Summary of what happened:
fMRIprep crashed with the following error as mentioned in the log. Was only running fmriprep for PerceptionTest sessions.
Command used:
#!usr/bin/env bash
subject=01
nprocs=16
maxmem=80
#specify the directories
rawdatadir="/DATA1/satwick22/Documents/fMRI/multimodal_concepts/generic_object_decoding"
derivsdir="/DATA1/satwick22/Documents/fMRI/multimodal_concepts/preprocessed/fmriprep_run01"
workdir="/DATA1/satwick22/Documents/fMRI/wdir/fmriprep"
license_dir="$(pwd)/"
#run the fmriprep docker container
docker run -ti --rm \
--memory="$maxmem""g" \
-v "$rawdatadir":/data:ro \
-v "$derivsdir":/out \
-v "$workdir":/work \
-v "$license_dir":/licensedir \
nipreps/fmriprep:latest \
--skip-bids-validation \
--participant-label "$subject" \
--fs-no-reconall \
--output-spaces MNI305 \
--bold2t1w-dof 9 \
--nprocs "$nprocs" --mem "$maxmem""GB" \
--fs-license-file /licensedir/license.txt \
--bids-filter-file /licensedir/filtercfg.json \
/data /out participant -w /work
Version:
23.2.2
Environment (Docker, Singularity / Apptainer, custom installation):
Docker
Data formatted according to a validatable standard? Please provide the output of the validator:
3: [ERR] NIfTI file exist with both '.nii' and '.nii.gz' extensions. (code: 74 - DUPLICATE_NIFTI_FILES)
./sub-01/ses-perceptionTest01/anat/sub-01_ses-perceptionTest01_inplaneT2.nii
./sub-01/ses-perceptionTest01/anat/sub-01_ses-perceptionTest01_inplaneT2.nii.gz
./sub-01/ses-perceptionTest01/func/sub-01_ses-perceptionTest01_task-perception_run-01_bold.nii
./sub-01/ses-perceptionTest01/func/sub-01_ses-perceptionTest01_task-perception_run-01_bold.nii.gz
./sub-01/ses-perceptionTest01/func/sub-01_ses-perceptionTest01_task-perception_run-02_bold.nii
./sub-01/ses-perceptionTest01/func/sub-01_ses-perceptionTest01_task-perception_run-02_bold.nii.gz
./sub-01/ses-perceptionTest01/func/sub-01_ses-perceptionTest01_task-perception_run-03_bold.nii
./sub-01/ses-perceptionTest01/func/sub-01_ses-perceptionTest01_task-perception_run-03_bold.nii.gz
./sub-01/ses-perceptionTest01/func/sub-01_ses-perceptionTest01_task-perception_run-04_bold.nii
./sub-01/ses-perceptionTest01/func/sub-01_ses-perceptionTest01_task-perception_run-04_bold.nii.gz
... and 124 more files having this issue (Use --verbose to see them all).
Please visit https://neurostars.org/search?q=DUPLICATE_NIFTI_FILES for existing conversations about this issue.
