociatedWith": "urn:spm-Iqi6cYes",
"Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -171,12 +171,12 @@
}
},
{
- "@id": "urn:d62b2ec3-829d-47f0-8be5-78951d973045",
+ "@id": "urn:smooth10-FUAMZN5D",
"Label": "Smooth",
"Used": [
- "urn:ef9e05cf-67b3-40d2-8746-162f2fea45e7"
+ "urn:uuid:640338ab-1dde-494c-a012-ee8afd479306"
],
- "AssociatedWith": "urn:646036ac-d41f-4613-83a2-1ab3a0d849ca",
+ "AssociatedWith": "urn:spm-Iqi6cYes",
"Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
"Parameters": {
"fwhm": "[6, 6, 6]",
@@ -186,14 +186,14 @@
}
},
{
- "@id": "urn:46f37fcb-4a4e-4244-9b2f-7d258e66861e",
+ "@id": "urn:statdesi-orB8CKas",
"Label": "Stat Design",
"Used": [
- "urn:dc001804-b15a-44be-ad41-70c5ddbc74cb",
- "urn:b1b48e81-1b17-4657-9d77-27a71bfac7bb"
+ "urn:uuid:ae76fb47-5ccd-4dfc-8142-411e1b1b129f",
+ "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
],
- "AssociatedWith": "urn:646036ac-d41f-4613-83a2-1ab3a0d849ca",
- "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_temporal_derivative'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [1 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
+ "AssociatedWith": "urn:spm-Iqi6cYes",
+ "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_temporal_derivative'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [1 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
"Parameters": {
"dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_temporal_derivative'}",
"timing.units": "'secs'",
@@ -214,12 +214,12 @@
}
},
{
- "@id": "urn:bc40716c-b325-40dd-81fe-ffe9e270e07f",
+ "@id": "urn:estimate-1ESElFyw",
"Label": "Estimate stat.",
"Used": [
- "urn:c46590f7-4d38-4ee9-a0ba-28911704bd72"
+ "urn:uuid:4a6db4b0-3c55-4daa-83b4-3fce50530896"
],
- "AssociatedWith": "urn:646036ac-d41f-4613-83a2-1ab3a0d849ca",
+ "AssociatedWith": "urn:spm-Iqi6cYes",
"Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
"Parameters": {
"write_residuals": "0",
@@ -227,12 +227,12 @@
}
},
{
- "@id": "urn:25bf796d-6fa6-462b-9152-ac64033f2fb9",
+ "@id": "urn:estimate-rrWWlZyr",
"Label": "Estimate contrast",
"Used": [
- "urn:06f311d0-ac7b-4a4e-b730-32932e83b47d"
+ "urn:uuid:1ef58f22-1c60-40c8-a8cc-32c360c3b073"
],
- "AssociatedWith": "urn:646036ac-d41f-4613-83a2-1ab3a0d849ca",
+ "AssociatedWith": "urn:spm-Iqi6cYes",
"Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0 0 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
"Parameters": {
"consess{1}.tcon.name": "'tone counting vs baseline'",
@@ -242,12 +242,12 @@
}
},
{
- "@id": "urn:586156d3-de9c-47d0-aaa3-8c640989f434",
+ "@id": "urn:threshol-0BHNvztl",
"Label": "Threshold",
"Used": [
- "urn:130b871a-526a-49f0-aedb-a4fd309f803f"
+ "urn:uuid:24f0054d-e998-40fc-8931-a30b14234f5b"
],
- "AssociatedWith": "urn:646036ac-d41f-4613-83a2-1ab3a0d849ca",
+ "AssociatedWith": "urn:spm-Iqi6cYes",
"Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.none = 1;",
"Parameters": {
"conspec.titlestr": "''",
@@ -265,98 +265,96 @@
],
"Entities": [
{
- "@id": "urn:d1e011d7-e565-4bea-850c-263729ba79cd",
+ "@id": "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+ "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"digest": {
- "sha256": "52cc2a3822512db5be3accc8263f2ac1338f32fad8af63cc81fb5af2f335c509"
+ "sha256": "b3d8382360fbbc58cbd8c9e654ddda30b9f0318cf04ebd7539ec75bd724041d2"
}
},
{
- "@id": "urn:ae1735e0-33c8-4a6b-9a2d-f92b51e75ae8",
+ "@id": "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz",
"Label": "anat_sub-01_T1w.nii.gz",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+ "AtLocation": "ds011/sub-01/anat/sub-01_T1w.nii.gz",
"digest": {
- "sha256": "3d9457fa7712b355d6569522ca80a6dfd70a40b82e6aa0a9364513cf04916dbb"
+ "sha256": "70b9327067cc5200330e04e70b22a41db5aa3b78f978060f61f49bd3a45d125e"
}
},
{
- "@id": "urn:dfa18369-5868-428e-83a6-730b94365a17",
+ "@id": "urn:uuid:d28c66ee-9df4-4f48-bcdb-5cc80f2c82b8",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "GeneratedBy": "urn:68c34e3d-c21c-423c-8152-3fe74f2cf2a2"
+ "GeneratedBy": "urn:movefile-8gz2vYDp"
},
{
- "@id": "urn:1778c562-63a6-473a-baaf-fac05a57a5ba",
+ "@id": "urn:uuid:12c70fce-50a2-4587-a377-83845161d6f0",
"Label": "anat_sub-01_T1w.nii.gz",
- "GeneratedBy": "urn:d9ee762f-9dd7-491b-82a6-000d8178f364"
+ "GeneratedBy": "urn:movefile-ciNJaxWf"
},
{
- "@id": "urn:753c1b0c-e222-4f15-8866-5546c1c4ba3d",
+ "@id": "urn:uuid:b9734a59-46f3-4366-aac7-ce4e18652307",
"Label": "func_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:008ecd09-9993-4235-84a2-a437a35dab54"
+ "GeneratedBy": "urn:gunzip3-r9lvn8p1"
},
{
- "@id": "urn:25facea6-f5dd-4a26-a41b-2423688b11ae",
+ "@id": "urn:uuid:9bfb0b4b-b351-4f87-b425-5ab23b28e8b8",
"Label": "meanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:0aa34890-8756-4bfc-90db-e611bc459fb7"
+ "GeneratedBy": "urn:realign5-pT0fpiId"
},
{
- "@id": "urn:7817abad-c255-476c-bb68-b696ba85df03",
+ "@id": "urn:uuid:bdd303a3-95b8-429d-be7c-5526b3701b1b",
"Label": "anat_sub-01_T1w.nii",
- "GeneratedBy": "urn:bdda387f-4e42-4010-969a-58d6c75a23ae"
+ "GeneratedBy": "urn:gunzip4-Pq5ZEXnx"
},
{
- "@id": "urn:24dc3cb9-8070-4c72-873b-7984f8bce111",
+ "@id": "bids::c1anat_sub-01_T1w.nii",
"Label": "segment1",
- "Atlocation": "c1xxx.nii.gz",
- "GeneratedBy": "urn:eb164190-0156-408a-8695-eabc2105da90",
"AtLocation": "c1anat_sub-01_T1w.nii",
+ "GeneratedBy": "urn:segment7-TxjeajaC",
"digest": {
"sha256": "61ca923955d0a5c9088df9e258f41644067ec964e1c9a83284ba03b0515079b0"
}
},
{
- "@id": "urn:1f8622e8-1b41-46db-8ea0-c302e1a18b83",
+ "@id": "bids::c2anat_sub-01_T1w.nii",
"Label": "segment2",
- "Atlocation": "c2xxx.nii.gz",
- "GeneratedBy": "urn:eb164190-0156-408a-8695-eabc2105da90",
"AtLocation": "c2anat_sub-01_T1w.nii",
+ "GeneratedBy": "urn:segment7-TxjeajaC",
"digest": {
"sha256": "10ad88ebeebebd0bd03ccbdd4df92d500d28d14715fa5375fd35589caddf49a6"
}
},
{
- "@id": "urn:ef9e05cf-67b3-40d2-8746-162f2fea45e7",
+ "@id": "urn:uuid:640338ab-1dde-494c-a012-ee8afd479306",
"Label": "wsegment1",
- "GeneratedBy": "urn:12313157-10eb-4297-9463-d87018825ae9"
+ "GeneratedBy": "urn:normaliz-gxMyUxTC"
},
{
- "@id": "urn:b1b48e81-1b17-4657-9d77-27a71bfac7bb",
+ "@id": "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"Label": "ONSETS_sub-01-MultiCond.mat",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+ "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"digest": {
- "sha256": "be4671d4f9dc480dd3e5be19aeeab2756f7afdc3b32d81e071685d7a4eafcfed"
+ "sha256": "5599e80629bb4d66cdbfb357511c04060bd3d37cdbfe2a4cd701a2979e9f6610"
}
},
{
- "@id": "urn:dc001804-b15a-44be-ad41-70c5ddbc74cb",
+ "@id": "urn:uuid:ae76fb47-5ccd-4dfc-8142-411e1b1b129f",
"Label": "swsegment1",
- "GeneratedBy": "urn:d62b2ec3-829d-47f0-8be5-78951d973045"
+ "GeneratedBy": "urn:smooth10-FUAMZN5D"
},
{
- "@id": "urn:c46590f7-4d38-4ee9-a0ba-28911704bd72",
+ "@id": "urn:uuid:4a6db4b0-3c55-4daa-83b4-3fce50530896",
"Label": "SPM.mat",
- "GeneratedBy": "urn:46f37fcb-4a4e-4244-9b2f-7d258e66861e"
+ "GeneratedBy": "urn:statdesi-orB8CKas"
},
{
- "@id": "urn:06f311d0-ac7b-4a4e-b730-32932e83b47d",
+ "@id": "urn:uuid:1ef58f22-1c60-40c8-a8cc-32c360c3b073",
"Label": "SPM.mat",
- "GeneratedBy": "urn:bc40716c-b325-40dd-81fe-ffe9e270e07f"
+ "GeneratedBy": "urn:estimate-1ESElFyw"
},
{
- "@id": "urn:130b871a-526a-49f0-aedb-a4fd309f803f",
+ "@id": "urn:uuid:24f0054d-e998-40fc-8931-a30b14234f5b",
"Label": "SPM.mat",
- "GeneratedBy": "urn:25bf796d-6fa6-462b-9152-ac64033f2fb9"
+ "GeneratedBy": "urn:estimate-rrWWlZyr"
}
]
}
diff --git a/examples/from_parsers/spm/spm_temporal_derivative_batch.m b/examples/from_parsers/spm/spm_temporal_derivative_batch.m
index 11047f027..b691c9636 100644
--- a/examples/from_parsers/spm/spm_temporal_derivative_batch.m
+++ b/examples/from_parsers/spm/spm_temporal_derivative_batch.m
@@ -3,10 +3,10 @@
% spm SPM - SPM12 (12.1)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------
-matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};
-matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};
-matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};
-matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};
+matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};
+matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};
+matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};
+matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};
matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));
@@ -90,7 +90,7 @@
matlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;
matlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});
-matlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};
+matlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};
matlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});
matlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};
matlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;
diff --git a/examples/from_parsers/spm/spm_temporal_derivative_batch.png b/examples/from_parsers/spm/spm_temporal_derivative_batch.png
index 1921a1e0e..0b6e146e0 100644
Binary files a/examples/from_parsers/spm/spm_temporal_derivative_batch.png and b/examples/from_parsers/spm/spm_temporal_derivative_batch.png differ
diff --git a/examples/from_parsers/spm/spm_thr_clustfwep05_batch.jsonld b/examples/from_parsers/spm/spm_thr_clustfwep05_batch.jsonld
index 8a3922b12..5ba0324ef 100644
--- a/examples/from_parsers/spm/spm_thr_clustfwep05_batch.jsonld
+++ b/examples/from_parsers/spm/spm_thr_clustfwep05_batch.jsonld
@@ -4,63 +4,63 @@
"Records": {
"Software": [
{
- "@id": "urn:b1109425-53a2-4d85-9c69-6c3da5a73743",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:spm-0M07DSW9",
"@type": "prov:SoftwareAgent",
"Label": "SPM",
- "Version": "SPM12r7224"
+ "Version": "SPM12r7224",
+ "AltIdentifier": "RRID:SCR_007037"
}
],
"Activities": [
{
- "@id": "urn:577dbeef-ee03-40d7-aa64-023f1045a060",
+ "@id": "urn:movefile-xEUWiFIX",
"Label": "Move file",
"Used": [
- "urn:3ce38cf8-d9ad-4bb8-a6ee-d7c5c0a18511"
+ "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
],
- "AssociatedWith": "urn:b1109425-53a2-4d85-9c69-6c3da5a73743",
- "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
