Summary of what happened:
Hello everyone,
I need to validate a dataset so I can later run fMRIPrep. My dataset is in an HCP cluster, so it is not viable to use the web version. I built the singularity image from bids/validator - Docker Image using the latest version (2.2.10), and it works properly. However, I find that when it gives the errors, it lists only one or two files that present the error and then says “x more files with the same issue”. I was wondering if there is a way to list all the files that present a given error (e.g. identify all the files that present [ERROR] T1W_FILE_WITH_TOO_MANY_DIMENSIONS _T1w.nii[.gz] files must have exactly three dimensions.).
Thanks!
.
Command used (and if a helper script was used, a link to the helper script or the command generated):
module load apptainer
singularity exec \
-B ./<data_path>/data:ro \
bids_validator.simg \
deno run \
--allow-read=/data \
--allow-env \
/src/bids-validator.js /data
Version:
2.2.10
Environment (Docker, Singularity / Apptainer, custom installation):
Singularity (running in an HCP cluster using apptainer)
Data formatted according to a validatable standard? Please provide the output of the validator:
[ERROR] T1W_FILE_WITH_TOO_MANY_DIMENSIONS _T1w.nii[.gz] files must have exactly three dimensions.
/sub-TN3RVM/ses-HAB1/anat/sub-TN3RVM_ses-HAB1_T1w.nii.gz
/sub-NSQIVG/ses-HAB1/anat/sub-NSQIVG_ses-HAB1_T1w.nii.gz