1: [WARN] Not all subjects contain the same files. Each subject should contain the same number of files with the same naming unless some files are known to be missing. (code: 38 - INCONSISTENT_SUBJECTS)
./sub-01/ses-anatomy/anat/sub-01_ses-anatomy_T1w.nii
Evidence: Subject: sub-01; Missing file: sub-01_ses-anatomy_T1w.nii
./sub-01/ses-imageryTest03/func/sub-01_ses-imageryTest03_task-imagery_run-05_bold.nii.gz
Evidence: Subject: sub-01; Missing file: sub-01_ses-imageryTest03_task-imagery_run-05_bold.nii.gz
./sub-01/ses-imageryTest03/func/sub-01_ses-imageryTest03_task-imagery_run-05_events.tsv
Evidence: Subject: sub-01; Missing file: sub-01_ses-imageryTest03_task-imagery_run-05_events.tsv
./sub-01/ses-imageryTest03/func/sub-01_ses-imageryTest03_task-imagery_run-06_bold.nii.gz
Evidence: Subject: sub-01; Missing file: sub-01_ses-imageryTest03_task-imagery_run-06_bold.nii.gz
./sub-01/ses-imageryTest03/func/sub-01_ses-imageryTest03_task-imagery_run-06_events.tsv
Evidence: Subject: sub-01; Missing file: sub-01_ses-imageryTest03_task-imagery_run-06_events.tsv
./sub-01/ses-imageryTest03/func/sub-01_ses-imageryTest03_task-imagery_run-07_bold.nii.gz
Evidence: Subject: sub-01; Missing file: sub-01_ses-imageryTest03_task-imagery_run-07_bold.nii.gz
./sub-01/ses-imageryTest03/func/sub-01_ses-imageryTest03_task-imagery_run-07_events.tsv
Evidence: Subject: sub-01; Missing file: sub-01_ses-imageryTest03_task-imagery_run-07_events.tsv
./sub-01/ses-imageryTest03/func/sub-01_ses-imageryTest03_task-imagery_run-08_bold.nii.gz
Evidence: Subject: sub-01; Missing file: sub-01_ses-imageryTest03_task-imagery_run-08_bold.nii.gz
./sub-01/ses-imageryTest03/func/sub-01_ses-imageryTest03_task-imagery_run-08_events.tsv
Evidence: Subject: sub-01; Missing file: sub-01_ses-imageryTest03_task-imagery_run-08_events.tsv
./sub-01/ses-imageryTest03/func/sub-01_ses-imageryTest03_task-imagery_run-09_bold.nii.gz
Evidence: Subject: sub-01; Missing file: sub-01_ses-imageryTest03_task-imagery_run-09_bold.nii.gz
... and 315 more files having this issue (Use --verbose to see them all).
Please visit https://neurostars.org/search?q=INCONSISTENT_SUBJECTS for existing conversations about this issue.
2: [WARN] Not all subjects/sessions/runs have the same scanning parameters. (code: 39 - INCONSISTENT_PARAMETERS)
./sub-05/ses-anatomy/anat/sub-05_ses-anatomy_T1w.nii.gz
Please visit https://neurostars.org/search?q=INCONSISTENT_PARAMETERS for existing conversations about this issue.
2: [WARN] Not all subjects/sessions/runs have the same scanning parameters. (code: 39 - INCONSISTENT_PARAMETERS)
./sub-05/ses-anatomy/anat/sub-05_ses-anatomy_T1w.nii.gz
Please visit https://neurostars.org/search?q=INCONSISTENT_PARAMETERS for existing conversations about this issue.
3: [WARN] Tabular file contains custom columns not described in a data dictionary (code: 82 - CUSTOM_COLUMN_WITHOUT_DESCRIPTION)
./sub-01/ses-imageryTest01/func/sub-01_ses-imageryTest01_task-imagery_run-01_events.tsv
Evidence: Columns: trial_no, event_type, category_id, evaluation not defined, please define in: /events.json, /task-imagery_events.json,/run-01_events.json,/task-imagery_run-01_events.json,/sub-01/sub-01_events.json,/sub-01/sub-01_task-imagery_events.json,/sub
-01/sub-01_run-01_events.json,/sub-01/sub-01_task-imagery_run-01_events.json,/sub-01/ses-imageryTest01/sub-01_ses-imageryTest01_events.json,/sub-01/ses-imageryTest01/sub-01_ses-imageryTest01_task-imagery_events.json,/sub-01/ses-imageryTest01/sub-01_ses-imageryTest01_run-01_events.jso