+ "AssociatedWith": "urn:spm-0M07DSW9",
+ "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};",
"Parameters": {
- "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
+ "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'}"
}
},
{
- "@id": "urn:9fd0ca4c-fc1b-4432-aa2c-81fad09598a4",
+ "@id": "urn:movefile-NRl0j05C",
"Label": "Move file",
"Used": [
- "urn:ba826ece-23e7-4e53-99b9-4b46aaad83a1"
+ "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz"
],
- "AssociatedWith": "urn:b1109425-53a2-4d85-9c69-6c3da5a73743",
- "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
+ "AssociatedWith": "urn:spm-0M07DSW9",
+ "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};",
"Parameters": {
- "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
+ "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'}"
}
},
{
- "@id": "urn:0ca949c1-667d-4f2c-899b-823a46887441",
+ "@id": "urn:gunzip3-NJhcOouF",
"Label": "Gunzip",
"Used": [
- "urn:1b7cccab-fd35-487f-8618-d01f9bcaa4fb"
+ "urn:uuid:3a1d3aaa-f467-4762-8b65-74efb94acbdc"
],
- "AssociatedWith": "urn:b1109425-53a2-4d85-9c69-6c3da5a73743",
+ "AssociatedWith": "urn:spm-0M07DSW9",
"Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:655ebf55-3871-401e-af6d-9b51b8475106",
+ "@id": "urn:gunzip4-D4JR7Bc6",
"Label": "Gunzip",
"Used": [
- "urn:3e7153c9-1e34-421c-b825-35cd8d74eb15"
+ "urn:uuid:73cdb74c-9f64-4789-81b9-0e5bf20d453b"
],
- "AssociatedWith": "urn:b1109425-53a2-4d85-9c69-6c3da5a73743",
+ "AssociatedWith": "urn:spm-0M07DSW9",
"Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:d66a89e0-e899-4368-b615-3138cf30c215",
+ "@id": "urn:realign5-i7ADv0vS",
"Label": "Realign",
"Used": [
- "urn:dbf01613-5698-4ca9-b6c5-e1d7fcbcd75c"
+ "urn:uuid:e4dff923-f549-4834-b48a-b363ba87bbf6"
],
- "AssociatedWith": "urn:b1109425-53a2-4d85-9c69-6c3da5a73743",
+ "AssociatedWith": "urn:spm-0M07DSW9",
"Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
"Parameters": {
"eoptions.quality": "0.9",
@@ -78,13 +78,13 @@
}
},
{
- "@id": "urn:e386f822-5553-4832-8d3d-145ad7886285",
+ "@id": "urn:coregist-2O8MVi4F",
"Label": "Coregister",
"Used": [
- "urn:6e4f96b4-c210-48f8-92ab-727c45324f2c",
- "urn:cbaacc0b-fa57-4e78-8f67-1518f03bd398"
+ "urn:uuid:c991394e-1a6b-4dec-af39-37e0ce004fae",
+ "urn:uuid:ea2bad58-0c22-447c-8b66-1aeb5499512f"
],
- "AssociatedWith": "urn:b1109425-53a2-4d85-9c69-6c3da5a73743",
+ "AssociatedWith": "urn:spm-0M07DSW9",
"Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
"Parameters": {
"other": "{''}",
@@ -95,12 +95,12 @@
}
},
{
- "@id": "urn:bf572fa3-0641-448f-900b-a0d0b1b22531",
+ "@id": "urn:segment7-hPpFAHil",
"Label": "Segment",
"Used": [
- "urn:6e4f96b4-c210-48f8-92ab-727c45324f2c"
+ "urn:uuid:ea2bad58-0c22-447c-8b66-1aeb5499512f"
],
- "AssociatedWith": "urn:b1109425-53a2-4d85-9c69-6c3da5a73743",
+ "AssociatedWith": "urn:spm-0M07DSW9",
"Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
"Parameters": {
"channel.biasreg": "0.001",
@@ -140,13 +140,13 @@
}
},
{
- "@id": "urn:10492bfd-8ec0-4fe0-b867-bec8425d0dca",
+ "@id": "urn:normaliz-9GRC3VyJ",
"Label": "Normalize",
"Used": [
- "urn:77b55fda-08f6-4167-aaa8-81a868cd06bb",
- "urn:cbaacc0b-fa57-4e78-8f67-1518f03bd398"
+ "bids::c1anat_sub-01_T1w.nii",
+ "urn:uuid:c991394e-1a6b-4dec-af39-37e0ce004fae"
],
- "AssociatedWith": "urn:b1109425-53a2-4d85-9c69-6c3da5a73743",
+ "AssociatedWith": "urn:spm-0M07DSW9",
"Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -156,12 +156,12 @@
}
},
{
- "@id": "urn:b6fa3c79-0f4b-43ca-9e68-105676040d46",
+ "@id": "urn:normaliz-a6YDDjrt",
"Label": "Normalize",
"Used": [
- "urn:77b55fda-08f6-4167-aaa8-81a868cd06bb"
+ "bids::c1anat_sub-01_T1w.nii"
],
- "AssociatedWith": "urn:b1109425-53a2-4d85-9c69-6c3da5a73743",
+ "AssociatedWith": "urn:spm-0M07DSW9",
"Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -171,12 +171,12 @@
}
},
{
- "@id": "urn:f6c94055-f898-470c-8498-e56004edcadd",
+ "@id": "urn:smooth10-GkiH6I72",
"Label": "Smooth",
"Used": [
- "urn:0af1248e-e25c-46f3-b05a-9b3b2a617c5a"
+ "urn:uuid:34637116-2460-4e0d-a7f3-d79b7feb3fc8"
],
- "AssociatedWith": "urn:b1109425-53a2-4d85-9c69-6c3da5a73743",
+ "AssociatedWith": "urn:spm-0M07DSW9",
"Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
"Parameters": {
"fwhm": "[6, 6, 6]",
@@ -186,14 +186,14 @@
}
},
{
- "@id": "urn:fad5fe04-ff55-413d-ac3c-b845eb60abe7",
+ "@id": "urn:statdesi-25cin2BQ",
"Label": "Stat Design",
"Used": [
- "urn:69000e1a-e90e-4fe9-9148-a4e7bab105bc",
- "urn:56d76a74-54b9-4c18-94ef-0e7ffee7589d"
+ "urn:uuid:d939ba15-a30f-4d48-a4c2-9d3ca0eb2972",
+ "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
],
- "AssociatedWith": "urn:b1109425-53a2-4d85-9c69-6c3da5a73743",
- "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_cluster_p005'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
+ "AssociatedWith": "urn:spm-0M07DSW9",
+ "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_cluster_p005'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
"Parameters": {
"dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_cluster_p005'}",
"timing.units": "'secs'",
@@ -214,12 +214,12 @@
}
},
{
- "@id": "urn:5c4586db-865a-4612-818d-aedbe8a7214c",
+ "@id": "urn:estimate-rFIkwBPX",
"Label": "Estimate stat.",
"Used": [
- "urn:0891ae6e-341e-47ff-be6e-b7be11da7d54"
+ "urn:uuid:641e9a46-6810-4125-b85c-1aa5bb8119e7"
],
- "AssociatedWith": "urn:b1109425-53a2-4d85-9c69-6c3da5a73743",
+ "AssociatedWith": "urn:spm-0M07DSW9",
"Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
"Parameters": {
"write_residuals": "0",
@@ -227,12 +227,12 @@
}
},
{
- "@id": "urn:22332602-c1dd-46ac-8021-349e698a0939",
+ "@id": "urn:estimate-IqJTcXSm",
"Label": "Estimate contrast",
"Used": [
- "urn:5c2f4a20-c576-4e9f-b873-ce856594d1eb"
+ "urn:uuid:ddb595a9-6134-47dd-a3db-47d426702f79"
],
- "AssociatedWith": "urn:b1109425-53a2-4d85-9c69-6c3da5a73743",
+ "AssociatedWith": "urn:spm-0M07DSW9",
"Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
"Parameters": {
"consess{1}.tcon.name": "'tone counting vs baseline'",
@@ -242,12 +242,12 @@
}
},
{
- "@id": "urn:fa82d500-9b52-455b-842d-f82094ef7a6a",
+ "@id": "urn:threshol-hsW9nRZv",
"Label": "Threshold",
"Used": [
- "urn:357c4736-e0f2-4459-a14e-8796a5614330"
+ "urn:uuid:4bd3cab0-ba16-490e-b334-ca7c036cec4f"
],
- "AssociatedWith": "urn:b1109425-53a2-4d85-9c69-6c3da5a73743",
+ "AssociatedWith": "urn:spm-0M07DSW9",
"Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 116;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.tspm.basename = 'thresh';",
"Parameters": {
"conspec.titlestr": "''",
@@ -265,98 +265,96 @@
],
"Entities": [
{
- "@id": "urn:3ce38cf8-d9ad-4bb8-a6ee-d7c5c0a18511",
+ "@id": "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+ "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"digest": {
- "sha256": "52cc2a3822512db5be3accc8263f2ac1338f32fad8af63cc81fb5af2f335c509"
+ "sha256": "b3d8382360fbbc58cbd8c9e654ddda30b9f0318cf04ebd7539ec75bd724041d2"
}
},
{
- "@id": "urn:ba826ece-23e7-4e53-99b9-4b46aaad83a1",
+ "@id": "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz",
"Label": "anat_sub-01_T1w.nii.gz",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+ "AtLocation": "ds011/sub-01/anat/sub-01_T1w.nii.gz",
"digest": {
- "sha256": "3d9457fa7712b355d6569522ca80a6dfd70a40b82e6aa0a9364513cf04916dbb"
+ "sha256": "70b9327067cc5200330e04e70b22a41db5aa3b78f978060f61f49bd3a45d125e"
}
},
{
- "@id": "urn:1b7cccab-fd35-487f-8618-d01f9bcaa4fb",
+ "@id": "urn:uuid:3a1d3aaa-f467-4762-8b65-74efb94acbdc",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "GeneratedBy": "urn:577dbeef-ee03-40d7-aa64-023f1045a060"
+ "GeneratedBy": "urn:movefile-xEUWiFIX"
},
{
- "@id": "urn:3e7153c9-1e34-421c-b825-35cd8d74eb15",
+ "@id": "urn:uuid:73cdb74c-9f64-4789-81b9-0e5bf20d453b",
"Label": "anat_sub-01_T1w.nii.gz",
- "GeneratedBy": "urn:9fd0ca4c-fc1b-4432-aa2c-81fad09598a4"
+ "GeneratedBy": "urn:movefile-NRl0j05C"
},
{
- "@id": "urn:dbf01613-5698-4ca9-b6c5-e1d7fcbcd75c",
+ "@id": "urn:uuid:e4dff923-f549-4834-b48a-b363ba87bbf6",
"Label": "func_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:0ca949c1-667d-4f2c-899b-823a46887441"
+ "GeneratedBy": "urn:gunzip3-NJhcOouF"
},
{
- "@id": "urn:cbaacc0b-fa57-4e78-8f67-1518f03bd398",
+ "@id": "urn:uuid:c991394e-1a6b-4dec-af39-37e0ce004fae",
"Label": "meanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:d66a89e0-e899-4368-b615-3138cf30c215"
+ "GeneratedBy": "urn:realign5-i7ADv0vS"
},
{
- "@id": "urn:6e4f96b4-c210-48f8-92ab-727c45324f2c",
+ "@id": "urn:uuid:ea2bad58-0c22-447c-8b66-1aeb5499512f",
"Label": "anat_sub-01_T1w.nii",
- "GeneratedBy": "urn:655ebf55-3871-401e-af6d-9b51b8475106"
+ "GeneratedBy": "urn:gunzip4-D4JR7Bc6"
},
{
- "@id": "urn:77b55fda-08f6-4167-aaa8-81a868cd06bb",
+ "@id": "bids::c1anat_sub-01_T1w.nii",
"Label": "segment1",
- "Atlocation": "c1xxx.nii.gz",
- "GeneratedBy": "urn:bf572fa3-0641-448f-900b-a0d0b1b22531",
"AtLocation": "c1anat_sub-01_T1w.nii",
+ "GeneratedBy": "urn:segment7-hPpFAHil",
"digest": {
"sha256": "61ca923955d0a5c9088df9e258f41644067ec964e1c9a83284ba03b0515079b0"
}
},
{
- "@id": "urn:28cb7508-1b38-4619-b8bb-a2dc2b849553",
+ "@id": "bids::c2anat_sub-01_T1w.nii",
"Label": "segment2",
- "Atlocation": "c2xxx.nii.gz",
- "GeneratedBy": "urn:bf572fa3-0641-448f-900b-a0d0b1b22531",
"AtLocation": "c2anat_sub-01_T1w.nii",
+ "GeneratedBy": "urn:segment7-hPpFAHil",
"digest": {
"sha256": "10ad88ebeebebd0bd03ccbdd4df92d500d28d14715fa5375fd35589caddf49a6"
}
},
{
- "@id": "urn:0af1248e-e25c-46f3-b05a-9b3b2a617c5a",
+ "@id": "urn:uuid:34637116-2460-4e0d-a7f3-d79b7feb3fc8",
"Label": "wsegment1",
- "GeneratedBy": "urn:10492bfd-8ec0-4fe0-b867-bec8425d0dca"
+ "GeneratedBy": "urn:normaliz-9GRC3VyJ"
},
{
- "@id": "urn:56d76a74-54b9-4c18-94ef-0e7ffee7589d",
+ "@id": "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"Label": "ONSETS_sub-01-MultiCond.mat",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+ "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"digest": {
- "sha256": "be4671d4f9dc480dd3e5be19aeeab2756f7afdc3b32d81e071685d7a4eafcfed"
+ "sha256": "5599e80629bb4d66cdbfb357511c04060bd3d37cdbfe2a4cd701a2979e9f6610"
