Hi,
I’m running fmriprep version 20.0.7 and recently ran into a validation error when trying to include lesion mask (e.g., sub-001_T1w_label-lesion_roi.nii.gz). in my anat folder.
I tried to include a .bidsignore file with the following text (*lesion_roi.nii.gz) but it does not work. Its important to say that I have the data preprocessed without the lesion mask file, so my data is organized according to bids.
what should I do?
thank you,
Shaymaa
This is the command I’m running : fmriprep-docker /home/shymaa/Desktop/my_dataset/Participant /home/shymaa/Desktop/my_dataset/Participant/derivative participant --participant-label 12 --fs-license-file /home/shymaa/Desktop/license.txt
and this is the error:
1: [ERR] Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a “.bidsignore” file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder. (code: 1 - NOT_INCLUDED)
./sub-12/anat/sub-12_T1w_label-lesion_roi.nii.gz
Evidence: sub-12_T1w_label-lesion_roi.nii.gz
Please visit https://neurostars.org/search?q=NOT_INCLUDED for existing conversations about this issue.
2: [ERR] Sub label contain an Illegal Character hyphen or underscore. Please edit the filename as per BIDS spec. (code: 62 - SUBJECT_VALUE_CONTAINS_ILLEGAL_CHARACTER)
./sub-12/anat/sub-12_T1w_label-lesion_roi.nii.gz
Evidence: sub name contains illegal character:/sub-12/anat/sub-12_T1w_label-lesion_roi.nii.gz
Please visit https://neurostars.org/search?q=SUBJECT_VALUE_CONTAINS_ILLEGAL_CHARACTER 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.
Summary: Available Tasks: Available Modalities:
40 Files, 1.65GB T1w
13 - Subjects bold
1 - Session
If you have any questions, please post on https://neurostars.org/tags/bids.
Traceback (most recent call last):
File “/usr/local/miniconda/bin/fmriprep”, line 10, in
sys.exit(main())
File “/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/run.py”, line 17, in main
parse_args()
File “/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/parser.py”, line 703, in parse_args
config.environment.exec_env, opts.bids_dir, opts.participant_label
File “/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/utils/bids.py”, line 155, in validate_input_dir
subprocess.check_call([‘bids-validator’, bids_dir, ‘-c’, temp.name])
File “/usr/local/miniconda/lib/python3.7/subprocess.py”, line 341, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command ‘[‘bids-validator’, PosixPath(’/data’), ‘-c’, ‘/tmp/tmpvdqrc5ov’]’ returned non-zero exit status 1.
fMRIPrep: Please report errors to https://github.com/nipreps/fmriprep/issues