Slice-timing correction failure in fMRIPrep on 7T data

Software Support
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1

Summary of what happened:

Slice-timing correction failure in fMRIPrep on 7T data. Appears to be an error with the 3dTshift command.

Command used (and if a helper script was used, a link to the helper script or the command generated):

/opt/conda/bin/fmriprep /data /out participant --participant-label sub-pilot02 --mem-mb 50000

Version:

  • fMRIPrep version: 23.0.0

Environment (Docker, Singularity, custom installation):

Docker

Data formatted according to a validatable standard? Please provide the output of the validator:

Yes.

File Path: You have to define 'TaskName' for this file.

	Type:		Error
	File:		sub-pilot02_ses-Pilot002_task-olfunc_run-01_bold.nii.gz
	Location:		BIDS_OlfUnc/sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_run-01_bold.nii.gz
	Reason:		You have to define 'TaskName' for this file. It can be included one of the following locations: /task-olfunc_bold.json, /task-olfunc_run-01_bold.json, /sub-pilot02/sub-pilot02_task-olfunc_bold.json, /sub-pilot02/sub-pilot02_task-olfunc_run-01_bold.json, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_task-olfunc_bold.json, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_task-olfunc_run-01_bold.json, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_bold.json, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_run-01_bold.json
	Type:		Error
	File:		sub-pilot02_ses-Pilot002_task-olfunc_run-02_bold.nii.gz
	Location:		BIDS_OlfUnc/sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_run-02_bold.nii.gz
	Reason:		You have to define 'TaskName' for this file. It can be included one of the following locations: /task-olfunc_bold.json, /task-olfunc_run-02_bold.json, /sub-pilot02/sub-pilot02_task-olfunc_bold.json, /sub-pilot02/sub-pilot02_task-olfunc_run-02_bold.json, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_task-olfunc_bold.json, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_task-olfunc_run-02_bold.json, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_bold.json, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_run-02_bold.json
	Type:		Error
	File:		sub-pilot02_ses-Pilot002_task-olfunc_run-03_bold.nii.gz
	Location:		BIDS_OlfUnc/sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_run-03_bold.nii.gz
	Reason:		You have to define 'TaskName' for this file. It can be included one of the following locations: /task-olfunc_bold.json, /task-olfunc_run-03_bold.json, /sub-pilot02/sub-pilot02_task-olfunc_bold.json, /sub-pilot02/sub-pilot02_task-olfunc_run-03_bold.json, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_task-olfunc_bold.json, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_task-olfunc_run-03_bold.json, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_bold.json, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_run-03_bold.json
	Type:		Error
	File:		sub-pilot02_ses-Pilot002_task-olfunc_run-04_bold.nii.gz
	Location:		BIDS_OlfUnc/sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_run-04_bold.nii.gz
	Reason:		You have to define 'TaskName' for this file. It can be included one of the following locations: /task-olfunc_bold.json, /task-olfunc_run-04_bold.json, /sub-pilot02/sub-pilot02_task-olfunc_bold.json, /sub-pilot02/sub-pilot02_task-olfunc_run-04_bold.json, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_task-olfunc_bold.json, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_task-olfunc_run-04_bold.json, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_bold.json, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_run-04_bold.json
	Type:		Error
	File:		sub-pilot02_ses-Pilot002_task-olfunc_run-05_bold.nii.gz
	Location:		BIDS_OlfUnc/sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_run-05_bold.nii.gz
	Reason:		You have to define 'TaskName' for this file. It can be included one of the following locations: /task-olfunc_bold.json, /task-olfunc_run-05_bold.json, /sub-pilot02/sub-pilot02_task-olfunc_bold.json, /sub-pilot02/sub-pilot02_task-olfunc_run-05_bold.json, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_task-olfunc_bold.json, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_task-olfunc_run-05_bold.json, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_bold.json, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_run-05_bold.json
	Type:		Error
	File:		sub-pilot02_ses-Pilot002_task-olfunc_run-06_bold.nii.gz
	Location:		BIDS_OlfUnc/sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_run-06_bold.nii.gz
	Reason:		You have to define 'TaskName' for this file. It can be included one of the following locations: /task-olfunc_bold.json, /task-olfunc_run-06_bold.json, /sub-pilot02/sub-pilot02_task-olfunc_bold.json, /sub-pilot02/sub-pilot02_task-olfunc_run-06_bold.json, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_task-olfunc_bold.json, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_task-olfunc_run-06_bold.json, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_bold.json, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_run-06_bold.json
	Type:		Error
	File:		sub-pilot02_ses-Pilot002_task-olfunc_run-07_bold.nii.gz
	Location:		BIDS_OlfUnc/sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_run-07_bold.nii.gz
	Reason:		You have to define 'TaskName' for this file. It can be included one of the following locations: /task-olfunc_bold.json, /task-olfunc_run-07_bold.json, /sub-pilot02/sub-pilot02_task-olfunc_bold.json, /sub-pilot02/sub-pilot02_task-olfunc_run-07_bold.json, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_task-olfunc_bold.json, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_task-olfunc_run-07_bold.json, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_bold.json, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_run-07_bold.json
	Type:		Error
	File:		sub-pilot02_ses-Pilot002_task-olfunc_run-08_bold.nii.gz
	Location:		BIDS_OlfUnc/sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_run-08_bold.nii.gz
	Reason:		You have to define 'TaskName' for this file. It can be included one of the following locations: /task-olfunc_bold.json, /task-olfunc_run-08_bold.json, /sub-pilot02/sub-pilot02_task-olfunc_bold.json, /sub-pilot02/sub-pilot02_task-olfunc_run-08_bold.json, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_task-olfunc_bold.json, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_task-olfunc_run-08_bold.json, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_bold.json, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_run-08_bold.json

