Dev rr1 (#2)

* updated CLI for step1

* updated step2 CLI

* starting traditional approach

* point-wise glm done

* added plotting

* updated documentation

* working on figures

* added shading to plot_diff

* added tukey stats to memory plot

* restructuring

* renaming files

* reorganizing

* updated notes

* Update README.md

* Update README.md

* added GAM for MD

* added print out for memory stats, session

* updated notes, decreased shade opacity

* decreased opacity

README.md

@@ -1,13 +1,32 @@
 # emu_AFQ
 
-Scripts are named in their respective order.
+Repo containing code, documents, and data used in the manuscript "General Additive Models Address Statistical Issues in Diffusion MRI: An Example with Clinically Anxious Adolescents".
 
-afq_step1 - deals with pulling data and getting organized for pyAFQ.
+# Code
 
-afq_step2 - run pyAFQ CLI on data.
+Various scripts for organizing DWI data, running pyAFQ, and conducting statistical analyses. Scripts are named (a) for their respective order in the workflow, and (b) with a description of their function.
 
-afq_step3 - model tract FA values with a GAM, conduct tests.
+- step1_submit.sh : Set up, copy data, and wrap step1_setup.py
+- step1_setup.py : Configure config.toml for pyAFQ CLI
+- step2_submit.sh : Wrap step2_CLI.sh
+- step2_CLI.sh : Run AFQ via pyAFQ on Slurm scheduled resources
+- step3_manuscript_stats.R : Code used to conduct statistical analyses reported in the manuscript. Unused analyses, portions remain for potential future analyses and transparency.
+- step3_reduced_stats.R : Illustrative code to aid in the implementation of using a GAM method with AFQ output
+- step4_quick_stats.R : Quick queries for the manuscript
+- step5_reviewer_stats.R : Code written to address reviewer concerns, in addition to updates to step3_manuscript_stats.R and step4_quick_stats.R.
 
-afq_step4 - make quick figures, stats for manuscript.
 
-Other files: config.toml is the file referenced by afq_step2, and tract_profiles.csv is the output of afq_step2.
+# Data
+
+Contains data used in the manuscript.
+
+- tract_profiles.csv : pyAFQ output
+- Master_dataframe_G3.csv : pyAFQ output with demographic information added for groupings according to PARS-6 tertiles
+
+
+# Docs
+
+Documents used to conduct analyses or to aid in replication.
+
+- config.toml : Configuration file used with pyAFQ
+- R_session_info.txt : A complete description of all packages and versions used in the analyses

code/config.toml

@@ -0,0 +1,85 @@
+[BIDS]
+bids_path = "/scratch/madlab/emu_AFQ"
+bids_filters = "{'suffix': 'dwi'}"
+dmriprep = "all"
+custom_tractography_bids_filters = ""
+
+[REGISTRATION]
+b0_threshold = 50
+patch2self = false
+robust_tensor_fitting = false
+min_bval = ""
+max_bval = ""
+reg_template = "mni_T1"
+reg_subject = "power_map"
+brain_mask = "B0Mask({})"
+mapping = "SynMap(True, {}, {})"
+
+[PROFILE]
+profile_weights = "gauss"
+
+[BUNDLES]
+bundle_info = ""
+scalars = [ "dti_fa", "dti_md",]
+
+[COMPUTE]
+dask_it = false
+
+[VIZ]
+virtual_frame_buffer = false
+viz_backend = "plotly_no_gif"
+
+[TRACTOGRAPHY]
+directions = "prob"
+max_angle = 30.0
+sphere = ""
+seed_mask = ""
+seed_threshold = 0
+n_seeds = 1
+random_seeds = false
+rng_seed = ""
+stop_mask = ""
+stop_threshold = 0
+step_size = 0.5
+min_length = 10
+max_length = 1000
+odf_model = "DTI"
+tracker = "local"
+
+[SEGMENTATION]
+nb_points = false
+nb_streamlines = false
+seg_algo = "AFQ"
+reg_algo = ""
+clip_edges = false
+parallel_segmentation = "{'n_jobs': -1, 'engine': 'joblib', 'backend': 'loky'}"
+progressive = true
+greater_than = 50
+rm_small_clusters = 50
+model_clust_thr = 1.25
+reduction_thr = 25
+refine = false
+pruning_thr = 12
+b0_threshold = 50
+prob_threshold = 0
+dist_to_waypoint = ""
+rng = ""
+return_idx = false
+presegment_bundle_dict = ""
+presegment_kawrgs = "{}"
+filter_by_endpoints = true
+endpoint_info = ""
+dist_to_atlas = 4
+save_intermediates = ""
+
+[CLEANING]
+n_points = 100
+clean_rounds = 5
+distance_threshold = 5
+length_threshold = 4
+min_sl = 20
+stat = "mean"
+return_idx = false
+
+[files]
+dmriprep_folder = "/scratch/madlab/emu_AFQ/derivatives/dwi_preproc"

afq_step1_setup.py → code/step1_setup.py

@@ -1,55 +1,74 @@
-"""Setup config.toml file for AFQ
+"""Setup config.toml file for AFQ.
 
 This script will edit the BIDs file dataset_description.json
 with values needed by AFQ. It will then edit the AFQ
 configuration file config.toml with project-specific values.
 
-It is wrapped by afq_step1_submit.sh.
+It is wrapped by step1_submit.sh.
+
+Examples
+--------
+python step1_setup.py \\
+    -c config.toml \\
+    -b /scratch/madlab/emu_AFQ \\
+    -d /scratch/madlab/emu_AFQ/derivatives/dwi_preproc \\
+    -j /scratch/madlab/emu_AFQ/dataset_description.json \\
+    -p dwi_preproc
 """
 
 import os
+import sys
 import toml
 import json
-from argparse import ArgumentParser
+import textwrap
+from argparse import ArgumentParser, RawTextHelpFormatter
 
 
 def get_args():
-    parser = ArgumentParser("Receive bash args from afq_step1_submit.sh wrapper")
+    """Get and parse arguments."""
+    parser = ArgumentParser(description=__doc__, formatter_class=RawTextHelpFormatter)
     parser.add_argument(
-        "-c",
-        "--config-file",
-        help="/path/to/afq/config.toml",
+        "-p",
+        "--preproc-dwi",
         type=str,
-        required=True,
+        default="dwi_preproc",
+        help=textwrap.dedent(
+            """\
+            Description str for pre-processed DWI
+            (default : %(default)s)
+            """
+        ),
     )
-    parser.add_argument(
+    required_args = parser.add_argument_group("Required Arguments")
+    required_args.add_argument(
+        "-c", "--config-file", help="/path/to/afq/config.toml", type=str, required=True,
+    )
+    required_args.add_argument(
         "-b",
         "--bids-directory",
         help="/path/to/bids/project_directory",
         type=str,
         required=True,
     )
-    parser.add_argument(
+    required_args.add_argument(
         "-d",
         "--deriv-directory",
         help="/path/to/bids/project_directory/derivatives/pre-processed_dwi",
         type=str,
         required=True,
     )
-    parser.add_argument(
+    required_args.add_argument(
         "-j",
         "--json-file",
         help="/path/to/bids/project_directory/dataset_description.json",
         type=str,
         required=True,
     )
-    parser.add_argument(
-        "-p",
-        "--preproc-dwi",
-        help="Description str for pre-processed DWI",
-        type=str,
-        default="dwi_preproc",
-    )
+
+    if len(sys.argv) == 1:
+        parser.print_help(sys.stderr)
+        sys.exit(1)
+
     return parser