Skip to content
New issue

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

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

Already on GitHub? Sign in to your account

Make bids-validator conform to BIDS-App (or execution-spec right away) specification #2000

Open
yarikoptic opened this issue Jun 12, 2024 · 2 comments

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
Copy link
Collaborator

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 ;-)

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
Development

No branches or pull requests

2 participants