Hello. I have a multi-session dataset where participants obtain multiple T1w scans. Running fmriprep generates an anat/ folder with mean T1w images, however, the filenames it generates does not seem to pass the BIDS specification. Anyone know the reason why that is?
fmriprep v23.0.1
bids-validator v1.12.0
Log:
[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 GitHub - bids-standard/bids-validator: Validator for the Brain Imaging Data Structure 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-SID000002/anat/
Evidence: sub-SID000002_acq-MPRAGEXp3X08mm_desc-brain_mask.json
./sub-SID000002/anat/sub-SID000002_acq-MPRAGEXp3X08mm_desc-brain_mask.nii.gz
Evidence: sub-SID000002_acq-MPRAGEXp3X08mm_desc-brain_mask.nii.gz
./sub-SID000002/anat/sub-SID000002_acq-MPRAGEXp3X08mm_desc-preproc_T1w.json
Evidence: sub-SID000002_acq-MPRAGEXp3X08mm_desc-preproc_T1w.json
./sub-SID000002/anat/sub-SID000002_acq-MPRAGEXp3X08mm_desc-preproc_T1w.nii.gz
Evidence: sub-SID000002_acq-MPRAGEXp3X08mm_desc-preproc_T1w.nii.gz
... and 24255 more files having this issue (Use --verbose to see them all).
Similarly, fmriprep-generated /figures/ folders generates filenames with the ses- entity in it, which then gets flagged by the BIDS-validator as not matching the directory it is “supposed” to be in.
Log:
[ERR] Session label in the filename doesn’t match with the path of the file. File seems to be saved in incorrect session directory. (code: 65 - SESSION_LABEL_IN_FILENAME_DOESNOT_MATCH_DIRECTORY)
./sub-SID000002/figures/
Evidence: File: /sub-SID000002/figures/sub-SID000002_ses-01_acq-mb8_fmapid-auto00000_desc-pepolar_fieldmap.svg is saved in incorrect session directory as per ses-id in filename.
./sub-SID000002/figures/sub-SID000002_ses-01_acq-mb8_fmapid-auto00005_desc-pepolar_fieldmap.svg
Evidence: File: /sub-SID000002/figures/sub-SID000002_ses-01_acq-mb8_fmapid-auto00005_desc-pepolar_fieldmap.svg is saved in incorrect session directory as per ses-id in filename.
./sub-SID000002/figures/sub-SID000002_ses-01_acq-mb8_fmapid-auto00007_desc-pepolar_fieldmap.svg
Evidence: File: /sub-SID000002/figures/sub-SID000002_ses-01_acq-mb8_fmapid-auto00007_desc-pepolar_fieldmap.svg is saved in incorrect session directory as per ses-id in filename.
./sub-SID000002/figures/sub-SID000002_ses-01_acq-mb8_fmapid-auto00010_desc-pepolar_fieldmap.svg
Evidence: File: /sub-SID000002/figures/sub-SID000002_ses-01_acq-mb8_fmapid-auto00010_desc-pepolar_fieldmap.svg is saved in incorrect session directory as per ses-id in filename.
./sub-SID000002/figures/sub-SID000002_ses-01_acq-mb8_fmapid-auto00015_desc-pepolar_fieldmap.svg
Evidence: File: /sub-SID000002/figures/sub-SID000002_ses-01_acq-mb8_fmapid-auto00015_desc-pepolar_fieldmap.svg is saved in incorrect session directory as per ses-id in filename.
./sub-SID000002/figures/sub-SID000002_ses-01_task-movemap_acq-mb8_run-1_desc-aroma_bold.svg
Evidence: File: /sub-SID000002/figures/sub-SID000002_ses-01_task-movemap_acq-mb8_run-1_desc-aroma_bold.svg is saved in incorrect session directory as per ses-id in filename.
./sub-SID000002/figures/sub-SID000002_ses-01_task-movemap_acq-mb8_run-1_desc-carpetplot_bold.svg
Evidence: File: /sub-SID000002/figures/sub-SID000002_ses-01_task-movemap_acq-mb8_run-1_desc-carpetplot_bold.svg is saved in incorrect session directory as per ses-id in filename.
./sub-SID000002/figures/sub-SID000002_ses-01_task-movemap_acq-mb8_run-1_desc-compcorvar_bold.svg
Evidence: File: /sub-SID000002/figures/sub-SID000002_ses-01_task-movemap_acq-mb8_run-1_desc-compcorvar_bold.svg is saved in incorrect session directory as per ses-id in filename.
./sub-SID000002/figures/sub-SID000002_ses-01_task-movemap_acq-mb8_run-1_desc-confoundcorr_bold.svg
Evidence: File: /sub-SID000002/figures/sub-SID000002_ses-01_task-movemap_acq-mb8_run-1_desc-confoundcorr_bold.svg is saved in incorrect session directory as per ses-id in filename.
./sub-SID000002/figures/sub-SID000002_ses-01_task-movemap_acq-mb8_run-1_desc-flirtbbr_bold.svg
Evidence: File: /sub-SID000002/figures/sub-SID000002_ses-01_task-movemap_acq-mb8_run-1_desc-flirtbbr_bold.svg is saved in incorrect session directory as per ses-id in filename.
… and 7656 more files having this issue (Use --verbose to see them all).