======================================================


File Path: Task scans should have a corresponding events.tsv file. If this is a resting state scan you can ignore this warning or rename the task to include the word "rest".

	Type:		Warning
	File:		sub-pilot02_ses-Pilot002_task-olfunc_run-01_bold.nii.gz
	Location:		BIDS_OlfUnc/sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_run-01_bold.nii.gz
	Reason:		Task scans should have a corresponding events.tsv file. It can be included one of the following locations: /events.tsv, /task-olfunc_events.tsv, /run-01_events.tsv, /task-olfunc_run-01_events.tsv, /sub-pilot02/sub-pilot02_events.tsv, /sub-pilot02/sub-pilot02_task-olfunc_events.tsv, /sub-pilot02/sub-pilot02_run-01_events.tsv, /sub-pilot02/sub-pilot02_task-olfunc_run-01_events.tsv, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_events.tsv, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_task-olfunc_events.tsv, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_run-01_events.tsv, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_task-olfunc_run-01_events.tsv, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_events.tsv, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_events.tsv, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_run-01_events.tsv, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_run-01_events.tsv
	Type:		Warning
	File:		sub-pilot02_ses-Pilot002_task-olfunc_run-02_bold.nii.gz
	Location:		BIDS_OlfUnc/sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_run-02_bold.nii.gz
	Reason:		Task scans should have a corresponding events.tsv file. It can be included one of the following locations: /events.tsv, /task-olfunc_events.tsv, /run-02_events.tsv, /task-olfunc_run-02_events.tsv, /sub-pilot02/sub-pilot02_events.tsv, /sub-pilot02/sub-pilot02_task-olfunc_events.tsv, /sub-pilot02/sub-pilot02_run-02_events.tsv, /sub-pilot02/sub-pilot02_task-olfunc_run-02_events.tsv, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_events.tsv, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_task-olfunc_events.tsv, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_run-02_events.tsv, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_task-olfunc_run-02_events.tsv, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_events.tsv, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_events.tsv, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_run-02_events.tsv, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_run-02_events.tsv
	Type:		Warning
	File:		sub-pilot02_ses-Pilot002_task-olfunc_run-03_bold.nii.gz
	Location:		BIDS_OlfUnc/sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_run-03_bold.nii.gz
	Reason:		Task scans should have a corresponding events.tsv file. It can be included one of the following locations: /events.tsv, /task-olfunc_events.tsv, /run-03_events.tsv, /task-olfunc_run-03_events.tsv, /sub-pilot02/sub-pilot02_events.tsv, /sub-pilot02/sub-pilot02_task-olfunc_events.tsv, /sub-pilot02/sub-pilot02_run-03_events.tsv, /sub-pilot02/sub-pilot02_task-olfunc_run-03_events.tsv, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_events.tsv, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_task-olfunc_events.tsv, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_run-03_events.tsv, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_task-olfunc_run-03_events.tsv, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_events.tsv, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_events.tsv, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_run-03_events.tsv, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_run-03_events.tsv
	Type:		Warning
	File:		sub-pilot02_ses-Pilot002_task-olfunc_run-04_bold.nii.gz
	Location:		BIDS_OlfUnc/sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_run-04_bold.nii.gz
	Reason:		Task scans should have a corresponding events.tsv file. It can be included one of the following locations: /events.tsv, /task-olfunc_events.tsv, /run-04_events.tsv, /task-olfunc_run-04_events.tsv, /sub-pilot02/sub-pilot02_events.tsv, /sub-pilot02/sub-pilot02_task-olfunc_events.tsv, /sub-pilot02/sub-pilot02_run-04_events.tsv, /sub-pilot02/sub-pilot02_task-olfunc_run-04_events.tsv, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_events.tsv, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_task-olfunc_events.tsv, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_run-04_events.tsv, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_task-olfunc_run-04_events.tsv, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_events.tsv, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_events.tsv, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_run-04_events.tsv, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_run-04_events.tsv