}
},
{
- "@id": "urn:69000e1a-e90e-4fe9-9148-a4e7bab105bc",
+ "@id": "urn:uuid:d939ba15-a30f-4d48-a4c2-9d3ca0eb2972",
"Label": "swsegment1",
- "GeneratedBy": "urn:f6c94055-f898-470c-8498-e56004edcadd"
+ "GeneratedBy": "urn:smooth10-GkiH6I72"
},
{
- "@id": "urn:0891ae6e-341e-47ff-be6e-b7be11da7d54",
+ "@id": "urn:uuid:641e9a46-6810-4125-b85c-1aa5bb8119e7",
"Label": "SPM.mat",
- "GeneratedBy": "urn:fad5fe04-ff55-413d-ac3c-b845eb60abe7"
+ "GeneratedBy": "urn:statdesi-25cin2BQ"
},
{
- "@id": "urn:5c2f4a20-c576-4e9f-b873-ce856594d1eb",
+ "@id": "urn:uuid:ddb595a9-6134-47dd-a3db-47d426702f79",
"Label": "SPM.mat",
- "GeneratedBy": "urn:5c4586db-865a-4612-818d-aedbe8a7214c"
+ "GeneratedBy": "urn:estimate-rFIkwBPX"
},
{
- "@id": "urn:357c4736-e0f2-4459-a14e-8796a5614330",
+ "@id": "urn:uuid:4bd3cab0-ba16-490e-b334-ca7c036cec4f",
"Label": "SPM.mat",
- "GeneratedBy": "urn:22332602-c1dd-46ac-8021-349e698a0939"
+ "GeneratedBy": "urn:estimate-IqJTcXSm"
}
]
}
diff --git a/examples/from_parsers/spm/spm_thr_clustfwep05_batch.m b/examples/from_parsers/spm/spm_thr_clustfwep05_batch.m
index 5033a6315..26bca723e 100644
--- a/examples/from_parsers/spm/spm_thr_clustfwep05_batch.m
+++ b/examples/from_parsers/spm/spm_thr_clustfwep05_batch.m
@@ -3,10 +3,10 @@
% spm SPM - SPM12 (12.1)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------
-matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};
-matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};
-matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};
-matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};
+matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};
+matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};
+matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};
+matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};
matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));
@@ -90,7 +90,7 @@
matlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;
matlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});
-matlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};
+matlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};
matlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});
matlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};
matlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;
diff --git a/examples/from_parsers/spm/spm_thr_clustfwep05_batch.png b/examples/from_parsers/spm/spm_thr_clustfwep05_batch.png
index 55bdcd29b..046b1575e 100644
Binary files a/examples/from_parsers/spm/spm_thr_clustfwep05_batch.png and b/examples/from_parsers/spm/spm_thr_clustfwep05_batch.png differ
diff --git a/examples/from_parsers/spm/spm_thr_clustunck10_batch.jsonld b/examples/from_parsers/spm/spm_thr_clustunck10_batch.jsonld
index 85751cd81..3c16abf87 100644
--- a/examples/from_parsers/spm/spm_thr_clustunck10_batch.jsonld
+++ b/examples/from_parsers/spm/spm_thr_clustunck10_batch.jsonld
@@ -4,63 +4,63 @@
"Records": {
"Software": [
{
- "@id": "urn:f3864eb5-3dee-4f42-aebc-78dac92cd7ea",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:spm-Eyt4IuQT",
"@type": "prov:SoftwareAgent",
"Label": "SPM",
- "Version": "SPM12r7224"
+ "Version": "SPM12r7224",
+ "AltIdentifier": "RRID:SCR_007037"
}
],
"Activities": [
{
- "@id": "urn:c6797c80-a805-4854-ae91-70a8444c022d",
+ "@id": "urn:movefile-6M2dWydM",
"Label": "Move file",
"Used": [
- "urn:0651b820-6157-4a1d-a001-93201fb81bda"
+ "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
],
- "AssociatedWith": "urn:f3864eb5-3dee-4f42-aebc-78dac92cd7ea",
- "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
+ "AssociatedWith": "urn:spm-Eyt4IuQT",
+ "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};",
"Parameters": {
- "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
+ "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'}"
}
},
{
- "@id": "urn:4305cc71-294c-407a-be2e-082e60ec59c2",
+ "@id": "urn:movefile-lMbd62mT",
"Label": "Move file",
"Used": [
- "urn:496059e9-1914-47b7-998c-2b3ab7cef31e"
+ "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz"
],
- "AssociatedWith": "urn:f3864eb5-3dee-4f42-aebc-78dac92cd7ea",
- "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
+ "AssociatedWith": "urn:spm-Eyt4IuQT",
+ "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};",
"Parameters": {
- "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
+ "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'}"
}
},
{
- "@id": "urn:14538410-322b-433e-89a1-fb485be42a81",
+ "@id": "urn:gunzip3-dfRVUaru",
"Label": "Gunzip",
"Used": [
- "urn:8387f2d4-1fd6-4431-b2d2-fb5c9be44109"
+ "urn:uuid:aeb68c71-9731-4d2d-9ea0-12c4b3cfaea2"
],
- "AssociatedWith": "urn:f3864eb5-3dee-4f42-aebc-78dac92cd7ea",
+ "AssociatedWith": "urn:spm-Eyt4IuQT",
"Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:f9444c1b-dbca-4dc3-b0e8-69fb0f84eaab",
+ "@id": "urn:gunzip4-hjYeNgdg",
"Label": "Gunzip",
"Used": [
- "urn:c27daab7-7b46-4a97-aef8-e9def2558de6"
+ "urn:uuid:f5dceeb4-5e21-462a-9be8-d084ddbf7932"
],
- "AssociatedWith": "urn:f3864eb5-3dee-4f42-aebc-78dac92cd7ea",
+ "AssociatedWith": "urn:spm-Eyt4IuQT",
"Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:98f84370-938e-4751-9130-dacf85d9b5fd",
+ "@id": "urn:realign5-YeQbKxpG",
"Label": "Realign",
"Used": [
- "urn:3c1ac51f-9d28-4ce9-a5ee-787dc723fe39"
+ "urn:uuid:1fdcb68d-e374-4d38-bcc6-20e33e2b5d16"
],
- "AssociatedWith": "urn:f3864eb5-3dee-4f42-aebc-78dac92cd7ea",
+ "AssociatedWith": "urn:spm-Eyt4IuQT",
"Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
"Parameters": {
"eoptions.quality": "0.9",
@@ -78,13 +78,13 @@
}
},
{
- "@id": "urn:6f283968-276a-4175-ab1d-ad170199c3f3",
+ "@id": "urn:coregist-e324XMg9",
"Label": "Coregister",
"Used": [
- "urn:223f4f8a-3be2-4725-8506-7e8836fba053",
- "urn:3a0e0646-3ab7-484c-95b6-6cb11ae88870"
+ "urn:uuid:0d8b8014-e217-4f92-a442-a7d19c708320",
+ "urn:uuid:5a8a8ad7-73f8-456f-afe3-ac53d237dfd1"
],
- "AssociatedWith": "urn:f3864eb5-3dee-4f42-aebc-78dac92cd7ea",
+ "AssociatedWith": "urn:spm-Eyt4IuQT",
"Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
"Parameters": {
"other": "{''}",
@@ -95,12 +95,12 @@
}
},
{
- "@id": "urn:44d74964-f3dc-46e0-a792-cd386dd5389f",
+ "@id": "urn:segment7-2TUAqTwk",
"Label": "Segment",
"Used": [
- "urn:223f4f8a-3be2-4725-8506-7e8836fba053"
+ "urn:uuid:5a8a8ad7-73f8-456f-afe3-ac53d237dfd1"
],
- "AssociatedWith": "urn:f3864eb5-3dee-4f42-aebc-78dac92cd7ea",
+ "AssociatedWith": "urn:spm-Eyt4IuQT",
"Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
"Parameters": {
"channel.biasreg": "0.001",
@@ -140,13 +140,13 @@
}
},
{
- "@id": "urn:40667860-a8a0-4bbb-8e21-a110c83b1cf2",
+ "@id": "urn:normaliz-vR7z5lUJ",
"Label": "Normalize",
"Used": [
- "urn:25e399d4-7e91-428b-ad79-8f22dee7bb11",
- "urn:3a0e0646-3ab7-484c-95b6-6cb11ae88870"
+ "bids::c1anat_sub-01_T1w.nii",
+ "urn:uuid:0d8b8014-e217-4f92-a442-a7d19c708320"
],
- "AssociatedWith": "urn:f3864eb5-3dee-4f42-aebc-78dac92cd7ea",
+ "AssociatedWith": "urn:spm-Eyt4IuQT",
"Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -156,12 +156,12 @@
}
},
{
- "@id": "urn:14381320-683a-4404-9dcf-f73101d00876",
+ "@id": "urn:normaliz-ZinH9mGC",
"Label": "Normalize",
"Used": [
- "urn:25e399d4-7e91-428b-ad79-8f22dee7bb11"
+ "bids::c1anat_sub-01_T1w.nii"
],
- "AssociatedWith": "urn:f3864eb5-3dee-4f42-aebc-78dac92cd7ea",
+ "AssociatedWith": "urn:spm-Eyt4IuQT",
"Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -171,12 +171,12 @@
}
},
{
- "@id": "urn:44183f80-97dc-4bbb-be0f-10eedc9caec1",
+ "@id": "urn:smooth10-IethF8hX",
"Label": "Smooth",
"Used": [
- "urn:1bc7a644-c310-44ec-8396-52c25d33a2de"
+ "urn:uuid:6865890c-2e7f-4d7b-846d-40e2034cb7a9"
],
- "AssociatedWith": "urn:f3864eb5-3dee-4f42-aebc-78dac92cd7ea",
+ "AssociatedWith": "urn:spm-Eyt4IuQT",
"Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
"Parameters": {
"fwhm": "[6, 6, 6]",
@@ -186,14 +186,14 @@
}
},
{
- "@id": "urn:6b9530f5-6075-4b7d-873b-15df208d2e88",
+ "@id": "urn:statdesi-v3Y21fTt",
"Label": "Stat Design",
"Used": [
- "urn:266d9fa3-6f0b-4e1d-b2b2-aaaabb98cef2",
- "urn:2629ff4e-7046-4bbb-9ced-42483142f1ba"
+ "urn:uuid:c9a1d982-a774-4e4a-b4de-119da8e1ddc2",
+ "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
],
- "AssociatedWith": "urn:f3864eb5-3dee-4f42-aebc-78dac92cd7ea",
- "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_cluster_k10'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
+ "AssociatedWith": "urn:spm-Eyt4IuQT",
+ "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_cluster_k10'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
"Parameters": {
"dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_cluster_k10'}",
"timing.units": "'secs'",
@@ -214,12 +214,12 @@
}
},
{
- "@id": "urn:f9aa4808-f717-4c6f-a4b1-0a6939095264",
+ "@id": "urn:estimate-JtC0qUcj",
"Label": "Estimate stat.",
"Used": [
- "urn:bd26eb50-469a-4def-8b96-63879625c1ac"
+ "urn:uuid:b097d4f8-8924-49fc-b7bf-d36e399f4f21"
],
- "AssociatedWith": "urn:f3864eb5-3dee-4f42-aebc-78dac92cd7ea",
+ "AssociatedWith": "urn:spm-Eyt4IuQT",
"Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
"Parameters": {
"write_residuals": "0",
@@ -227,12 +227,12 @@
}
},
{
- "@id": "urn:372bd721-7ab0-4667-b4b6-a5412ee5062f",
+ "@id": "urn:estimate-VEN2wZN2",
"Label": "Estimate contrast",
"Used": [
- "urn:a5773a3d-e278-40b2-b7a2-d22deb1d7ac4"
+ "urn:uuid:8fdee69d-4f68-4c41-9e25-d5bc958272db"
],
- "AssociatedWith": "urn:f3864eb5-3dee-4f42-aebc-78dac92cd7ea",
+ "AssociatedWith": "urn:spm-Eyt4IuQT",
"Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
"Parameters": {
"consess{1}.tcon.name": "'tone counting vs baseline'",
@@ -242,12 +242,12 @@
}
},
{
- "@id": "urn:53cba1ab-9277-4f22-9bcf-c2d36879bb3b",
+ "@id": "urn:threshol-6Xp8i3BJ",
"Label": "Threshold",
"Used": [
- "urn:ccb1560a-9028-47f0-ab4c-966f54c83553"
+ "urn:uuid:7a4e0b61-870e-4ea1-804a-c5cb1dcca2d2"
],
- "AssociatedWith": "urn:f3864eb5-3dee-4f42-aebc-78dac92cd7ea",
+ "AssociatedWith": "urn:spm-Eyt4IuQT",
"Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 10;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.tspm.basename = 'thresh';",