n,/sub-01/ses-imageryTest01/sub-01_ses-imageryTest01_task-imagery_run-01_events.json,/sub-01/ses-imageryTest01/func/sub-01_ses-imageryTest01_events.json,/sub-01/ses-imageryTest01/func/sub-01_ses-imageryTest01_task-imagery_events.json,/sub-01/ses-imageryTest01/func/sub-01_ses-imageryT
est01_run-01_events.json,/sub-01/ses-imageryTest01/func/sub-01_ses-imageryTest01_task-imagery_run-01_events.json
./sub-01/ses-imageryTest01/func/sub-01_ses-imageryTest01_task-imagery_run-02_events.tsv
Evidence: Columns: trial_no, event_type, category_id, evaluation not defined, please define in: /events.json, /task-imagery_events.json,/run-02_events.json,/task-imagery_run-02_events.json,/sub-01/sub-01_events.json,/sub-01/sub-01_task-imagery_events.json,/sub
-01/sub-01_run-02_events.json,/sub-01/sub-01_task-imagery_run-02_events.json,/sub-01/ses-imageryTest01/sub-01_ses-imageryTest01_events.json,/sub-01/ses-imageryTest01/sub-01_ses-imageryTest01_task-imagery_events.json,/sub-01/ses-imageryTest01/sub-01_ses-imageryTest01_run-02_events.jso
n,/sub-01/ses-imageryTest01/sub-01_ses-imageryTest01_task-imagery_run-02_events.json,/sub-01/ses-imageryTest01/func/sub-01_ses-imageryTest01_events.json,/sub-01/ses-imageryTest01/func/sub-01_ses-imageryTest01_task-imagery_events.json,/sub-01/ses-imageryTest01/func/sub-01_ses-imageryT
est01_run-02_events.json,/sub-01/ses-imageryTest01/func/sub-01_ses-imageryTest01_task-imagery_run-02_events.json
./sub-01/ses-imageryTest01/func/sub-01_ses-imageryTest01_task-imagery_run-03_events.tsv
Evidence: Columns: trial_no, event_type, category_id, evaluation not defined, please define in: /events.json, /task-imagery_events.json,/run-03_events.json,/task-imagery_run-03_events.json,/sub-01/sub-01_events.json,/sub-01/sub-01_task-imagery_events.json,/sub
-01/sub-01_run-03_events.json,/sub-01/sub-01_task-imagery_run-03_events.json,/sub-01/ses-imageryTest01/sub-01_ses-imageryTest01_events.json,/sub-01/ses-imageryTest01/sub-01_ses-imageryTest01_task-imagery_events.json,/sub-01/ses-imageryTest01/sub-01_ses-imageryTest01_run-03_events.jso
n,/sub-01/ses-imageryTest01/sub-01_ses-imageryTest01_task-imagery_run-03_events.json,/sub-01/ses-imageryTest01/func/sub-01_ses-imageryTest01_events.json,/sub-01/ses-imageryTest01/func/sub-01_ses-imageryTest01_task-imagery_events.json,/sub-01/ses-imageryTest01/func/sub-01_ses-imageryT
est01_run-03_events.json,/sub-01/ses-imageryTest01/func/sub-01_ses-imageryTest01_task-imagery_run-03_events.json
./sub-01/ses-imageryTest01/func/sub-01_ses-imageryTest01_task-imagery_run-04_events.tsv
Evidence: Columns: trial_no, event_type, category_id, evaluation not defined, please define in: /events.json, /task-imagery_events.json,/run-04_events.json,/task-imagery_run-04_events.json,/sub-01/sub-01_events.json,/sub-01/sub-01_task-imagery_events.json,/sub
-01/sub-01_run-04_events.json,/sub-01/sub-01_task-imagery_run-04_events.json,/sub-01/ses-imageryTest01/sub-01_ses-imageryTest01_events.json,/sub-01/ses-imageryTest01/sub-01_ses-imageryTest01_task-imagery_events.json,/sub-01/ses-imageryTest01/sub-01_ses-imageryTest01_run-04_events.jso
n,/sub-01/ses-imageryTest01/sub-01_ses-imageryTest01_task-imagery_run-04_events.json,/sub-01/ses-imageryTest01/func/sub-01_ses-imageryTest01_events.json,/sub-01/ses-imageryTest01/func/sub-01_ses-imageryTest01_task-imagery_events.json,/sub-01/ses-imageryTest01/func/sub-01_ses-imageryT