	Type:		Warning
	File:		sub-pilot02_ses-Pilot002_task-olfunc_run-05_bold.nii.gz
	Location:		BIDS_OlfUnc/sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_run-05_bold.nii.gz
	Reason:		Task scans should have a corresponding events.tsv file. It can be included one of the following locations: /events.tsv, /task-olfunc_events.tsv, /run-05_events.tsv, /task-olfunc_run-05_events.tsv, /sub-pilot02/sub-pilot02_events.tsv, /sub-pilot02/sub-pilot02_task-olfunc_events.tsv, /sub-pilot02/sub-pilot02_run-05_events.tsv, /sub-pilot02/sub-pilot02_task-olfunc_run-05_events.tsv, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_events.tsv, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_task-olfunc_events.tsv, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_run-05_events.tsv, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_task-olfunc_run-05_events.tsv, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_events.tsv, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_events.tsv, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_run-05_events.tsv, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_run-05_events.tsv
	Type:		Warning
	File:		sub-pilot02_ses-Pilot002_task-olfunc_run-06_bold.nii.gz
	Location:		BIDS_OlfUnc/sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_run-06_bold.nii.gz
	Reason:		Task scans should have a corresponding events.tsv file. It can be included one of the following locations: /events.tsv, /task-olfunc_events.tsv, /run-06_events.tsv, /task-olfunc_run-06_events.tsv, /sub-pilot02/sub-pilot02_events.tsv, /sub-pilot02/sub-pilot02_task-olfunc_events.tsv, /sub-pilot02/sub-pilot02_run-06_events.tsv, /sub-pilot02/sub-pilot02_task-olfunc_run-06_events.tsv, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_events.tsv, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_task-olfunc_events.tsv, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_run-06_events.tsv, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_task-olfunc_run-06_events.tsv, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_events.tsv, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_events.tsv, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_run-06_events.tsv, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_run-06_events.tsv
	Type:		Warning
	File:		sub-pilot02_ses-Pilot002_task-olfunc_run-07_bold.nii.gz
	Location:		BIDS_OlfUnc/sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_run-07_bold.nii.gz
	Reason:		Task scans should have a corresponding events.tsv file. It can be included one of the following locations: /events.tsv, /task-olfunc_events.tsv, /run-07_events.tsv, /task-olfunc_run-07_events.tsv, /sub-pilot02/sub-pilot02_events.tsv, /sub-pilot02/sub-pilot02_task-olfunc_events.tsv, /sub-pilot02/sub-pilot02_run-07_events.tsv, /sub-pilot02/sub-pilot02_task-olfunc_run-07_events.tsv, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_events.tsv, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_task-olfunc_events.tsv, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_run-07_events.tsv, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_task-olfunc_run-07_events.tsv, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_events.tsv, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_events.tsv, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_run-07_events.tsv, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_run-07_events.tsv
	Type:		Warning
	File:		sub-pilot02_ses-Pilot002_task-olfunc_run-08_bold.nii.gz
	Location:		BIDS_OlfUnc/sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_run-08_bold.nii.gz
	Reason:		Task scans should have a corresponding events.tsv file. It can be included one of the following locations: /events.tsv, /task-olfunc_events.tsv, /run-08_events.tsv, /task-olfunc_run-08_events.tsv, /sub-pilot02/sub-pilot02_events.tsv, /sub-pilot02/sub-pilot02_task-olfunc_events.tsv, /sub-pilot02/sub-pilot02_run-08_events.tsv, /sub-pilot02/sub-pilot02_task-olfunc_run-08_events.tsv, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_events.tsv, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_task-olfunc_events.tsv, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_run-08_events.tsv, /sub-pilot02/ses-Pilot002/sub-pilot02_ses-Pilot002_task-olfunc_run-08_events.tsv, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_events.tsv, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_events.tsv, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_run-08_events.tsv, /sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_run-08_events.tsv

