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C-PAC v1.8.1-dev @ 53ab684 ― brainlife #21

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shnizzedy opened this issue Sep 14, 2021 · 0 comments
Open

C-PAC v1.8.1-dev @ 53ab684 ― brainlife #21

shnizzedy opened this issue Sep 14, 2021 · 0 comments
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debug Pipeline run failed due to an error or crash. help wanted Extra attention is needed log A summary of a run attempt

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@shnizzedy
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Description

FCP-INDI/C-PAC#1531 on Brainlife

Version

v1.8.1-dev @ FCP-INDI/C-PAC@53ab684

Container

fix_multiple_custom_regressors

System

brainlife.io

Data Size

No response

Results

https://brainlife.io/project/5f299e1fbeafe973f362a972/process/613fa01c2fe7651a3dd7a27d

crash-20210913-200944-user-func_motion_correct_mcflirt_97.a0-e2636568-1252-41fa-ac10-84fbf70d9b67.txt:

Node: cpac_sub-A00010893_ses-DS2.func_motion_correct_mcflirt_97
Working directory: /output/working/cpac_sub-A00010893_ses-DS2/_scan_rest/func_motion_correct_mcflirt_97

Node inputs:

args = <undefined>
bins = <undefined>
cost = <undefined>
dof = <undefined>
environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
in_file = /output/working/cpac_sub-A00010893_ses-DS2/_scan_rest/func_reorient_93/sub-A00010893_ses-DS2_task-rest_bold_calc_tshift_resample.nii.gz
init = <undefined>
interpolation = <undefined>
mean_vol = <undefined>
out_file = <undefined>
output_type = NIFTI_GZ
ref_file = /output/working/cpac_sub-A00010893_ses-DS2/_scan_rest/func_get_fmriprep_ref_81/ref_bold.nii.gz
ref_vol = <undefined>
rotation = <undefined>
save_mats = True
save_plots = True
save_rms = True
scaling = <undefined>
smooth = <undefined>
stages = <undefined>
stats_imgs = <undefined>
use_contour = <undefined>
use_gradient = <undefined>

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/linear.py", line 46, in run
    node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
    result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
    return self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 764, in _run_command
    dirs2keep=dirs2keep,
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/utils.py", line 1527, in clean_working_directory
    os.remove(f)
FileNotFoundError: [Errno 2] No such file or directory: '/output/working/cpac_sub-A00010893_ses-DS2/_scan_rest/func_motion_correct_mcflirt_97/sub-A00010893_ses-DS2_task-rest_bold_calc_tshift_resample_mcf.nii.gz.mat/MAT_0735'


When creating this crashfile, the results file corresponding
to the node could not be found.

ls /output/working/cpac_sub-A00010893_ses-DS2/_scan_rest/func_motion_correct_mcflirt_97/sub-A00010893_ses-DS2_task-rest_bold_calc_tshift_resample_mcf.nii.gz.mat:

MAT_0000  MAT_0089  MAT_0179  MAT_0366  MAT_0440  MAT_0542  MAT_0670  MAT_0788
MAT_0006  MAT_0091  MAT_0194  MAT_0381  MAT_0445  MAT_0547  MAT_0671  MAT_0797
MAT_0018  MAT_0095  MAT_0202  MAT_0382  MAT_0450  MAT_0550  MAT_0687  MAT_0799
MAT_0025  MAT_0097  MAT_0203  MAT_0383  MAT_0453  MAT_0557  MAT_0688  MAT_0800
MAT_0026  MAT_0098  MAT_0205  MAT_0385  MAT_0455  MAT_0570  MAT_0700  MAT_0811
MAT_0028  MAT_0102  MAT_0206  MAT_0390  MAT_0476  MAT_0578  MAT_0704  MAT_0826
MAT_0038  MAT_0103  MAT_0213  MAT_0394  MAT_0486  MAT_0585  MAT_0711  MAT_0836
MAT_0041  MAT_0113  MAT_0218  MAT_0399  MAT_0487  MAT_0591  MAT_0718  MAT_0840
MAT_0046  MAT_0118  MAT_0222  MAT_0400  MAT_0492  MAT_0598  MAT_0723  MAT_0843
MAT_0049  MAT_0120  MAT_0223  MAT_0401  MAT_0493  MAT_0600  MAT_0725  MAT_0850
MAT_0054  MAT_0121  MAT_0229  MAT_0404  MAT_0497  MAT_0605  MAT_0727  MAT_0855
MAT_0055  MAT_0122  MAT_0231  MAT_0405  MAT_0500  MAT_0609  MAT_0730  MAT_0856
MAT_0057  MAT_0133  MAT_0234  MAT_0408  MAT_0503  MAT_0618  MAT_0748  MAT_0860
MAT_0061  MAT_0142  MAT_0249  MAT_0415  MAT_0510  MAT_0630  MAT_0759  MAT_0871
MAT_0065  MAT_0147  MAT_0257  MAT_0418  MAT_0511  MAT_0631  MAT_0761  MAT_0888
MAT_0071  MAT_0149  MAT_0258  MAT_0423  MAT_0512  MAT_0632  MAT_0763  MAT_0894
MAT_0072  MAT_0154  MAT_0261  MAT_0424  MAT_0513  MAT_0635  MAT_0768  MAT_0895
MAT_0078  MAT_0159  MAT_0301  MAT_0425  MAT_0525  MAT_0643  MAT_0783
MAT_0079  MAT_0160  MAT_0322  MAT_0431  MAT_0540  MAT_0659  MAT_0785