"Parameters": {
"conspec.titlestr": "''",
@@ -265,98 +265,96 @@
],
"Entities": [
{
- "@id": "urn:0651b820-6157-4a1d-a001-93201fb81bda",
+ "@id": "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+ "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"digest": {
- "sha256": "52cc2a3822512db5be3accc8263f2ac1338f32fad8af63cc81fb5af2f335c509"
+ "sha256": "b3d8382360fbbc58cbd8c9e654ddda30b9f0318cf04ebd7539ec75bd724041d2"
}
},
{
- "@id": "urn:496059e9-1914-47b7-998c-2b3ab7cef31e",
+ "@id": "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz",
"Label": "anat_sub-01_T1w.nii.gz",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+ "AtLocation": "ds011/sub-01/anat/sub-01_T1w.nii.gz",
"digest": {
- "sha256": "3d9457fa7712b355d6569522ca80a6dfd70a40b82e6aa0a9364513cf04916dbb"
+ "sha256": "70b9327067cc5200330e04e70b22a41db5aa3b78f978060f61f49bd3a45d125e"
}
},
{
- "@id": "urn:8387f2d4-1fd6-4431-b2d2-fb5c9be44109",
+ "@id": "urn:uuid:aeb68c71-9731-4d2d-9ea0-12c4b3cfaea2",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "GeneratedBy": "urn:c6797c80-a805-4854-ae91-70a8444c022d"
+ "GeneratedBy": "urn:movefile-6M2dWydM"
},
{
- "@id": "urn:c27daab7-7b46-4a97-aef8-e9def2558de6",
+ "@id": "urn:uuid:f5dceeb4-5e21-462a-9be8-d084ddbf7932",
"Label": "anat_sub-01_T1w.nii.gz",
- "GeneratedBy": "urn:4305cc71-294c-407a-be2e-082e60ec59c2"
+ "GeneratedBy": "urn:movefile-lMbd62mT"
},
{
- "@id": "urn:3c1ac51f-9d28-4ce9-a5ee-787dc723fe39",
+ "@id": "urn:uuid:1fdcb68d-e374-4d38-bcc6-20e33e2b5d16",
"Label": "func_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:14538410-322b-433e-89a1-fb485be42a81"
+ "GeneratedBy": "urn:gunzip3-dfRVUaru"
},
{
- "@id": "urn:3a0e0646-3ab7-484c-95b6-6cb11ae88870",
+ "@id": "urn:uuid:0d8b8014-e217-4f92-a442-a7d19c708320",
"Label": "meanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:98f84370-938e-4751-9130-dacf85d9b5fd"
+ "GeneratedBy": "urn:realign5-YeQbKxpG"
},
{
- "@id": "urn:223f4f8a-3be2-4725-8506-7e8836fba053",
+ "@id": "urn:uuid:5a8a8ad7-73f8-456f-afe3-ac53d237dfd1",
"Label": "anat_sub-01_T1w.nii",
- "GeneratedBy": "urn:f9444c1b-dbca-4dc3-b0e8-69fb0f84eaab"
+ "GeneratedBy": "urn:gunzip4-hjYeNgdg"
},
{
- "@id": "urn:25e399d4-7e91-428b-ad79-8f22dee7bb11",
+ "@id": "bids::c1anat_sub-01_T1w.nii",
"Label": "segment1",
- "Atlocation": "c1xxx.nii.gz",
- "GeneratedBy": "urn:44d74964-f3dc-46e0-a792-cd386dd5389f",
"AtLocation": "c1anat_sub-01_T1w.nii",
+ "GeneratedBy": "urn:segment7-2TUAqTwk",
"digest": {
"sha256": "61ca923955d0a5c9088df9e258f41644067ec964e1c9a83284ba03b0515079b0"
}
},
{
- "@id": "urn:83df4d40-0769-4504-832a-88276820c98a",
+ "@id": "bids::c2anat_sub-01_T1w.nii",
"Label": "segment2",
- "Atlocation": "c2xxx.nii.gz",
- "GeneratedBy": "urn:44d74964-f3dc-46e0-a792-cd386dd5389f",
"AtLocation": "c2anat_sub-01_T1w.nii",
+ "GeneratedBy": "urn:segment7-2TUAqTwk",
"digest": {
"sha256": "10ad88ebeebebd0bd03ccbdd4df92d500d28d14715fa5375fd35589caddf49a6"
}
},
{
- "@id": "urn:1bc7a644-c310-44ec-8396-52c25d33a2de",
+ "@id": "urn:uuid:6865890c-2e7f-4d7b-846d-40e2034cb7a9",
"Label": "wsegment1",
- "GeneratedBy": "urn:40667860-a8a0-4bbb-8e21-a110c83b1cf2"
+ "GeneratedBy": "urn:normaliz-vR7z5lUJ"
},
{
- "@id": "urn:2629ff4e-7046-4bbb-9ced-42483142f1ba",
+ "@id": "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"Label": "ONSETS_sub-01-MultiCond.mat",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+ "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"digest": {
- "sha256": "be4671d4f9dc480dd3e5be19aeeab2756f7afdc3b32d81e071685d7a4eafcfed"
+ "sha256": "5599e80629bb4d66cdbfb357511c04060bd3d37cdbfe2a4cd701a2979e9f6610"
}
},
{
- "@id": "urn:266d9fa3-6f0b-4e1d-b2b2-aaaabb98cef2",
+ "@id": "urn:uuid:c9a1d982-a774-4e4a-b4de-119da8e1ddc2",
"Label": "swsegment1",
- "GeneratedBy": "urn:44183f80-97dc-4bbb-be0f-10eedc9caec1"
+ "GeneratedBy": "urn:smooth10-IethF8hX"
},
{
- "@id": "urn:bd26eb50-469a-4def-8b96-63879625c1ac",
+ "@id": "urn:uuid:b097d4f8-8924-49fc-b7bf-d36e399f4f21",
"Label": "SPM.mat",
- "GeneratedBy": "urn:6b9530f5-6075-4b7d-873b-15df208d2e88"
+ "GeneratedBy": "urn:statdesi-v3Y21fTt"
},
{
- "@id": "urn:a5773a3d-e278-40b2-b7a2-d22deb1d7ac4",
+ "@id": "urn:uuid:8fdee69d-4f68-4c41-9e25-d5bc958272db",
"Label": "SPM.mat",
- "GeneratedBy": "urn:f9aa4808-f717-4c6f-a4b1-0a6939095264"
+ "GeneratedBy": "urn:estimate-JtC0qUcj"
},
{
- "@id": "urn:ccb1560a-9028-47f0-ab4c-966f54c83553",
+ "@id": "urn:uuid:7a4e0b61-870e-4ea1-804a-c5cb1dcca2d2",
"Label": "SPM.mat",
- "GeneratedBy": "urn:372bd721-7ab0-4667-b4b6-a5412ee5062f"
+ "GeneratedBy": "urn:estimate-VEN2wZN2"
}
]
}
diff --git a/examples/from_parsers/spm/spm_thr_clustunck10_batch.m b/examples/from_parsers/spm/spm_thr_clustunck10_batch.m
index a9e4d501c..607424cca 100644
--- a/examples/from_parsers/spm/spm_thr_clustunck10_batch.m
+++ b/examples/from_parsers/spm/spm_thr_clustunck10_batch.m
@@ -3,10 +3,10 @@
% spm SPM - SPM12 (12.1)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------
-matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};
-matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};
-matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};
-matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};
+matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};
+matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};
+matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};
+matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};
matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));
@@ -90,7 +90,7 @@
matlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;
matlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});
-matlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};
+matlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};
matlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});
matlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};
matlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;
diff --git a/examples/from_parsers/spm/spm_thr_clustunck10_batch.png b/examples/from_parsers/spm/spm_thr_clustunck10_batch.png
index 83e619504..475eb6345 100644
Binary files a/examples/from_parsers/spm/spm_thr_clustunck10_batch.png and b/examples/from_parsers/spm/spm_thr_clustunck10_batch.png differ
diff --git a/examples/from_parsers/spm/spm_thr_voxelfdrp05_batch.jsonld b/examples/from_parsers/spm/spm_thr_voxelfdrp05_batch.jsonld
index 0a4c425f8..8c34e40d3 100644
--- a/examples/from_parsers/spm/spm_thr_voxelfdrp05_batch.jsonld
+++ b/examples/from_parsers/spm/spm_thr_voxelfdrp05_batch.jsonld
@@ -4,63 +4,63 @@
"Records": {
"Software": [
{
- "@id": "urn:4a53d31b-ba56-4ff3-9b15-e37074df2718",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:spm-9bcWvatM",
"@type": "prov:SoftwareAgent",
"Label": "SPM",
- "Version": "SPM12r7224"
+ "Version": "SPM12r7224",
+ "AltIdentifier": "RRID:SCR_007037"
}
],
"Activities": [
{
- "@id": "urn:6fac3dd4-3655-4d3d-a4f5-73b727d0283d",
+ "@id": "urn:movefile-oKHoqlpV",
"Label": "Move file",
"Used": [
- "urn:2cf7336e-cc7b-4dc7-80e4-7fbd39e41e15"
+ "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
],
- "AssociatedWith": "urn:4a53d31b-ba56-4ff3-9b15-e37074df2718",
- "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
+ "AssociatedWith": "urn:spm-9bcWvatM",
+ "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};",
"Parameters": {
- "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
+ "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'}"
}
},
{
- "@id": "urn:24a2e1fd-6f79-48cf-a9b4-0b3c50c00ef7",
+ "@id": "urn:movefile-Wjq8qqkf",
"Label": "Move file",
"Used": [
- "urn:d1d57963-2edd-4c3a-935e-79e9d3ae925b"
+ "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz"
],
- "AssociatedWith": "urn:4a53d31b-ba56-4ff3-9b15-e37074df2718",
- "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
+ "AssociatedWith": "urn:spm-9bcWvatM",
+ "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};",
"Parameters": {
- "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
+ "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'}"
}
},
{
- "@id": "urn:8e23621e-af1f-4f36-aa91-fe74af747392",
+ "@id": "urn:gunzip3-AAN8zM3m",
"Label": "Gunzip",
"Used": [
- "urn:14ddd282-4294-4c2e-a111-1bc95e4f5a39"
+ "urn:uuid:8fa22cb9-7c76-486f-9d5b-8cba8bd3acee"
],
- "AssociatedWith": "urn:4a53d31b-ba56-4ff3-9b15-e37074df2718",
+ "AssociatedWith": "urn:spm-9bcWvatM",
"Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:df85adc5-0547-478e-a8d0-34cb2391ce58",
+ "@id": "urn:gunzip4-aws2OWPG",
"Label": "Gunzip",
"Used": [
- "urn:dca2af2a-8bf2-48b5-be14-e6e569647003"
+ "urn:uuid:b8523047-5639-4e6e-adec-6daec8a60280"
],
- "AssociatedWith": "urn:4a53d31b-ba56-4ff3-9b15-e37074df2718",
+ "AssociatedWith": "urn:spm-9bcWvatM",
"Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:32ec3ee6-1e9d-47e1-90db-591150f53238",
+ "@id": "urn:realign5-6rhsn0th",
"Label": "Realign",
"Used": [
- "urn:2461ed0f-a5f5-47b8-96f4-be8d20fc72ec"
+ "urn:uuid:d93c3829-c444-49f3-a3c6-6f836e61bd6a"
],
- "AssociatedWith": "urn:4a53d31b-ba56-4ff3-9b15-e37074df2718",
+ "AssociatedWith": "urn:spm-9bcWvatM",
"Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
"Parameters": {
"eoptions.quality": "0.9",
@@ -78,13 +78,13 @@
}
},
{
- "@id": "urn:37c3c064-fdc2-41a0-9c52-90aac989eb63",
+ "@id": "urn:coregist-uXQiSgZ5",
"Label": "Coregister",
"Used": [
- "urn:9157ac14-4b38-4ffb-9216-f2597912fe25",
- "urn:caf58ed5-15de-4ac6-aa9d-3a9c22c728fc"
+ "urn:uuid:858135c7-7aac-4fee-9ffb-2109e784abc0",
+ "urn:uuid:d8124621-a9cb-4ed9-b26d-0adfb02e6e84"
],
- "AssociatedWith": "urn:4a53d31b-ba56-4ff3-9b15-e37074df2718",
+ "AssociatedWith": "urn:spm-9bcWvatM",
"Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
"Parameters": {
"other": "{''}",
@@ -95,12 +95,12 @@
}
},
{
- "@id": "urn:c09a6590-cb1b-443f-991f-902132a59ae4",
+ "@id": "urn:segment7-1oFMwhYt",
"Label": "Segment",
"Used": [
- "urn:9157ac14-4b38-4ffb-9216-f2597912fe25"
+ "urn:uuid:d8124621-a9cb-4ed9-b26d-0adfb02e6e84"
],
- "AssociatedWith": "urn:4a53d31b-ba56-4ff3-9b15-e37074df2718",
+ "AssociatedWith": "urn:spm-9bcWvatM",
"Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