======================================================


File Path: Not all subjects/sessions/runs have the same scanning parameters.

	Type:		Warning
	File:		sub-pilot02_ses-Pilot002_task-olfunc_run-03_bold.nii.gz
	Location:		BIDS_OlfUnc/sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_run-03_bold.nii.gz
	Reason:		 The most common set of dimensions is: 148,148,90,235 (voxels), This file has the dimensions: 148,148,90,152 (voxels).
	Type:		Warning
	File:		sub-pilot02_ses-Pilot002_task-olfunc_run-05_bold.nii.gz
	Location:		BIDS_OlfUnc/sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_run-05_bold.nii.gz
	Reason:		 The most common set of dimensions is: 148,148,90,235 (voxels), This file has the dimensions: 148,148,90,125 (voxels).
	Type:		Warning
	File:		sub-pilot02_ses-Pilot002_task-olfunc_run-06_bold.nii.gz
	Location:		BIDS_OlfUnc/sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_run-06_bold.nii.gz
	Reason:		 The most common set of dimensions is: 148,148,90,235 (voxels), This file has the dimensions: 148,148,90,260 (voxels).
	Type:		Warning
	File:		sub-pilot02_ses-Pilot002_task-olfunc_run-07_bold.nii.gz
	Location:		BIDS_OlfUnc/sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_run-07_bold.nii.gz
	Reason:		 The most common set of dimensions is: 148,148,90,235 (voxels), This file has the dimensions: 148,148,90,89 (voxels).
	Type:		Warning
	File:		sub-pilot02_ses-Pilot002_task-olfunc_run-08_bold.nii.gz
	Location:		BIDS_OlfUnc/sub-pilot02/ses-Pilot002/func/sub-pilot02_ses-Pilot002_task-olfunc_run-08_bold.nii.gz
	Reason:		 The most common set of dimensions is: 148,148,90,235 (voxels), This file has the dimensions: 148,148,90,260 (voxels).

======================================================


File Path: The recommended file /README is missing. See Section 03 (Modality agnostic files) of the BIDS specification.

	Type:		Warning

======================================================


File Path: The Authors field of dataset_description.json should contain an array of fields - with one author per field. This was triggered because there are no authors, which will make DOI registration from dataset metadata impossible.

	Type:		Warning

======================================================

Relevant log outputs (up to 20 lines):

The following time slicing-error occurs for multiple functional scans for this subject.