est01_run-04_events.json,/sub-01/ses-imageryTest01/func/sub-01_ses-imageryTest01_task-imagery_run-04_events.json
./sub-01/ses-imageryTest01/func/sub-01_ses-imageryTest01_task-imagery_run-05_events.tsv
Evidence: Columns: trial_no, event_type, category_id, evaluation not defined, please define in: /events.json, /task-imagery_events.json,/run-05_events.json,/task-imagery_run-05_events.json,/sub-01/sub-01_events.json,/sub-01/sub-01_task-imagery_events.json,/sub
-01/sub-01_run-05_events.json,/sub-01/sub-01_task-imagery_run-05_events.json,/sub-01/ses-imageryTest01/sub-01_ses-imageryTest01_events.json,/sub-01/ses-imageryTest01/sub-01_ses-imageryTest01_task-imagery_events.json,/sub-01/ses-imageryTest01/sub-01_ses-imageryTest01_run-05_events.jso
n,/sub-01/ses-imageryTest01/sub-01_ses-imageryTest01_task-imagery_run-05_events.json,/sub-01/ses-imageryTest01/func/sub-01_ses-imageryTest01_events.json,/sub-01/ses-imageryTest01/func/sub-01_ses-imageryTest01_task-imagery_events.json,/sub-01/ses-imageryTest01/func/sub-01_ses-imageryT
est01_run-05_events.json,/sub-01/ses-imageryTest01/func/sub-01_ses-imageryTest01_task-imagery_run-05_events.json
./sub-01/ses-imageryTest01/func/sub-01_ses-imageryTest01_task-imagery_run-06_events.tsv
Evidence: Columns: trial_no, event_type, category_id, evaluation not defined, please define in: /events.json, /task-imagery_events.json,/run-06_events.json,/task-imagery_run-06_events.json,/sub-01/sub-01_events.json,/sub-01/sub-01_task-imagery_events.json,/sub
-01/sub-01_run-06_events.json,/sub-01/sub-01_task-imagery_run-06_events.json,/sub-01/ses-imageryTest01/sub-01_ses-imageryTest01_events.json,/sub-01/ses-imageryTest01/sub-01_ses-imageryTest01_task-imagery_events.json,/sub-01/ses-imageryTest01/sub-01_ses-imageryTest01_run-06_events.jso
n,/sub-01/ses-imageryTest01/sub-01_ses-imageryTest01_task-imagery_run-06_events.json,/sub-01/ses-imageryTest01/func/sub-01_ses-imageryTest01_events.json,/sub-01/ses-imageryTest01/func/sub-01_ses-imageryTest01_task-imagery_events.json,/sub-01/ses-imageryTest01/func/sub-01_ses-imageryT
est01_run-06_events.json,/sub-01/ses-imageryTest01/func/sub-01_ses-imageryTest01_task-imagery_run-06_events.json
./sub-01/ses-imageryTest01/func/sub-01_ses-imageryTest01_task-imagery_run-07_events.tsv
Evidence: Columns: trial_no, event_type, category_id, evaluation not defined, please define in: /events.json, /task-imagery_events.json,/run-07_events.json,/task-imagery_run-07_events.json,/sub-01/sub-01_events.json,/sub-01/sub-01_task-imagery_events.json,/sub
-01/sub-01_run-07_events.json,/sub-01/sub-01_task-imagery_run-07_events.json,/sub-01/ses-imageryTest01/sub-01_ses-imageryTest01_events.json,/sub-01/ses-imageryTest01/sub-01_ses-imageryTest01_task-imagery_events.json,/sub-01/ses-imageryTest01/sub-01_ses-imageryTest01_run-07_events.jso
n,/sub-01/ses-imageryTest01/sub-01_ses-imageryTest01_task-imagery_run-07_events.json,/sub-01/ses-imageryTest01/func/sub-01_ses-imageryTest01_events.json,/sub-01/ses-imageryTest01/func/sub-01_ses-imageryTest01_task-imagery_events.json,/sub-01/ses-imageryTest01/func/sub-01_ses-imageryT
est01_run-07_events.json,/sub-01/ses-imageryTest01/func/sub-01_ses-imageryTest01_task-imagery_run-07_events.json
