An error occurred while running fmriprep

Software Support
1

Summary of what happened:

The error message is shown in the following image.

error
error1928Ă—440 339 KB

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

docker run --rm -v /home/zhouyuan/fan/Data/Data_GL/tmp_2/:/wd -v /home/zhouyuan/fan/Data/Data_GL/BIDS_Data/youngHC/:/input -v /home/zhouyuan/fan/Data/Data_GL/out/:/out -v /home/zhouyuan/fan/freesurferlicense:/freesurfer_license nipreps/fmriprep:latest /input /out participant -w /wd --output-spaces T1w MNI152NLin6Asym:res-2 MNI152NLin2009cAsym:res-2 --fs-license-file /freesurfer_license/license.txt --cifti 91k --skip-bids-validation

Version: fmriprep 23.1.4

Environment (Docker, Singularity, custom installation):

Docker

Data formatted :

data
data1006Ă—370 48.6 KB

2

Hi @Donggua,

May you try adding —it after —rm in your Docker arguments? Also try removing the —skip-bids-validation argument and sharing the results of validation.

Best,
Steven

1 Like
3

After modifying the execution command, a new error occurred. :face_exhaling:

docker run --rm -it -v /home/zhouyuan/fan/Data/Data_GL/tmp_2/:/wd -v /home/zhouyuan/fan/Data/Data_GL/BIDS_Data/youngHC/:/input -v /home/zhouyuan/fan/Data/Data_GL/out/:/out -v /home/zhouyuan/fan/freesurferlicense:/freesurfer_license nipreps/fmriprep:latest /input /out participant -w /wd --output-spaces T1w MNI152NLin6Asym:res-2 MNI152NLin2009cAsym:res-2 --fs-license-file /freesurfer_license/license.txt --cifti 91k

error message


*bids-validator@1.11.0
(node:9) Warning: Closing directory handle on garbage collection
(Use `node --trace-warnings ...` to show where the warning was created)
	1: [ERR] This file ends in the .gz extension but is not actually gzipped. (code: 28 - GZ_NOT_GZIPPED)
		./sub-HC001/anat/sub-HC001_T1w.nii.gz
		./sub-HC001/func/sub-HC001_task-rest_bold.nii.gz
		./sub-HC002/anat/sub-HC002_T1w.nii.gz
		./sub-HC002/func/sub-HC002_task-rest_bold.nii.gz
		./sub-HC003/anat/sub-HC003_T1w.nii.gz
		./sub-HC003/func/sub-HC003_task-rest_bold.nii.gz
		./sub-HC004/anat/sub-HC004_T1w.nii.gz
		./sub-HC004/func/sub-HC004_task-rest_bold.nii.gz
		./sub-HC005/anat/sub-HC005_T1w.nii.gz
		./sub-HC005/func/sub-HC005_task-rest_bold.nii.gz
		... and 48 more files having this issue (Use --verbose to see them all).

	Please visit https://neurostars.org/search?q=GZ_NOT_GZIPPED for existing conversations about this issue.

	1: [WARN] The recommended file /README is missing. See Section 03 (Modality agnostic files) of the BIDS specification. (code: 101 - README_FILE_MISSING)

	Please visit https://neurostars.org/search?q=README_FILE_MISSING for existing conversations about this issue.

	2: [WARN] 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. (code: 113 - NO_AUTHORS)

	Please visit https://neurostars.org/search?q=NO_AUTHORS for existing conversations about this issue.

        Summary:                 Available Tasks:        Available Modalities: 
        117 Files, 2.14GB                                MRI                   
        29 - Subjects                                                          
        1 - Session                                                            


	If you have any questions, please post on https://neurostars.org/tags/bids.
Traceback (most recent call last):
  File "/opt/conda/envs/fmriprep/bin/fmriprep", line 8, in <module>
    sys.exit(main())
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/cli/run.py", line 43, in main
    parse_args()
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/cli/parser.py", line 812, in parse_args
    validate_input_dir(config.environment.exec_env, opts.bids_dir, opts.participant_label)
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/utils/bids.py", line 185, in validate_input_dir
    subprocess.check_call(['bids-validator', str(bids_dir), '-c', temp.name])
  File "/opt/conda/envs/fmriprep/lib/python3.10/subprocess.py", line 369, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['bids-validator', '/input', '-c', '/tmp/tmpzkxeoenf.json']' returned non-zero exit status 1.*
4

Hi @Donggua,

Can you talk about how you prepared the data?

Best,
Steven

5

Hi Steven,
The original data files had the extension “.nii”, but when organizing these data into BIDS format, I renamed them with the extension “.nii.gz” .

6

Hi @Donggua,

You would need to use the gzip command for that. But, BIDS should also accept .nii so try removing all the .gz from the file names.

Best,
Steven

8

Thank you so much, once again you have solved my problem. :handshake:

1 Like