Node Name: fmriprep_23_0_wf.single_subject_pilot02_wf.func_preproc_ses_Pilot002_task_olfunc_run_03_wf.bold_stc_wf.slice_timing_correction

File: /out/sub-pilot02/log/20230405-221626_785a0198-3dd5-447f-94e6-00302d40cbc1/crash-20230405-221757-root-slice_timing_correction-26fbfec0-bed4-4533-aad2-e32529b3a342.txt
Working Directory: /tmp/work/fmriprep_23_0_wf/single_subject_pilot02_wf/func_preproc_ses_Pilot002_task_olfunc_run_03_wf/bold_stc_wf/slice_timing_correction
Inputs:
args:
environ: {}
ignore:
in_file:
interp:
num_threads: 1
out_file:
outputtype: NIFTI_GZ
rlt:
rltplus:
slice_encoding_direction: k
slice_timing: [0.0, 0.4675, 0.9325, 1.4, 1.8675, 0.3325, 0.8, 1.2675, 1.7325, 0.2, 0.6675, 1.1325, 1.6, 0.0675, 0.5325, 1.0, 1.4675, 1.9325, 0.4, 0.8675, 1.3325, 1.8, 0.2675, 0.7325, 1.2, 1.6675, 0.1325, 0.6, 1.0675, 1.5325, 0.0, 0.4675, 0.9325, 1.4, 1.8675, 0.3325, 0.8, 1.2675, 1.7325, 0.2, 0.6675, 1.1325, 1.6, 0.0675, 0.5325, 1.0, 1.4675, 1.9325, 0.4, 0.8675, 1.3325, 1.8, 0.2675, 0.7325, 1.2, 1.6675, 0.1325, 0.6, 1.0675, 1.5325, 0.0, 0.4675, 0.9325, 1.4, 1.8675, 0.3325, 0.8, 1.2675, 1.7325, 0.2, 0.6675, 1.1325, 1.6, 0.0675, 0.5325, 1.0, 1.4675, 1.9325, 0.4, 0.8675, 1.3325, 1.8, 0.2675, 0.7325, 1.2, 1.6675, 0.1325, 0.6, 1.0675, 1.5325]
tpattern:
tr: 2s
tslice:
tzero: 0.966
Traceback (most recent call last):
  File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
    raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node slice_timing_correction.

Cmdline:
	3dTshift -ignore 0 -prefix sub-pilot02_ses-Pilot002_task-olfunc_run-03_bold_tshift.nii.gz -tpattern @slice_timing.1D -TR 2s -tzero 0.966 /tmp/work/fmriprep_23_0_wf/single_subject_pilot02_wf/func_preproc_ses_Pilot002_task_olfunc_run_03_wf/bold_stc_wf/slice_timing_correction/sub-pilot02_ses-Pilot002_task-olfunc_run-03_bold.nii.gz
Stdout:

Stderr:
	++ 3dTshift: AFNI version=AFNI_23.0.04 (Feb 13 2023) [64-bit]
	** AFNI converts NIFTI_datatype=512 (UINT16) in file /tmp/work/fmriprep_23_0_wf/single_subject_pilot02_wf/func_preproc_ses_Pilot002_task_olfunc_run_03_wf/bold_stc_wf/slice_timing_correction/sub-pilot02_ses-Pilot002_task-olfunc_run-03_bold.nii.gz to FLOAT32
	     Warnings of this type will be muted for this session.
	     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
	Killed
Traceback:
	Traceback (most recent call last):
	  File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 454, in aggregate_outputs
	    setattr(outputs, key, val)
	  File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/traits_extension.py", line 330, in validate
	    value = super(File, self).validate(objekt, name, value, return_pathlike=True)
	  File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate
	    self.error(objekt, name, str(value))
	  File "/opt/conda/lib/python3.9/site-packages/traits/base_trait_handler.py", line 74, in error
	    raise TraitError(
	traits.trait_errors.TraitError: The 'out_file' trait of a TShiftOutputSpec instance must be a pathlike object or string representing an existing file, but a value of '/tmp/work/fmriprep_23_0_wf/single_subject_pilot02_wf/func_preproc_ses_Pilot002_task_olfunc_run_03_wf/bold_stc_wf/slice_timing_correction/sub-pilot02_ses-Pilot002_task-olfunc_run-03_bold_tshift.nii.gz'  was specified.

