Separating the validation of BIDS datasets from BIDS apps

[gki...@gmail.com]

Hi All,

I've opened an issue here which proposes to make BIDS dataset validation optional in BIDS apps.

The reasons for this are:

1. Datasets stored on network (or other "far") mountpoints can be slow to access, and crawling every file within a large dataset would take a long time
2. Re-running this validation for every task you launch is redundant, and it makes more sense (to me) to either a) launch a single validation task prior to launching jobs, or b) validate datasets on "ingest" to wherever you wish to store or mount them, though I understand not everyone is using databases or anything fancier than a filesystem, so in some cases this step could be overlooked
3. Since validator versions vary independently from tool versions, depending when a tool was last updated the version of the validator used may be different, meaning different apps may give different validation results for the same dataset

Since I understand this may be a part of people's workflows, and this precedent has been set in the FreeSurfer BIDS app, I propose that all apps which currently use the validator add the --skip_bids_validator option to their command-line.

I've opened a PR on the BIDS example and linked to it in the above issue.

Cheers,

Greg

[Chris Gorgolewski]

+1 This already has been requested. Definitely good to add this option.

Best,

Chris

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