updating names of files in scans.tsv after running cubids apply

[B-Sevchik]

Summary

I would like cubids to have the ability to change the scans.tsv files for all of the subjects in which running cubids apply has changed the names of files due to variants.

Additional details

The benefit would be not having to manually update scans.tsv after cubids apply edits.

Next steps

[mattcieslak]

Does cubids apply not produce a new summary tsv? I thought it did (but it's been awhile). If it doesn't can you just rerun cubids group again to get a new scans.tsv?

[B-Sevchik]

Yeah, cubids apply does produce a new summary tsv! The issue is that neither cubids apply or cubids group seems to change/update the scans.tsv files. These are the files heudiconv produces for each subject/session that list the scans for that subject/session, so the validation error I got was because the scans.tsv still had the old names of the files that weren't updated when the file names with variants were updated after running cubids apply.