Run Command:

main:

#!/bin/bash
#PBS -l nodes=1:ppn=8,walltime=48:00:00
#PBS -l vmem=30gb
#PBS -N cpac

# parse config.json for input parameters
preconfig=$(jq -r .preconfig config.json)
if [ "$preconfig" == "" ] || [ "$preconfig" == "null" ] || [ "$preconfig" == "default" ]
    then
        preconfig=""
    else
        preconfig="--preconfig $preconfig"
fi

# get latest image if we don't already have one
if [ -f cpac-singularity-image.simg ]
  then
    echo "using existing C-PAC Singularity image"
  else
    echo "getting C-PAC Singularity image"
    time curl -LOJ https://9514-4733263-gh.circle-artifacts.com/0/cpac-singularity-image.simg
fi

# convert brainlife structure to BIDS
if [ ! -d bids ]
  then
    echo "restructuring data"
    bl2bids
fi

set -x
set -e

# run C-PAC
echo "running C-PAC"
mkdir -p output tmp

time singularity run -e -B $PWD/bids:/bids -B $PWD/output:/output -B $PWD/tmp:/tmp cpac-singularity-image.simg /bids /output participant $preconfig --save_working_dir

with config.json:

{
    "t1": "../613fa01c2fe7651348d7a289/59a5f2a1c1e7111a78d11a54/t1.nii.gz",
    "bold": "../613fa01c2fe7651348d7a289/59cc5342f45e7344b8c8aff0/bold.nii.gz",
    "events": "../613fa01c2fe7651348d7a289/59cc5342f45e7344b8c8aff0/events.tsv",
    "events_json": "../613fa01c2fe7651348d7a289/59cc5342f45e7344b8c8aff0/events.json",
    "sbref": "../613fa01c2fe7651348d7a289/59cc5342f45e7344b8c8aff0/sbref.nii.gz",
    "sbref_json": "../613fa01c2fe7651348d7a289/59cc5342f45e7344b8c8aff0/sbref.json",
    "physio": "../613fa01c2fe7651348d7a289/59cc5342f45e7344b8c8aff0/physio.tsv.gz",
    "physio_json": "../613fa01c2fe7651348d7a289/59cc5342f45e7344b8c8aff0/physio.json",
    "preconfig": "fmriprep-options",
    "_app": "5f3593e84615e04651bf9364",
    "_tid": 2,
    "_inputs": [
        {
            "id": "t1",
            "datatype": "58c33bcee13a50849b25879a",
            "meta": {
                "subject": "A00010893",
                "session": "DS2"
            },
            "tags": [
                "DS2"
            ],
            "datatype_tags": [],
            "subdir": "59a5f2a1c1e7111a78d11a54",
            "dataset_id": "59a5f2a1c1e7111a78d11a54",
            "project": "59a57af4b5e93a0023001416",
            "task_id": "613fa01c2fe7651348d7a289",
            "keys": [
                "t1"
            ]
        },
        {
            "id": "func",
            "datatype": "59b685a08e5d38b0b331ddc5",
            "meta": {
                "subject": "A00010893",
                "session": "DS2",
                "task": "rest",
                "acquisition": "645"
            },
            "tags": [
                "DS2",
                "rest",
                "645"
            ],
            "datatype_tags": [
                "rest"
            ],
            "subdir": "59cc5342f45e7344b8c8aff0",
            "dataset_id": "59cc5342f45e7344b8c8aff0",
            "project": "59a57af4b5e93a0023001416",
            "task_id": "613fa01c2fe7651348d7a289",
            "keys": [
                "bold",
                "events",
                "events_json",
                "sbref",
                "sbref_json",
                "physio",
                "physio_json"
            ]
        }
    ],
    "_outputs": [
        {
            "id": "output",
            "datatype": "59c3eae633fc1cf9ead71679",
            "desc": "C-PAC",
            "meta": {
                "subject": "A00010893",
                "session": "DS2"
            },
            "subdir": "output",
            "datatype_tags": [
                "c-pac"
            ]
        }
    ]
}

Pipeline Config

https://github.com/FCP-INDI/C-PAC/blob/53ab684fd21ddc2644b55d3a0c06a2d31db97f24/CPAC/resources/configs/pipeline_config_fmriprep-options.yml

cpac_pipeline_config_2021-09-13T19-05-33Z.yml

Data Config

cpac_data_config_2021-09-13T19-05-33Z.yml

Default Pipeline Diff

cpac_pipeline_config_2021-09-13T19-05-33Z_min.yml

Screenshots of brain extraction and registration wireframe overlays from QC pages

No response

Node timing information

No response

Extracted time series 1D and nuisance regressors 1D correlations against previous version or some benchmark

No response
@shnizzedy shnizzedy added log A summary of a run attempt debug Pipeline run failed due to an error or crash. help wanted Extra attention is needed labels Sep 14, 2021
@shnizzedy shnizzedy mentioned this issue Sep 15, 2021
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