"Parameters": {
"channel.biasreg": "0.001",
@@ -140,13 +140,13 @@
}
},
{
- "@id": "urn:1ae03796-c374-4c1d-b521-97bc6aeb3c76",
+ "@id": "urn:normaliz-XNMcYmPX",
"Label": "Normalize",
"Used": [
- "urn:40f61898-bf4a-46a7-9bd8-4190732dcdb7",
- "urn:caf58ed5-15de-4ac6-aa9d-3a9c22c728fc"
+ "bids::c1anat_sub-01_T1w.nii",
+ "urn:uuid:858135c7-7aac-4fee-9ffb-2109e784abc0"
],
- "AssociatedWith": "urn:4a53d31b-ba56-4ff3-9b15-e37074df2718",
+ "AssociatedWith": "urn:spm-9bcWvatM",
"Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -156,12 +156,12 @@
}
},
{
- "@id": "urn:b082c399-b8dc-4e48-bc93-46517e9ad1b3",
+ "@id": "urn:normaliz-YUhm2lc5",
"Label": "Normalize",
"Used": [
- "urn:40f61898-bf4a-46a7-9bd8-4190732dcdb7"
+ "bids::c1anat_sub-01_T1w.nii"
],
- "AssociatedWith": "urn:4a53d31b-ba56-4ff3-9b15-e37074df2718",
+ "AssociatedWith": "urn:spm-9bcWvatM",
"Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -171,12 +171,12 @@
}
},
{
- "@id": "urn:11f223e3-299f-4f87-b5c6-b2cd5e69c374",
+ "@id": "urn:smooth10-pO6CXV88",
"Label": "Smooth",
"Used": [
- "urn:9403d5c6-51b2-46bd-9794-981da1e12b27"
+ "urn:uuid:11e832e4-d52e-4d41-aa63-1013364f30be"
],
- "AssociatedWith": "urn:4a53d31b-ba56-4ff3-9b15-e37074df2718",
+ "AssociatedWith": "urn:spm-9bcWvatM",
"Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
"Parameters": {
"fwhm": "[6, 6, 6]",
@@ -186,14 +186,14 @@
}
},
{
- "@id": "urn:1c5facbc-99e5-4301-ba64-ab4aadc48e17",
+ "@id": "urn:statdesi-uWpA1oPb",
"Label": "Stat Design",
"Used": [
- "urn:4fbd6045-cae5-4f0a-8b65-857ef927274f",
- "urn:75142b97-c286-40c1-a0df-a19fee33956c"
+ "urn:uuid:f6b16b8e-ba13-4b03-957f-fbe68afe59df",
+ "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
],
- "AssociatedWith": "urn:4a53d31b-ba56-4ff3-9b15-e37074df2718",
- "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_FDR_p005'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
+ "AssociatedWith": "urn:spm-9bcWvatM",
+ "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_FDR_p005'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
"Parameters": {
"dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_FDR_p005'}",
"timing.units": "'secs'",
@@ -214,12 +214,12 @@
}
},
{
- "@id": "urn:d59db5b5-4ab3-4475-bb6e-9e3510819631",
+ "@id": "urn:estimate-PLgbjc6p",
"Label": "Estimate stat.",
"Used": [
- "urn:fe68686f-5fe0-4994-a9b1-200e446ff6b9"
+ "urn:uuid:30abb4c8-1be8-45e1-8509-67d5ed09efed"
],
- "AssociatedWith": "urn:4a53d31b-ba56-4ff3-9b15-e37074df2718",
+ "AssociatedWith": "urn:spm-9bcWvatM",
"Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
"Parameters": {
"write_residuals": "0",
@@ -227,12 +227,12 @@
}
},
{
- "@id": "urn:dde554f4-eccf-4317-9518-efa60214f791",
+ "@id": "urn:estimate-hoQcZWBN",
"Label": "Estimate contrast",
"Used": [
- "urn:636d3259-22bf-4dd3-a14a-b564569cac0d"
+ "urn:uuid:c0fb8d7f-a541-432b-a819-abdc9366765e"
],
- "AssociatedWith": "urn:4a53d31b-ba56-4ff3-9b15-e37074df2718",
+ "AssociatedWith": "urn:spm-9bcWvatM",
"Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
"Parameters": {
"consess{1}.tcon.name": "'tone counting vs baseline'",
@@ -242,12 +242,12 @@
}
},
{
- "@id": "urn:589b1c78-c52c-4441-951b-48ba0f8ae0bd",
+ "@id": "urn:threshol-fvHJxXb9",
"Label": "Threshold",
"Used": [
- "urn:954dc233-a400-4356-98f9-d818f2b94a91"
+ "urn:uuid:2864188c-4e65-4ac4-acd8-096759441ba7"
],
- "AssociatedWith": "urn:4a53d31b-ba56-4ff3-9b15-e37074df2718",
+ "AssociatedWith": "urn:spm-9bcWvatM",
"Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'FDR';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.05;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.tspm.basename = 'thresh';",
"Parameters": {
"conspec.titlestr": "''",
@@ -265,98 +265,96 @@
],
"Entities": [
{
- "@id": "urn:2cf7336e-cc7b-4dc7-80e4-7fbd39e41e15",
+ "@id": "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+ "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"digest": {
- "sha256": "52cc2a3822512db5be3accc8263f2ac1338f32fad8af63cc81fb5af2f335c509"
+ "sha256": "b3d8382360fbbc58cbd8c9e654ddda30b9f0318cf04ebd7539ec75bd724041d2"
}
},
{
- "@id": "urn:d1d57963-2edd-4c3a-935e-79e9d3ae925b",
+ "@id": "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz",
"Label": "anat_sub-01_T1w.nii.gz",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+ "AtLocation": "ds011/sub-01/anat/sub-01_T1w.nii.gz",
"digest": {
- "sha256": "3d9457fa7712b355d6569522ca80a6dfd70a40b82e6aa0a9364513cf04916dbb"
+ "sha256": "70b9327067cc5200330e04e70b22a41db5aa3b78f978060f61f49bd3a45d125e"
}
},
{
- "@id": "urn:14ddd282-4294-4c2e-a111-1bc95e4f5a39",
+ "@id": "urn:uuid:8fa22cb9-7c76-486f-9d5b-8cba8bd3acee",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "GeneratedBy": "urn:6fac3dd4-3655-4d3d-a4f5-73b727d0283d"
+ "GeneratedBy": "urn:movefile-oKHoqlpV"
},
{
- "@id": "urn:dca2af2a-8bf2-48b5-be14-e6e569647003",
+ "@id": "urn:uuid:b8523047-5639-4e6e-adec-6daec8a60280",
"Label": "anat_sub-01_T1w.nii.gz",
- "GeneratedBy": "urn:24a2e1fd-6f79-48cf-a9b4-0b3c50c00ef7"
+ "GeneratedBy": "urn:movefile-Wjq8qqkf"
},
{
- "@id": "urn:2461ed0f-a5f5-47b8-96f4-be8d20fc72ec",
+ "@id": "urn:uuid:d93c3829-c444-49f3-a3c6-6f836e61bd6a",
"Label": "func_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:8e23621e-af1f-4f36-aa91-fe74af747392"
+ "GeneratedBy": "urn:gunzip3-AAN8zM3m"
},
{
- "@id": "urn:caf58ed5-15de-4ac6-aa9d-3a9c22c728fc",
+ "@id": "urn:uuid:858135c7-7aac-4fee-9ffb-2109e784abc0",
"Label": "meanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:32ec3ee6-1e9d-47e1-90db-591150f53238"
+ "GeneratedBy": "urn:realign5-6rhsn0th"
},
{
- "@id": "urn:9157ac14-4b38-4ffb-9216-f2597912fe25",
+ "@id": "urn:uuid:d8124621-a9cb-4ed9-b26d-0adfb02e6e84",
"Label": "anat_sub-01_T1w.nii",
- "GeneratedBy": "urn:df85adc5-0547-478e-a8d0-34cb2391ce58"
+ "GeneratedBy": "urn:gunzip4-aws2OWPG"
},
{
- "@id": "urn:40f61898-bf4a-46a7-9bd8-4190732dcdb7",
+ "@id": "bids::c1anat_sub-01_T1w.nii",
"Label": "segment1",
- "Atlocation": "c1xxx.nii.gz",
- "GeneratedBy": "urn:c09a6590-cb1b-443f-991f-902132a59ae4",
"AtLocation": "c1anat_sub-01_T1w.nii",
+ "GeneratedBy": "urn:segment7-1oFMwhYt",
"digest": {
"sha256": "61ca923955d0a5c9088df9e258f41644067ec964e1c9a83284ba03b0515079b0"
}
},
{
- "@id": "urn:ba3fdc68-178d-4cf7-ad77-704f1b52cedd",
+ "@id": "bids::c2anat_sub-01_T1w.nii",
"Label": "segment2",
- "Atlocation": "c2xxx.nii.gz",
- "GeneratedBy": "urn:c09a6590-cb1b-443f-991f-902132a59ae4",
"AtLocation": "c2anat_sub-01_T1w.nii",
+ "GeneratedBy": "urn:segment7-1oFMwhYt",
"digest": {
"sha256": "10ad88ebeebebd0bd03ccbdd4df92d500d28d14715fa5375fd35589caddf49a6"
}
},
{
- "@id": "urn:9403d5c6-51b2-46bd-9794-981da1e12b27",
+ "@id": "urn:uuid:11e832e4-d52e-4d41-aa63-1013364f30be",
"Label": "wsegment1",
- "GeneratedBy": "urn:1ae03796-c374-4c1d-b521-97bc6aeb3c76"
+ "GeneratedBy": "urn:normaliz-XNMcYmPX"
},
{
- "@id": "urn:75142b97-c286-40c1-a0df-a19fee33956c",
+ "@id": "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"Label": "ONSETS_sub-01-MultiCond.mat",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+ "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"digest": {
- "sha256": "be4671d4f9dc480dd3e5be19aeeab2756f7afdc3b32d81e071685d7a4eafcfed"
+ "sha256": "5599e80629bb4d66cdbfb357511c04060bd3d37cdbfe2a4cd701a2979e9f6610"
}
},
{
- "@id": "urn:4fbd6045-cae5-4f0a-8b65-857ef927274f",
+ "@id": "urn:uuid:f6b16b8e-ba13-4b03-957f-fbe68afe59df",
"Label": "swsegment1",
- "GeneratedBy": "urn:11f223e3-299f-4f87-b5c6-b2cd5e69c374"
+ "GeneratedBy": "urn:smooth10-pO6CXV88"
},
{
- "@id": "urn:fe68686f-5fe0-4994-a9b1-200e446ff6b9",
+ "@id": "urn:uuid:30abb4c8-1be8-45e1-8509-67d5ed09efed",
"Label": "SPM.mat",
- "GeneratedBy": "urn:1c5facbc-99e5-4301-ba64-ab4aadc48e17"
+ "GeneratedBy": "urn:statdesi-uWpA1oPb"
},
{
- "@id": "urn:636d3259-22bf-4dd3-a14a-b564569cac0d",
+ "@id": "urn:uuid:c0fb8d7f-a541-432b-a819-abdc9366765e",
"Label": "SPM.mat",
- "GeneratedBy": "urn:d59db5b5-4ab3-4475-bb6e-9e3510819631"
+ "GeneratedBy": "urn:estimate-PLgbjc6p"
},
{
- "@id": "urn:954dc233-a400-4356-98f9-d818f2b94a91",
+ "@id": "urn:uuid:2864188c-4e65-4ac4-acd8-096759441ba7",
"Label": "SPM.mat",
- "GeneratedBy": "urn:dde554f4-eccf-4317-9518-efa60214f791"
+ "GeneratedBy": "urn:estimate-hoQcZWBN"
}
]
}
diff --git a/examples/from_parsers/spm/spm_thr_voxelfdrp05_batch.m b/examples/from_parsers/spm/spm_thr_voxelfdrp05_batch.m
index 4384597de..d3d4b6a41 100644
--- a/examples/from_parsers/spm/spm_thr_voxelfdrp05_batch.m
+++ b/examples/from_parsers/spm/spm_thr_voxelfdrp05_batch.m
@@ -3,10 +3,10 @@
% spm SPM - SPM12 (12.1)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------
-matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};
-matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};
-matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};
-matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};
+matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};
+matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};
+matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};
+matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};
matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));
@@ -90,7 +90,7 @@
matlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;
matlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});
-matlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};
+matlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};
matlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});
matlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};
matlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;
diff --git a/examples/from_parsers/spm/spm_thr_voxelfdrp05_batch.png b/examples/from_parsers/spm/spm_thr_voxelfdrp05_batch.png
index a2a1ec926..5dfb550db 100644
Binary files a/examples/from_parsers/spm/spm_thr_voxelfdrp05_batch.png and b/examples/from_parsers/spm/spm_thr_voxelfdrp05_batch.png differ
diff --git a/examples/from_parsers/spm/spm_thr_voxelfwep05_batch.jsonld b/examples/from_parsers/spm/spm_thr_voxelfwep05_batch.jsonld
index 399441087..dfa1ad3c1 100644
--- a/examples/from_parsers/spm/spm_thr_voxelfwep05_batch.jsonld
