Summary of what happened:
I ran the BIDS validator on my dataset and I’m getting an internal error that I haven’t seen before. This dataset previously passed BIDS validation a couple months ago but I have added new data to it since then. It also lists that I have 27 sessions but I should have ~90-100 sessions total across all subjects.
Command used (and if a helper script was used, a link to the helper script or the command generated):
bidsdir=/zwork/hannah/mbp/data/
SING_IMG=/zwork/hannah/mbp/data/code/diconv/bids-validator_latest.simg
cmd='singularity exec --bind ${bidsdir}:${bidsdir}:ro ${SING_IMG} \bids-validator ${bidsdir}'
eval $cmd
Version:
1.14.6
Environment (Docker, Singularity / Apptainer, custom installation):
Running in a singularity container
Data formatted according to a validatable standard? Please provide the output of the validator:
bids-validator@1.14.6
(node:1618782) Warning: Closing directory handle on garbage collection
(Use `node --trace-warnings ...` to show where the warning was created)
1: [ERR] Internal error. SOME VALIDATION STEPS MAY NOT HAVE OCCURRED (code: 0 - INTERNAL ERROR)
Evidence: TypeError: Cannot read properties of undefined (reading 'split')
at splitDateString (/usr/local/lib/node_modules/bids-validator/dist/commonjs/cli.js:100086:29)
at parseISO (/usr/local/lib/node_modules/bids-validator/dist/commonjs/cli.js:100035:23)
at /usr/local/lib/node_modules/bids-validator/dist/commonjs/cli.js:100228:28
at Array.map (<anonymous>)
at checkAcqTimeFormat (/usr/local/lib/node_modules/bids-validator/dist/commonjs/cli.js:100225:12)
at TSV (/usr/local/lib/node_modules/bids-validator/dist/commonjs/cli.js:100933:7)
at /usr/local/lib/node_modules/bids-validator/dist/commonjs/cli.js:101382:9
Please visit https://neurostars.org/search?q=INTERNAL ERROR for existing conversations about this issue.
Summary: Available Tasks: Available Modalities:
2217 Files, 125.4GB MRI
17 - Subjects
27 - Sessions
If you have any questions, please post on https://neurostars.org/tags/bids.