./sub-01/ses-imageryTest01/func/sub-01_ses-imageryTest01_task-imagery_run-08_events.tsv
Evidence: Columns: trial_no, event_type, category_id, evaluation not defined, please define in: /events.json, /task-imagery_events.json,/run-08_events.json,/task-imagery_run-08_events.json,/sub-01/sub-01_events.json,/sub-01/sub-01_task-imagery_events.json,/sub
-01/sub-01_run-08_events.json,/sub-01/sub-01_task-imagery_run-08_events.json,/sub-01/ses-imageryTest01/sub-01_ses-imageryTest01_events.json,/sub-01/ses-imageryTest01/sub-01_ses-imageryTest01_task-imagery_events.json,/sub-01/ses-imageryTest01/sub-01_ses-imageryTest01_run-08_events.jso
n,/sub-01/ses-imageryTest01/sub-01_ses-imageryTest01_task-imagery_run-08_events.json,/sub-01/ses-imageryTest01/func/sub-01_ses-imageryTest01_events.json,/sub-01/ses-imageryTest01/func/sub-01_ses-imageryTest01_task-imagery_events.json,/sub-01/ses-imageryTest01/func/sub-01_ses-imageryT
est01_run-08_events.json,/sub-01/ses-imageryTest01/func/sub-01_ses-imageryTest01_task-imagery_run-08_events.json
./sub-01/ses-imageryTest02/func/sub-01_ses-imageryTest02_task-imagery_run-01_events.tsv
Evidence: Columns: trial_no, event_type, category_id, evaluation not defined, please define in: /events.json, /task-imagery_events.json,/run-01_events.json,/task-imagery_run-01_events.json,/sub-01/sub-01_events.json,/sub-01/sub-01_task-imagery_events.json,/sub
-01/sub-01_run-01_events.json,/sub-01/sub-01_task-imagery_run-01_events.json,/sub-01/ses-imageryTest02/sub-01_ses-imageryTest02_events.json,/sub-01/ses-imageryTest02/sub-01_ses-imageryTest02_task-imagery_events.json,/sub-01/ses-imageryTest02/sub-01_ses-imageryTest02_run-01_events.jso
n,/sub-01/ses-imageryTest02/sub-01_ses-imageryTest02_task-imagery_run-01_events.json,/sub-01/ses-imageryTest02/func/sub-01_ses-imageryTest02_events.json,/sub-01/ses-imageryTest02/func/sub-01_ses-imageryTest02_task-imagery_events.json,/sub-01/ses-imageryTest02/func/sub-01_ses-imageryT
est02_run-01_events.json,/sub-01/ses-imageryTest02/func/sub-01_ses-imageryTest02_task-imagery_run-01_events.json
./sub-01/ses-imageryTest02/func/sub-01_ses-imageryTest02_task-imagery_run-02_events.tsv
Evidence: Columns: trial_no, event_type, category_id, evaluation not defined, please define in: /events.json, /task-imagery_events.json,/run-02_events.json,/task-imagery_run-02_events.json,/sub-01/sub-01_events.json,/sub-01/sub-01_task-imagery_events.json,/sub
-01/sub-01_run-02_events.json,/sub-01/sub-01_task-imagery_run-02_events.json,/sub-01/ses-imageryTest02/sub-01_ses-imageryTest02_events.json,/sub-01/ses-imageryTest02/sub-01_ses-imageryTest02_task-imagery_events.json,/sub-01/ses-imageryTest02/sub-01_ses-imageryTest02_run-02_events.jso
n,/sub-01/ses-imageryTest02/sub-01_ses-imageryTest02_task-imagery_run-02_events.json,/sub-01/ses-imageryTest02/func/sub-01_ses-imageryTest02_events.json,/sub-01/ses-imageryTest02/func/sub-01_ses-imageryTest02_task-imagery_events.json,/sub-01/ses-imageryTest02/func/sub-01_ses-imageryT
est02_run-02_events.json,/sub-01/ses-imageryTest02/func/sub-01_ses-imageryTest02_task-imagery_run-02_events.json
... and 385 more files having this issue (Use --verbose to see them all).
Please visit https://neurostars.org/search?q=CUSTOM_COLUMN_WITHOUT_DESCRIPTION for existing conversations about this issue.
Please visit https://neurostars.org/search?q=CUSTOM_COLUMN_WITHOUT_DESCRIPTION for existing conversations about this issue.