+++ b/examples/from_parsers/spm/spm_thr_voxelfwep05_batch.jsonld
@@ -4,63 +4,63 @@
"Records": {
"Software": [
{
- "@id": "urn:132f8ed1-de07-49fe-bbcd-0e7d8bf4dc50",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:spm-yjAds0ke",
"@type": "prov:SoftwareAgent",
"Label": "SPM",
- "Version": "SPM12r7224"
+ "Version": "SPM12r7224",
+ "AltIdentifier": "RRID:SCR_007037"
}
],
"Activities": [
{
- "@id": "urn:6a2d483a-c551-4640-840d-afcc913d7b0c",
+ "@id": "urn:movefile-jgpFGx7p",
"Label": "Move file",
"Used": [
- "urn:d09a9e6e-3b93-45ac-bc47-55d3f9553c11"
+ "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
],
- "AssociatedWith": "urn:132f8ed1-de07-49fe-bbcd-0e7d8bf4dc50",
- "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
+ "AssociatedWith": "urn:spm-yjAds0ke",
+ "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};",
"Parameters": {
- "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
+ "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'}"
}
},
{
- "@id": "urn:3ae2add0-3e15-43a4-8ed1-2a271df38148",
+ "@id": "urn:movefile-oi25dFW5",
"Label": "Move file",
"Used": [
- "urn:63092bb5-c00b-4806-ada8-4e675ca40481"
+ "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz"
],
- "AssociatedWith": "urn:132f8ed1-de07-49fe-bbcd-0e7d8bf4dc50",
- "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
+ "AssociatedWith": "urn:spm-yjAds0ke",
+ "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};",
"Parameters": {
- "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
+ "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'}"
}
},
{
- "@id": "urn:499b5597-193b-4c01-8748-0353d72e7812",
+ "@id": "urn:gunzip3-rcniALDA",
"Label": "Gunzip",
"Used": [
- "urn:b6cfbd28-f1b1-428c-8aee-21fa321a24c3"
+ "urn:uuid:66498c32-4cc1-4b35-8a3b-7ef1e48f870b"
],
- "AssociatedWith": "urn:132f8ed1-de07-49fe-bbcd-0e7d8bf4dc50",
+ "AssociatedWith": "urn:spm-yjAds0ke",
"Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:571a134a-fc64-4cdd-a0f4-2ce78588cf20",
+ "@id": "urn:gunzip4-unV7YNDw",
"Label": "Gunzip",
"Used": [
- "urn:3de80e83-be49-40e6-9e70-c25dd5f971ad"
+ "urn:uuid:be46fe75-48d3-4aec-b827-72eb76cf3e4b"
],
- "AssociatedWith": "urn:132f8ed1-de07-49fe-bbcd-0e7d8bf4dc50",
+ "AssociatedWith": "urn:spm-yjAds0ke",
"Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:ca817d3b-0fca-4f15-82b4-edda7393cefa",
+ "@id": "urn:realign5-K1X4d2V7",
"Label": "Realign",
"Used": [
- "urn:c32531f4-eacb-40a9-923b-70b1748c51c5"
+ "urn:uuid:0e8c2114-421b-4c1f-9770-b7ec22289e5b"
],
- "AssociatedWith": "urn:132f8ed1-de07-49fe-bbcd-0e7d8bf4dc50",
+ "AssociatedWith": "urn:spm-yjAds0ke",
"Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
"Parameters": {
"eoptions.quality": "0.9",
@@ -78,13 +78,13 @@
}
},
{
- "@id": "urn:2d92b15d-ceb0-4828-90ca-44d8cb55b37f",
+ "@id": "urn:coregist-CYH6rn5i",
"Label": "Coregister",
"Used": [
- "urn:58f887a8-b7b6-4ae0-ac2a-6f8113ecf719",
- "urn:a4bcce4e-9230-4c91-afc0-6657745b8701"
+ "urn:uuid:116af5c8-b8ba-4dc0-8992-24147d8fa74f",
+ "urn:uuid:a921f85d-f605-4362-954a-0cb2364b9106"
],
- "AssociatedWith": "urn:132f8ed1-de07-49fe-bbcd-0e7d8bf4dc50",
+ "AssociatedWith": "urn:spm-yjAds0ke",
"Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
"Parameters": {
"other": "{''}",
@@ -95,12 +95,12 @@
}
},
{
- "@id": "urn:af9f6f85-8adc-4ef9-a88c-8402725f2373",
+ "@id": "urn:segment7-kfGSAqvJ",
"Label": "Segment",
"Used": [
- "urn:a4bcce4e-9230-4c91-afc0-6657745b8701"
+ "urn:uuid:116af5c8-b8ba-4dc0-8992-24147d8fa74f"
],
- "AssociatedWith": "urn:132f8ed1-de07-49fe-bbcd-0e7d8bf4dc50",
+ "AssociatedWith": "urn:spm-yjAds0ke",
"Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
"Parameters": {
"channel.biasreg": "0.001",
@@ -140,13 +140,13 @@
}
},
{
- "@id": "urn:cb81e16e-cab3-408f-93d8-37aefc195994",
+ "@id": "urn:normaliz-qr8A88OY",
"Label": "Normalize",
"Used": [
- "urn:3bdef291-db22-4670-b345-fff8811f30ac",
- "urn:58f887a8-b7b6-4ae0-ac2a-6f8113ecf719"
+ "bids::c1anat_sub-01_T1w.nii",
+ "urn:uuid:a921f85d-f605-4362-954a-0cb2364b9106"
],
- "AssociatedWith": "urn:132f8ed1-de07-49fe-bbcd-0e7d8bf4dc50",
+ "AssociatedWith": "urn:spm-yjAds0ke",
"Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -156,12 +156,12 @@
}
},
{
- "@id": "urn:e289288b-2ab9-40af-bfb8-5ccf11862589",
+ "@id": "urn:normaliz-RHavIjbG",
"Label": "Normalize",
"Used": [
- "urn:3bdef291-db22-4670-b345-fff8811f30ac"
+ "bids::c1anat_sub-01_T1w.nii"
],
- "AssociatedWith": "urn:132f8ed1-de07-49fe-bbcd-0e7d8bf4dc50",
+ "AssociatedWith": "urn:spm-yjAds0ke",
"Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -171,12 +171,12 @@
}
},
{
- "@id": "urn:a7c0d8c8-7be5-4ebc-8f07-ebd395edf9a2",
+ "@id": "urn:smooth10-LW7JBDgU",
"Label": "Smooth",
"Used": [
- "urn:012baa80-344e-4625-9fe2-288360cec634"
+ "urn:uuid:be60ffac-85d7-4c57-b3a3-64e06e72d7b6"
],
- "AssociatedWith": "urn:132f8ed1-de07-49fe-bbcd-0e7d8bf4dc50",
+ "AssociatedWith": "urn:spm-yjAds0ke",
"Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
"Parameters": {
"fwhm": "[6, 6, 6]",
@@ -186,14 +186,14 @@
}
},
{
- "@id": "urn:42974bae-1dd8-4079-a97d-4ba1ccc9632e",
+ "@id": "urn:statdesi-QtqAmLov",
"Label": "Stat Design",
"Used": [
- "urn:8433fb76-022b-4846-b2d4-fdc2cbeae320",
- "urn:7c2dc4f8-24fc-4996-ab18-2e8059b863d6"
+ "urn:uuid:4380232a-e050-464e-8f0f-3bd6d53cd023",
+ "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
],
- "AssociatedWith": "urn:132f8ed1-de07-49fe-bbcd-0e7d8bf4dc50",
- "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_FWE_p005'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
+ "AssociatedWith": "urn:spm-yjAds0ke",
+ "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_FWE_p005'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
"Parameters": {
"dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_FWE_p005'}",
"timing.units": "'secs'",
@@ -214,12 +214,12 @@
}
},
{
- "@id": "urn:6ed86163-23f8-47e8-89ec-54d1da8e4826",
+ "@id": "urn:estimate-IK95mkJW",
"Label": "Estimate stat.",
"Used": [
- "urn:84181693-0714-48f4-9e3b-b1b52f2f8877"
+ "urn:uuid:1ce4a608-dfe0-4e27-ac4f-77f4f7897c8d"
],
- "AssociatedWith": "urn:132f8ed1-de07-49fe-bbcd-0e7d8bf4dc50",
+ "AssociatedWith": "urn:spm-yjAds0ke",
"Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
"Parameters": {
"write_residuals": "0",
@@ -227,12 +227,12 @@
}
},
{
- "@id": "urn:fb0604a6-1759-4f62-97f1-fc18df7e0e79",
+ "@id": "urn:estimate-82zqDQEd",
"Label": "Estimate contrast",
"Used": [
- "urn:04b2168c-1bb1-445f-b71d-0bc0f29ada87"
+ "urn:uuid:63e6bd7b-8840-4c4a-8706-995cdcdecacb"
],
- "AssociatedWith": "urn:132f8ed1-de07-49fe-bbcd-0e7d8bf4dc50",
+ "AssociatedWith": "urn:spm-yjAds0ke",
"Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
"Parameters": {
"consess{1}.tcon.name": "'tone counting vs baseline'",
@@ -242,12 +242,12 @@
}
},
{
- "@id": "urn:ac224bd4-b45c-4ad9-a7c7-14bff747481d",
+ "@id": "urn:threshol-0yyntHMZ",
"Label": "Threshold",
"Used": [
- "urn:a4725cde-22c1-43e1-bb39-8ca323359467"
+ "urn:uuid:449e7341-030f-47de-ab61-25a597c0a2fc"
],
- "AssociatedWith": "urn:132f8ed1-de07-49fe-bbcd-0e7d8bf4dc50",
+ "AssociatedWith": "urn:spm-yjAds0ke",
"Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'FWE';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.05;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.tspm.basename = 'thresh';",
"Parameters": {
"conspec.titlestr": "''",
@@ -265,98 +265,96 @@
],
"Entities": [
{
- "@id": "urn:d09a9e6e-3b93-45ac-bc47-55d3f9553c11",
+ "@id": "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+ "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"digest": {
- "sha256": "52cc2a3822512db5be3accc8263f2ac1338f32fad8af63cc81fb5af2f335c509"
+ "sha256": "b3d8382360fbbc58cbd8c9e654ddda30b9f0318cf04ebd7539ec75bd724041d2"
}
},
{
- "@id": "urn:63092bb5-c00b-4806-ada8-4e675ca40481",
+ "@id": "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz",
"Label": "anat_sub-01_T1w.nii.gz",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+ "AtLocation": "ds011/sub-01/anat/sub-01_T1w.nii.gz",
"digest": {
- "sha256": "3d9457fa7712b355d6569522ca80a6dfd70a40b82e6aa0a9364513cf04916dbb"
+ "sha256": "70b9327067cc5200330e04e70b22a41db5aa3b78f978060f61f49bd3a45d125e"
}
},
{
- "@id": "urn:b6cfbd28-f1b1-428c-8aee-21fa321a24c3",
+ "@id": "urn:uuid:66498c32-4cc1-4b35-8a3b-7ef1e48f870b",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "GeneratedBy": "urn:6a2d483a-c551-4640-840d-afcc913d7b0c"
+ "GeneratedBy": "urn:movefile-jgpFGx7p"
},
{
- "@id": "urn:3de80e83-be49-40e6-9e70-c25dd5f971ad",
+ "@id": "urn:uuid:be46fe75-48d3-4aec-b827-72eb76cf3e4b",
"Label": "anat_sub-01_T1w.nii.gz",
- "GeneratedBy": "urn:3ae2add0-3e15-43a4-8ed1-2a271df38148"
+ "GeneratedBy": "urn:movefile-oi25dFW5"
},
{
- "@id": "urn:c32531f4-eacb-40a9-923b-70b1748c51c5",
+ "@id": "urn:uuid:0e8c2114-421b-4c1f-9770-b7ec22289e5b",
"Label": "func_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:499b5597-193b-4c01-8748-0353d72e7812"
+ "GeneratedBy": "urn:gunzip3-rcniALDA"
},
{
- "@id": "urn:58f887a8-b7b6-4ae0-ac2a-6f8113ecf719",
+ "@id": "urn:uuid:a921f85d-f605-4362-954a-0cb2364b9106",
"Label": "meanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:ca817d3b-0fca-4f15-82b4-edda7393cefa"
+ "GeneratedBy": "urn:realign5-K1X4d2V7"
},
{
- "@id": "urn:a4bcce4e-9230-4c91-afc0-6657745b8701",
+ "@id": "urn:uuid:116af5c8-b8ba-4dc0-8992-24147d8fa74f",
"Label": "anat_sub-01_T1w.nii",
- "GeneratedBy": "urn:571a134a-fc64-4cdd-a0f4-2ce78588cf20"
+ "GeneratedBy": "urn:gunzip4-unV7YNDw"
},
{
- "@id": "urn:3bdef291-db22-4670-b345-fff8811f30ac",
+ "@id": "bids::c1anat_sub-01_T1w.nii",
"Label": "segment1",
- "Atlocation": "c1xxx.nii.gz",
- "GeneratedBy": "urn:af9f6f85-8adc-4ef9-a88c-8402725f2373",
"AtLocation": "c1anat_sub-01_T1w.nii",
+ "GeneratedBy": "urn:segment7-kfGSAqvJ",
"digest": {
"sha256": "61ca923955d0a5c9088df9e258f41644067ec964e1c9a83284ba03b0515079b0"
}
},
{
- "@id": "urn:51f3d7f5-903a-4125-a257-f7bc9e65398b",
+ "@id": "bids::c2anat_sub-01_T1w.nii",
"Label": "segment2",
- "Atlocation": "c2xxx.nii.gz",
- "GeneratedBy": "urn:af9f6f85-8adc-4ef9-a88c-8402725f2373",
"AtLocation": "c2anat_sub-01_T1w.nii",
+ "GeneratedBy": "urn:segment7-kfGSAqvJ",
