Skip to content
New issue

Have a question about this project? # for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “#”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? # to your account

Make bids-validator conform to BIDS-App (or execution-spec right away) specification #16

Open
yarikoptic opened this issue Jun 12, 2024 · 2 comments
Labels
help wanted Extra attention is needed

Comments

@yarikoptic
Copy link
Contributor

ATM it is

Usage: bids-validator <dataset_directory> [options]

whenever BIDS-app interface, as described in new exec spec (bep027) https://bids-standard.github.io/execution-spec/inputs.html#backwards-compatibility

bids-app InputDataset OutputLocation AnalysisLevel [options]
...
CLI flag: --subject-label

. Or may be just following new options as described at https://bids-standard.github.io/execution-spec/inputs.html#list-of-custom-object-properties-and-roles-within-the-bids-application-specification

It would have been quite convenient to be able to limit bids-validation to a specific subject or session, and only at "dataset" level provide overall report.

@effigies effigies added the help wanted Extra attention is needed label Jun 12, 2024
@effigies
Copy link
Contributor

If we do want to adopt it, we are required to specify OutputLocation, which we could default to stdout with -o/--output -. I'm not sure what AnalysisLevel would correspond to, but that's also required. Maybe --analyze dataset that's set by default and any other value is an error.

Otherwise, seems fine. --subject-label X Y would simply filter contexts on entities.subject == 'X' || entities.subject == 'Y'. Similarly with any entity you care to define.

@yarikoptic
Copy link
Contributor Author

NB For BIDS exec spec itself might be worth defaulting OutputLocation to . to encourage YODA style composition ;-)

# for free to join this conversation on GitHub. Already have an account? # to comment
Labels
help wanted Extra attention is needed
Projects
None yet
Development

No branches or pull requests

2 participants