4: [WARN] Not all subjects contain the same sessions. (code: 97 - MISSING_SESSION)
./sub-01/ses-imageryTest04
Evidence: Subject: sub-01; Missing session: ses-imageryTest04
./sub-01/ses-imageryTest05
Evidence: Subject: sub-01; Missing session: ses-imageryTest05
./sub-01/ses-perceptionTest05
Evidence: Subject: sub-01; Missing session: ses-perceptionTest05
./sub-01/ses-perceptionTest06
Evidence: Subject: sub-01; Missing session: ses-perceptionTest06
./sub-01/ses-perceptionTraining04
Evidence: Subject: sub-01; Missing session: ses-perceptionTraining04
./sub-01/ses-perceptionTraining05
Evidence: Subject: sub-01; Missing session: ses-perceptionTraining05
./sub-02/ses-imageryTest04
Evidence: Subject: sub-02; Missing session: ses-imageryTest04
./sub-02/ses-imageryTest05
Evidence: Subject: sub-02; Missing session: ses-imageryTest05
./sub-02/ses-perceptionTest05
Evidence: Subject: sub-02; Missing session: ses-perceptionTest05
./sub-02/ses-perceptionTest06
Evidence: Subject: sub-02; Missing session: ses-perceptionTest06
... and 13 more files having this issue (Use --verbose to see them all).
Relevant log outputs:
Traceback:
Traceback (most recent call last):
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 397, in run
runtime = self._run_interface(runtime)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/interfaces/resampling.py", line 103, in _run_interface
resampled = resample_image(
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/interfaces/resampling.py", line 567, in resample_image
mapped_coordinates = ref2vox.map(coordinates)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nitransforms/manip.py", line 139, in map
x = xfm.map(x, inverse=inverse)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nitransforms/nonlinear.py", line 166, in map
return self._field[indexes]
IndexError: index 156 is out of bounds for axis 0 with size 156
240507-17:33:50,167 nipype.workflow INFO:
[Node] Finished "resample", elapsed time 7.044079s.
240507-17:33:52,845 nipype.workflow ERROR:
could not run node: fmriprep_23_2_wf.sub_01_wf.bold_ses_perceptionTest01_task_perception_run_01_wf.bold_std_wf.resample.a0
240507-17:33:52,851 nipype.workflow ERROR:
could not run node: fmriprep_23_2_wf.sub_01_wf.bold_ses_perceptionTest01_task_perception_run_02_wf.bold_std_wf.resample.a0
240507-17:33:52,856 nipype.workflow ERROR:
could not run node: fmriprep_23_2_wf.sub_01_wf.bold_ses_perceptionTest01_task_perception_run_03_wf.bold_std_wf.resample.a0
240507-17:33:52,862 nipype.workflow ERROR:
could not run node: fmriprep_23_2_wf.sub_01_wf.bold_ses_perceptionTest01_task_perception_run_04_wf.bold_std_wf.resample.a0
240507-17:33:52,867 nipype.workflow ERROR:
could not run node: fmriprep_23_2_wf.sub_01_wf.bold_ses_perceptionTest01_task_perception_run_05_wf.bold_std_wf.resample.a0
240507-17:33:52,873 nipype.workflow ERROR:
could not run node: fmriprep_23_2_wf.sub_01_wf.bold_ses_perceptionTest01_task_perception_run_06_wf.bold_std_wf.resample.a0
240507-17:33:52,880 nipype.workflow ERROR:
could not run node: fmriprep_23_2_wf.sub_01_wf.bold_ses_perceptionTest01_task_perception_run_07_wf.bold_std_wf.resample.a0
240507-17:33:52,886 nipype.workflow ERROR:
could not run node: fmriprep_23_2_wf.sub_01_wf.bold_ses_perceptionTest01_task_perception_run_08_wf.bold_std_wf.resample.a0
240507-17:33:52,893 nipype.workflow ERROR:
could not run node: fmriprep_23_2_wf.sub_01_wf.bold_ses_perceptionTest01_task_perception_run_09_wf.bold_std_wf.resample.a0
240507-17:33:52,900 nipype.workflow ERROR:
could not run node: fmriprep_23_2_wf.sub_01_wf.bold_ses_perceptionTest01_task_perception_run_10_wf.bold_std_wf.resample.a0
240507-17:33:53,131 nipype.workflow CRITICAL:
fMRIPrep failed: 10 raised. Re-raising first.
240507-17:33:59,558 cli ERROR:
Preprocessing did not finish successfully. Errors occurred while processing data from participants: 01 (10). Check the HTML reports for details.