	During handling of the above exception, another exception occurred:

	Traceback (most recent call last):
	  File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 401, in run
	    outputs = self.aggregate_outputs(runtime)
	  File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 461, in aggregate_outputs
	    raise FileNotFoundError(msg)
	FileNotFoundError: No such file or directory '/tmp/work/fmriprep_23_0_wf/single_subject_pilot02_wf/func_preproc_ses_Pilot002_task_olfunc_run_03_wf/bold_stc_wf/slice_timing_correction/sub-pilot02_ses-Pilot002_task-olfunc_run-03_bold_tshift.nii.gz' for output

Screenshots / relevant information:

2

Hi @samlyons and welcome to neurostars!

Please do the following:

  1. Fix the TaskName error causing your data to not be BIDS valid
  2. Repeat your command but add a working directory with the -w /path/to/workdir argument

Best,
Steven

3

Hi @Steven,

Thanks for your help! I fixed those two issues, but I get the same error re: 3dTshift in several of my runs (error log below). Any thoughts about why this error might arise? (My fervent googling hasn’t returned much!)

Main command:

fmriprep-docker ./ ./derivatives participant --participant-label sub-pilot02 --fs-license-file ../license.txt --mem-mb 50000 -w ../

Error Log:

Node: fmriprep_23_0_wf.single_subject_pilot02_wf.func_preproc_ses_Pilot002_task_olfunc_run_03_wf.bold_stc_wf.slice_timing_correction
Working directory: /scratch/fmriprep_23_0_wf/single_subject_pilot02_wf/func_preproc_ses_Pilot002_task_olfunc_run_03_wf/bold_stc_wf/slice_timing_correction

Node inputs:

args = <undefined>
environ = {}
ignore = <undefined>
in_file = <undefined>
interp = <undefined>
num_threads = 1
out_file = <undefined>
outputtype = NIFTI_GZ
rlt = <undefined>
rltplus = <undefined>
slice_encoding_direction = k
slice_timing = [0.0, 0.4675, 0.9325, 1.4, 1.8675, 0.3325, 0.8, 1.2675, 1.7325, 0.2, 0.6675, 1.1325, 1.6, 0.0675, 0.5325, 1.0, 1.4675, 1.9325, 0.4, 0.8675, 1.3325, 1.8, 0.2675, 0.7325, 1.2, 1.6675, 0.1325, 0.6, 1.0675, 1.5325, 0.0, 0.4675, 0.9325, 1.4, 1.8675, 0.3325, 0.8, 1.2675, 1.7325, 0.2, 0.6675, 1.1325, 1.6, 0.0675, 0.5325, 1.0, 1.4675, 1.9325, 0.4, 0.8675, 1.3325, 1.8, 0.2675, 0.7325, 1.2, 1.6675, 0.1325, 0.6, 1.0675, 1.5325, 0.0, 0.4675, 0.9325, 1.4, 1.8675, 0.3325, 0.8, 1.2675, 1.7325, 0.2, 0.6675, 1.1325, 1.6, 0.0675, 0.5325, 1.0, 1.4675, 1.9325, 0.4, 0.8675, 1.3325, 1.8, 0.2675, 0.7325, 1.2, 1.6675, 0.1325, 0.6, 1.0675, 1.5325]
tpattern = <undefined>
tr = 2s
tslice = <undefined>
tzero = 0.966

Traceback (most recent call last):
  File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
    raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node slice_timing_correction.

Cmdline:
	3dTshift -ignore 0 -prefix sub-pilot02_ses-Pilot002_task-olfunc_run-03_bold_tshift.nii.gz -tpattern @slice_timing.1D -TR 2s -tzero 0.966 /scratch/fmriprep_23_0_wf/single_subject_pilot02_wf/func_preproc_ses_Pilot002_task_olfunc_run_03_wf/bold_stc_wf/slice_timing_correction/sub-pilot02_ses-Pilot002_task-olfunc_run-03_bold.nii.gz
Stdout:

Stderr:
	++ 3dTshift: AFNI version=AFNI_23.0.04 (Feb 13 2023) [64-bit]
	** AFNI converts NIFTI_datatype=512 (UINT16) in file /scratch/fmriprep_23_0_wf/single_subject_pilot02_wf/func_preproc_ses_Pilot002_task_olfunc_run_03_wf/bold_stc_wf/slice_timing_correction/sub-pilot02_ses-Pilot002_task-olfunc_run-03_bold.nii.gz to FLOAT32
	     Warnings of this type will be muted for this session.
	     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
	Killed
Traceback:
	Traceback (most recent call last):
	  File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 454, in aggregate_outputs
	    setattr(outputs, key, val)
	  File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/traits_extension.py", line 330, in validate
	    value = super(File, self).validate(objekt, name, value, return_pathlike=True)
	  File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate
	    self.error(objekt, name, str(value))
	  File "/opt/conda/lib/python3.9/site-packages/traits/base_trait_handler.py", line 74, in error
	    raise TraitError(
	traits.trait_errors.TraitError: The 'out_file' trait of a TShiftOutputSpec instance must be a pathlike object or string representing an existing file, but a value of '/scratch/fmriprep_23_0_wf/single_subject_pilot02_wf/func_preproc_ses_Pilot002_task_olfunc_run_03_wf/bold_stc_wf/slice_timing_correction/sub-pilot02_ses-Pilot002_task-olfunc_run-03_bold_tshift.nii.gz' <class 'str'> was specified.

	During handling of the above exception, another exception occurred:

	Traceback (most recent call last):
	  File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 401, in run
	    outputs = self.aggregate_outputs(runtime)
	  File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 461, in aggregate_outputs
	    raise FileNotFoundError(msg)
	FileNotFoundError: No such file or directory '/scratch/fmriprep_23_0_wf/single_subject_pilot02_wf/func_preproc_ses_Pilot002_task_olfunc_run_03_wf/bold_stc_wf/slice_timing_correction/sub-pilot02_ses-Pilot002_task-olfunc_run-03_bold_tshift.nii.gz' for output 'out_file' of a TShift interface
4

hmmm, I’ve never used the docker fmriprep wrapper, just in case, can you try the following command (substituting paths as necessary)? Also, make sure your working directory is not contained in your BIDS directory, and use a working directory that is empty.

BIDS=/path/to/bids/
WORK=/path/to/work/
LICENSE=/path/to/license.txt

docker run -ti --rm -v $BIDS \
    -v $LICENSE -v $WORK \
    nipreps/fmriprep:23.0.1 \
    $BIDS $BIDS/derivatives participant \
    --participant-label sub-pilot02 \
    --fs-license-file $LICENSE -w $WORK \
    --mem-mb 50000
5

Thanks @Steven! I tried running a version of that below. (Done with python + there was a Windows/docker-related binding problem that required some extra fiddling.) Things are running as before unfortunately! I still get the same slice-timing 3dTshift error.

set BIDS_SRC $HOME/Documents/BIDS_OlfUnc
set BIDS_TRG /data

set WORK_SRC $HOME/Documents/WORKDIRECTORY
set WORK_TRG /work

set LICENSE_SRC $HOME/Documents/license.txt
set LICENSE_TRG /license.txt

docker run -ti --rm `
-v ${BIDS_SRC}:${BIDS_TRG} `
-v ${WORK_SRC}:${WORK_TRG} `
-v ${LICENSE_SRC}:${LICENSE_TRG} `
nipreps/fmriprep:23.0.1 $BIDS_TRG ${BIDS_TRG}/derivatives `
participant --participant-label sub-pilot02 `
--fs-license-file $LICENSE_TRG -w $WORK_TRG
6

So I think this ended up just being a memory issue! I reran everything using 2 functional runs instead of the original 8, and the error goes away. (I replicated this a few times with different runs to be sure.)

7

Hi @samlyons -

This is probably too late to be useful, but indeed, in the initial post, stderr contains the word “Killed”, which means that the available memory was being nearly all used up, and as a result the process was abruptly/brutally stopped by the operating system. Essentially, any time that is seen, a memory issue is occurring, so what you have diagnosed sounds correct.

–pt

1 Like