"digest": {
"sha256": "10ad88ebeebebd0bd03ccbdd4df92d500d28d14715fa5375fd35589caddf49a6"
}
},
{
- "@id": "urn:012baa80-344e-4625-9fe2-288360cec634",
+ "@id": "urn:uuid:be60ffac-85d7-4c57-b3a3-64e06e72d7b6",
"Label": "wsegment1",
- "GeneratedBy": "urn:cb81e16e-cab3-408f-93d8-37aefc195994"
+ "GeneratedBy": "urn:normaliz-qr8A88OY"
},
{
- "@id": "urn:7c2dc4f8-24fc-4996-ab18-2e8059b863d6",
+ "@id": "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"Label": "ONSETS_sub-01-MultiCond.mat",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+ "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"digest": {
- "sha256": "be4671d4f9dc480dd3e5be19aeeab2756f7afdc3b32d81e071685d7a4eafcfed"
+ "sha256": "5599e80629bb4d66cdbfb357511c04060bd3d37cdbfe2a4cd701a2979e9f6610"
}
},
{
- "@id": "urn:8433fb76-022b-4846-b2d4-fdc2cbeae320",
+ "@id": "urn:uuid:4380232a-e050-464e-8f0f-3bd6d53cd023",
"Label": "swsegment1",
- "GeneratedBy": "urn:a7c0d8c8-7be5-4ebc-8f07-ebd395edf9a2"
+ "GeneratedBy": "urn:smooth10-LW7JBDgU"
},
{
- "@id": "urn:84181693-0714-48f4-9e3b-b1b52f2f8877",
+ "@id": "urn:uuid:1ce4a608-dfe0-4e27-ac4f-77f4f7897c8d",
"Label": "SPM.mat",
- "GeneratedBy": "urn:42974bae-1dd8-4079-a97d-4ba1ccc9632e"
+ "GeneratedBy": "urn:statdesi-QtqAmLov"
},
{
- "@id": "urn:04b2168c-1bb1-445f-b71d-0bc0f29ada87",
+ "@id": "urn:uuid:63e6bd7b-8840-4c4a-8706-995cdcdecacb",
"Label": "SPM.mat",
- "GeneratedBy": "urn:6ed86163-23f8-47e8-89ec-54d1da8e4826"
+ "GeneratedBy": "urn:estimate-IK95mkJW"
},
{
- "@id": "urn:a4725cde-22c1-43e1-bb39-8ca323359467",
+ "@id": "urn:uuid:449e7341-030f-47de-ab61-25a597c0a2fc",
"Label": "SPM.mat",
- "GeneratedBy": "urn:fb0604a6-1759-4f62-97f1-fc18df7e0e79"
+ "GeneratedBy": "urn:estimate-82zqDQEd"
}
]
}
diff --git a/examples/from_parsers/spm/spm_thr_voxelfwep05_batch.m b/examples/from_parsers/spm/spm_thr_voxelfwep05_batch.m
index d80f328a6..f944277d3 100644
--- a/examples/from_parsers/spm/spm_thr_voxelfwep05_batch.m
+++ b/examples/from_parsers/spm/spm_thr_voxelfwep05_batch.m
@@ -3,10 +3,10 @@
% spm SPM - SPM12 (12.1)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------
-matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};
-matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};
-matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};
-matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};
+matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};
+matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};
+matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};
+matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};
matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));
@@ -90,7 +90,7 @@
matlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;
matlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});
-matlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};
+matlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};
matlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});
matlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};
matlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;
diff --git a/examples/from_parsers/spm/spm_thr_voxelfwep05_batch.png b/examples/from_parsers/spm/spm_thr_voxelfwep05_batch.png
index 08a249966..a2dd7a9b6 100644
Binary files a/examples/from_parsers/spm/spm_thr_voxelfwep05_batch.png and b/examples/from_parsers/spm/spm_thr_voxelfwep05_batch.png differ
diff --git a/examples/from_parsers/spm/spm_thr_voxelunct4_batch.jsonld b/examples/from_parsers/spm/spm_thr_voxelunct4_batch.jsonld
index 7ffb564c9..71d198e5b 100644
--- a/examples/from_parsers/spm/spm_thr_voxelunct4_batch.jsonld
+++ b/examples/from_parsers/spm/spm_thr_voxelunct4_batch.jsonld
@@ -4,63 +4,63 @@
"Records": {
"Software": [
{
- "@id": "urn:6fec5948-e934-4d57-885e-2f9ff5bb37ab",
- "RRID": "RRID:SCR_007037",
+ "@id": "urn:urn:spm-VHiUsL5F",
"@type": "prov:SoftwareAgent",
"Label": "SPM",
- "Version": "SPM12r7224"
+ "Version": "SPM12r7224",
+ "AltIdentifier": "RRID:SCR_007037"
}
],
"Activities": [
{
- "@id": "urn:7c2e9e77-f441-4a6e-a902-d2101c32b8eb",
+ "@id": "urn:movefile-ROutyaPT",
"Label": "Move file",
"Used": [
- "urn:a424e26a-4756-4ebf-aee7-78caa8508f49"
+ "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz"
],
- "AssociatedWith": "urn:6fec5948-e934-4d57-885e-2f9ff5bb37ab",
- "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
+ "AssociatedWith": "urn:spm-VHiUsL5F",
+ "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};",
"Parameters": {
- "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
+ "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'}"
}
},
{
- "@id": "urn:a9ba8f6c-c396-418e-a76a-08e1034d485c",
+ "@id": "urn:movefile-4PSvH3CK",
"Label": "Move file",
"Used": [
- "urn:c769e5d3-d624-487f-8403-8a811b38236f"
+ "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz"
],
- "AssociatedWith": "urn:6fec5948-e934-4d57-885e-2f9ff5bb37ab",
- "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
+ "AssociatedWith": "urn:spm-VHiUsL5F",
+ "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};",
"Parameters": {
- "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
+ "action.copyto": "{'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'}"
}
},
{
- "@id": "urn:f7b45616-d40f-4f94-9390-20175b6abab7",
+ "@id": "urn:gunzip3-vYPrtqD5",
"Label": "Gunzip",
"Used": [
- "urn:49ddb519-977c-4811-810f-148fd1d470bf"
+ "urn:uuid:b9c13da5-bd20-4982-8e24-84e88a4ae030"
],
- "AssociatedWith": "urn:6fec5948-e934-4d57-885e-2f9ff5bb37ab",
+ "AssociatedWith": "urn:spm-VHiUsL5F",
"Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:33aca4fb-d789-4ab3-96b7-d6f51bb3f6c5",
+ "@id": "urn:gunzip4-u7pnp8ps",
"Label": "Gunzip",
"Used": [
- "urn:b998fe7f-cac5-417b-a893-9c24f9d9c772"
+ "urn:uuid:e8972264-3d5c-41e9-9e79-3aa2517f2787"
],
- "AssociatedWith": "urn:6fec5948-e934-4d57-885e-2f9ff5bb37ab",
+ "AssociatedWith": "urn:spm-VHiUsL5F",
"Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:035743bc-1100-484b-94c6-b43764e0cd18",
+ "@id": "urn:realign5-8HqBQ0ss",
"Label": "Realign",
"Used": [
- "urn:7ad4dcb0-cec7-4d82-ab67-1da97d0a6e4e"
+ "urn:uuid:b9238bd2-fa85-4bcb-a4c2-08d2eec5e697"
],
- "AssociatedWith": "urn:6fec5948-e934-4d57-885e-2f9ff5bb37ab",
+ "AssociatedWith": "urn:spm-VHiUsL5F",
"Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
"Parameters": {
"eoptions.quality": "0.9",
@@ -78,13 +78,13 @@
}
},
{
- "@id": "urn:fe7f40a7-0fb0-4d06-bbd9-2b2eac246769",
+ "@id": "urn:coregist-SSyJLUBq",
"Label": "Coregister",
"Used": [
- "urn:9fe42f85-752e-4fee-8973-6463a374f383",
- "urn:bb39b855-9542-4c73-800c-28d70f33d72f"
+ "urn:uuid:9e132fb5-837a-4e40-b107-656f6b9a41f4",
+ "urn:uuid:fc1e9970-e3d1-4041-98fc-93127b2276d3"
],
- "AssociatedWith": "urn:6fec5948-e934-4d57-885e-2f9ff5bb37ab",
+ "AssociatedWith": "urn:spm-VHiUsL5F",
"Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
"Parameters": {
"other": "{''}",
@@ -95,12 +95,12 @@
}
},
{
- "@id": "urn:a9e915bc-4251-4ce4-aae6-e019c0098d4a",
+ "@id": "urn:segment7-w1flk7eY",
"Label": "Segment",
"Used": [
- "urn:bb39b855-9542-4c73-800c-28d70f33d72f"
+ "urn:uuid:9e132fb5-837a-4e40-b107-656f6b9a41f4"
],
- "AssociatedWith": "urn:6fec5948-e934-4d57-885e-2f9ff5bb37ab",
+ "AssociatedWith": "urn:spm-VHiUsL5F",
"Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
"Parameters": {
"channel.biasreg": "0.001",
@@ -140,13 +140,13 @@
}
},
{
- "@id": "urn:af3a6a6e-ab3b-495f-9d79-975b4fac173b",
+ "@id": "urn:normaliz-EnYVW6ta",
"Label": "Normalize",
"Used": [
- "urn:9fe42f85-752e-4fee-8973-6463a374f383",
- "urn:a3a0a820-1bda-451a-9a7a-8efcde1f9e21"
+ "bids::c1anat_sub-01_T1w.nii",
+ "urn:uuid:fc1e9970-e3d1-4041-98fc-93127b2276d3"
],
- "AssociatedWith": "urn:6fec5948-e934-4d57-885e-2f9ff5bb37ab",
+ "AssociatedWith": "urn:spm-VHiUsL5F",
"Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -156,12 +156,12 @@
}
},
{
- "@id": "urn:b3b270f2-332e-408c-9217-66156ffa79ff",
+ "@id": "urn:normaliz-6rnR9WUq",
"Label": "Normalize",
"Used": [
- "urn:a3a0a820-1bda-451a-9a7a-8efcde1f9e21"
+ "bids::c1anat_sub-01_T1w.nii"
],
- "AssociatedWith": "urn:6fec5948-e934-4d57-885e-2f9ff5bb37ab",
+ "AssociatedWith": "urn:spm-VHiUsL5F",
"Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -171,12 +171,12 @@
}
},
{
- "@id": "urn:b3ad7f23-b5b1-495b-bd54-c81324facbbf",
+ "@id": "urn:smooth10-3bFmW9kk",
"Label": "Smooth",
"Used": [
- "urn:a73f4c88-b010-423c-a66f-891d32b30cc8"
+ "urn:uuid:6ebfdade-3218-4c37-abda-28ad1f81b578"
],
- "AssociatedWith": "urn:6fec5948-e934-4d57-885e-2f9ff5bb37ab",
+ "AssociatedWith": "urn:spm-VHiUsL5F",
"Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
"Parameters": {
"fwhm": "[6, 6, 6]",
@@ -186,14 +186,14 @@
}
},
{
- "@id": "urn:45ff77e8-eb82-4175-80d0-f95a34bedc2d",
+ "@id": "urn:statdesi-NzpBsugX",
"Label": "Stat Design",
"Used": [
- "urn:fe7823e7-a7a4-4991-8938-14e7d736a233",
- "urn:7b8a0aed-a199-45c6-9984-691a3b9342b0"
+ "urn:uuid:f5296976-630d-4243-885f-f11f9ea2027d",
+ "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat"
],
- "AssociatedWith": "urn:6fec5948-e934-4d57-885e-2f9ff5bb37ab",
- "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_voxelwise_t4'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
+ "AssociatedWith": "urn:spm-VHiUsL5F",
+ "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_voxelwise_t4'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
"Parameters": {
"dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_voxelwise_t4'}",
"timing.units": "'secs'",
@@ -214,12 +214,12 @@
}
},
{
- "@id": "urn:6cc92bfd-ba05-4178-9439-f356bb45800e",
+ "@id": "urn:estimate-OmZfIRWm",
"Label": "Estimate stat.",
"Used": [
- "urn:1b5ca7ef-1b1c-417d-9180-6a48d5f2fcb6"
+ "urn:uuid:dc23b217-4d4d-4f85-8976-c35f199399ec"
],
- "AssociatedWith": "urn:6fec5948-e934-4d57-885e-2f9ff5bb37ab",
+ "AssociatedWith": "urn:spm-VHiUsL5F",
"Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
"Parameters": {
"write_residuals": "0",
@@ -227,12 +227,12 @@
}
},
{
- "@id": "urn:5f912f03-d39f-41da-8581-476057afa5b2",
+ "@id": "urn:estimate-5VIJTs0L",
"Label": "Estimate contrast",
"Used": [
- "urn:e455fbcd-8b0e-476b-964a-230f3fb1f315"
