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

RF: Add sanitized_id field to FieldmapEstimation #444

Merged
merged 3 commits into from
Jun 6, 2024

Conversation

effigies
Copy link
Member

@effigies effigies commented Jun 6, 2024

Replaces #434 along the lines described in #295 (comment).

I think probably the cleanest way forward for downstream is for functions to always store and pass the estimator object, and select bids_id or sanitized_id only when a string is needed and what kind of string is needed is known.

TBH, this is a needless headache that is going to invite bugs, and I think we should put a check in the validator warning about B0Field* that contains non-alphanumeric characters, including underscores.

@effigies effigies requested review from tsalo and mgxd June 6, 2024 12:15
Copy link
Contributor

@mgxd mgxd left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Looks good - even though testing seems to be broken atm, can you add a small test for this?

TBH, this is a needless headache that is going to invite bugs, and I think we should put a check in the validator warning about B0Field* that contains non-alphanumeric characters, including underscores.

Copy link
Contributor

@tsalo tsalo left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Thanks for fixing my original change. This PR makes sense to me.

I'm not sure how I feel about modifying the spec based on this though.

@effigies
Copy link
Member Author

effigies commented Jun 6, 2024

@mgxd Test failures resolved, new tests added.

@effigies
Copy link
Member Author

effigies commented Jun 6, 2024

WDYT about this being in a patch release vs a feature release?

@tsalo
Copy link
Contributor

tsalo commented Jun 6, 2024

I'd consider it a patch, since SDCFlows doesn't currently work with what the BIDS spec allows.

@mgxd
Copy link
Contributor

mgxd commented Jun 6, 2024

I guess this will cause significant cache invalidation (at least in fmriprep) for anyone using a non-sanitized B0FieldIdentifiers, so minor release feels safer

@effigies
Copy link
Member Author

effigies commented Jun 6, 2024

Okay. We'll just bump to 2.9.

@effigies effigies merged commit fa9e716 into nipreps:master Jun 6, 2024
20 checks passed
@effigies effigies deleted the fix/normalize-fmapids branch June 6, 2024 19:07
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

3 participants