+ "urn:uuid:74440f61-3749-47ff-bde5-b4c8a1a60240"
],
- "AssociatedWith": "urn:6fec5948-e934-4d57-885e-2f9ff5bb37ab",
+ "AssociatedWith": "urn:spm-VHiUsL5F",
"Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
"Parameters": {
"consess{1}.tcon.name": "'tone counting vs baseline'",
@@ -242,12 +242,12 @@
}
},
{
- "@id": "urn:1e091424-d3b1-4596-b5e1-2b5167927fa1",
+ "@id": "urn:threshol-limWhYjF",
"Label": "Threshold",
"Used": [
- "urn:b591dfe1-e4c6-4e46-9d53-c59c3a00c8bf"
+ "urn:uuid:18fe4543-ccde-4309-8280-1f29622ad95f"
],
- "AssociatedWith": "urn:6fec5948-e934-4d57-885e-2f9ff5bb37ab",
+ "AssociatedWith": "urn:spm-VHiUsL5F",
"Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 4;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.tspm.basename = 'thresh';",
"Parameters": {
"conspec.titlestr": "''",
@@ -265,98 +265,96 @@
],
"Entities": [
{
- "@id": "urn:a424e26a-4756-4ebf-aee7-78caa8508f49",
+ "@id": "bids:ds011:/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
+ "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"digest": {
- "sha256": "52cc2a3822512db5be3accc8263f2ac1338f32fad8af63cc81fb5af2f335c509"
+ "sha256": "b3d8382360fbbc58cbd8c9e654ddda30b9f0318cf04ebd7539ec75bd724041d2"
}
},
{
- "@id": "urn:c769e5d3-d624-487f-8403-8a811b38236f",
+ "@id": "bids:ds011:/sub-01/anat/sub-01_T1w.nii.gz",
"Label": "anat_sub-01_T1w.nii.gz",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
+ "AtLocation": "ds011/sub-01/anat/sub-01_T1w.nii.gz",
"digest": {
- "sha256": "3d9457fa7712b355d6569522ca80a6dfd70a40b82e6aa0a9364513cf04916dbb"
+ "sha256": "70b9327067cc5200330e04e70b22a41db5aa3b78f978060f61f49bd3a45d125e"
}
},
{
- "@id": "urn:49ddb519-977c-4811-810f-148fd1d470bf",
+ "@id": "urn:uuid:b9c13da5-bd20-4982-8e24-84e88a4ae030",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "GeneratedBy": "urn:7c2e9e77-f441-4a6e-a902-d2101c32b8eb"
+ "GeneratedBy": "urn:movefile-ROutyaPT"
},
{
- "@id": "urn:b998fe7f-cac5-417b-a893-9c24f9d9c772",
+ "@id": "urn:uuid:e8972264-3d5c-41e9-9e79-3aa2517f2787",
"Label": "anat_sub-01_T1w.nii.gz",
- "GeneratedBy": "urn:a9ba8f6c-c396-418e-a76a-08e1034d485c"
+ "GeneratedBy": "urn:movefile-4PSvH3CK"
},
{
- "@id": "urn:7ad4dcb0-cec7-4d82-ab67-1da97d0a6e4e",
+ "@id": "urn:uuid:b9238bd2-fa85-4bcb-a4c2-08d2eec5e697",
"Label": "func_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:f7b45616-d40f-4f94-9390-20175b6abab7"
+ "GeneratedBy": "urn:gunzip3-vYPrtqD5"
},
{
- "@id": "urn:9fe42f85-752e-4fee-8973-6463a374f383",
+ "@id": "urn:uuid:fc1e9970-e3d1-4041-98fc-93127b2276d3",
"Label": "meanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:035743bc-1100-484b-94c6-b43764e0cd18"
+ "GeneratedBy": "urn:realign5-8HqBQ0ss"
},
{
- "@id": "urn:bb39b855-9542-4c73-800c-28d70f33d72f",
+ "@id": "urn:uuid:9e132fb5-837a-4e40-b107-656f6b9a41f4",
"Label": "anat_sub-01_T1w.nii",
- "GeneratedBy": "urn:33aca4fb-d789-4ab3-96b7-d6f51bb3f6c5"
+ "GeneratedBy": "urn:gunzip4-u7pnp8ps"
},
{
- "@id": "urn:a3a0a820-1bda-451a-9a7a-8efcde1f9e21",
+ "@id": "bids::c1anat_sub-01_T1w.nii",
"Label": "segment1",
- "Atlocation": "c1xxx.nii.gz",
- "GeneratedBy": "urn:a9e915bc-4251-4ce4-aae6-e019c0098d4a",
"AtLocation": "c1anat_sub-01_T1w.nii",
+ "GeneratedBy": "urn:segment7-w1flk7eY",
"digest": {
"sha256": "61ca923955d0a5c9088df9e258f41644067ec964e1c9a83284ba03b0515079b0"
}
},
{
- "@id": "urn:e3afcce5-5eab-469d-a72b-caa4bf38c61d",
+ "@id": "bids::c2anat_sub-01_T1w.nii",
"Label": "segment2",
- "Atlocation": "c2xxx.nii.gz",
- "GeneratedBy": "urn:a9e915bc-4251-4ce4-aae6-e019c0098d4a",
"AtLocation": "c2anat_sub-01_T1w.nii",
+ "GeneratedBy": "urn:segment7-w1flk7eY",
"digest": {
"sha256": "10ad88ebeebebd0bd03ccbdd4df92d500d28d14715fa5375fd35589caddf49a6"
}
},
{
- "@id": "urn:a73f4c88-b010-423c-a66f-891d32b30cc8",
- "Label": "wmeanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:af3a6a6e-ab3b-495f-9d79-975b4fac173b"
+ "@id": "urn:uuid:6ebfdade-3218-4c37-abda-28ad1f81b578",
+ "Label": "wsegment1",
+ "GeneratedBy": "urn:normaliz-EnYVW6ta"
},
{
- "@id": "urn:7b8a0aed-a199-45c6-9984-691a3b9342b0",
+ "@id": "bids:ds011:/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"Label": "ONSETS_sub-01-MultiCond.mat",
- "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
+ "AtLocation": "ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"digest": {
- "sha256": "be4671d4f9dc480dd3e5be19aeeab2756f7afdc3b32d81e071685d7a4eafcfed"
+ "sha256": "5599e80629bb4d66cdbfb357511c04060bd3d37cdbfe2a4cd701a2979e9f6610"
}
},
{
- "@id": "urn:fe7823e7-a7a4-4991-8938-14e7d736a233",
- "Label": "swmeanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:b3ad7f23-b5b1-495b-bd54-c81324facbbf"
+ "@id": "urn:uuid:f5296976-630d-4243-885f-f11f9ea2027d",
+ "Label": "swsegment1",
+ "GeneratedBy": "urn:smooth10-3bFmW9kk"
},
{
- "@id": "urn:1b5ca7ef-1b1c-417d-9180-6a48d5f2fcb6",
+ "@id": "urn:uuid:dc23b217-4d4d-4f85-8976-c35f199399ec",
"Label": "SPM.mat",
- "GeneratedBy": "urn:45ff77e8-eb82-4175-80d0-f95a34bedc2d"
+ "GeneratedBy": "urn:statdesi-NzpBsugX"
},
{
- "@id": "urn:e455fbcd-8b0e-476b-964a-230f3fb1f315",
+ "@id": "urn:uuid:74440f61-3749-47ff-bde5-b4c8a1a60240",
"Label": "SPM.mat",
- "GeneratedBy": "urn:6cc92bfd-ba05-4178-9439-f356bb45800e"
+ "GeneratedBy": "urn:estimate-OmZfIRWm"
},
{
- "@id": "urn:b591dfe1-e4c6-4e46-9d53-c59c3a00c8bf",
+ "@id": "urn:uuid:18fe4543-ccde-4309-8280-1f29622ad95f",
"Label": "SPM.mat",
- "GeneratedBy": "urn:5f912f03-d39f-41da-8581-476057afa5b2"
+ "GeneratedBy": "urn:estimate-5VIJTs0L"
}
]
}
diff --git a/examples/from_parsers/spm/spm_thr_voxelunct4_batch.m b/examples/from_parsers/spm/spm_thr_voxelunct4_batch.m
index 344d48b20..99f464d54 100644
--- a/examples/from_parsers/spm/spm_thr_voxelunct4_batch.m
+++ b/examples/from_parsers/spm/spm_thr_voxelunct4_batch.m
@@ -3,10 +3,10 @@
% spm SPM - SPM12 (12.1)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------
-matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};
-matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};
-matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};
-matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};
+matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};
+matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/FUNCTIONAL'};
+matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'ds011/sub-01/anat/sub-01_T1w.nii.gz'};
+matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'ds011/derivatives/SPM/PREPROCESSING/ANATOMICAL'};
matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));
@@ -90,7 +90,7 @@
matlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;
matlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
matlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});
-matlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};
+matlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'ds011/derivatives/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};
matlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});
matlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};
matlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;
diff --git a/examples/from_parsers/spm/spm_thr_voxelunct4_batch.png b/examples/from_parsers/spm/spm_thr_voxelunct4_batch.png
index a430e32e0..a265034f1 100644
Binary files a/examples/from_parsers/spm/spm_thr_voxelunct4_batch.png and b/examples/from_parsers/spm/spm_thr_voxelunct4_batch.png differ
diff --git a/launch_parser_on_nidm.py b/launch_parser_on_nidm.py
index d32f133b0..7e1d08d3a 100755
--- a/launch_parser_on_nidm.py
+++ b/launch_parser_on_nidm.py
@@ -2,6 +2,7 @@
import argparse
import os
+from os.path import join
import random
import shutil
from datetime import datetime
@@ -12,22 +13,46 @@
from bids_prov.utils import CONTEXT_URL
from bids_prov.visualize import main as visualize
+def clean_bids_paths(spm_file):
+ """Remove parts of file paths contained in a nidm-example spm batch.m file"""
+
+ with open(spm_file, 'r') as file:
+ lines = file.readlines()
+
+ for index, line in enumerate(lines):
+ new_line = line.replace(
+ '/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/', 'ds011/')
+ new_line = new_line.replace(
+ '/storage/essicd/data/NIDM-Ex/Data/ds000052/', 'ds000052/derivatives/')
+ new_line = new_line.replace(
+ '/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/', 'ds011/derivatives/')
+ lines[index] = new_line
+
+ with open(spm_file, 'w') as file:
+ for line in lines:
+ file.write(line)
def process_file(context_write, root, file, filename_ss_ext, output_dir, parser_function, verbose, with_blocks=False):
"""Process a file using the given parser function and save the output to the output directory."""
+
context_write.write(f" file= {root}/{str(file)}\n")
- filename = root + "/" + str(file)
+ filename = join(output_dir,str(file))
+
if with_blocks is False:
- shutil.copyfile(filename, output_dir + "/" + str(file))
- output_base = output_dir + "/" + filename_ss_ext if with_blocks is False else output_dir + "/" + filename_ss_ext + "_block"
+ shutil.copyfile(join(root, str(file)), filename)
+ output_base = output_dir + "/" + filename_ss_ext
+ else:
+ output_base = output_dir + "/" + filename_ss_ext + "_block"
output_jsonld = output_base + ".jsonld"
output_png = output_base + ".png"
- if parser_function != afni_to_bids_prov:
- jsonld_same_as_existing = parser_function(root + "/" + str(file), CONTEXT_URL,
+
+ if parser_function in [spm_to_bids_prov, fsl_to_bids_prov]:
+ clean_bids_paths(filename)
+ jsonld_same_as_existing = parser_function(filename, CONTEXT_URL,
output_file=output_jsonld, verbose=verbose)
else:
- jsonld_same_as_existing = parser_function(root + "/" + str(file), CONTEXT_URL,
+ jsonld_same_as_existing = parser_function(filename, CONTEXT_URL,
output_file=output_jsonld, verbose=verbose, with_blocks=with_blocks)
if not jsonld_same_as_existing: # do not generate the png if the jsonld has not evolved
diff --git a/requirements.txt b/requirements.txt
index 9c026818f..53fece3f0 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -9,4 +9,5 @@ pyyaml
rdflib
boutiques
beautifulsoup4
-deepdiff
\ No newline at end of file
+deepdiff
+rfc3986
\ No newline at end of file