RFC: Replacing atlas entity with seg for specifying named segmentations

[Chris Markiewicz]

Hi all,

One thing we spent quite a bit of time discussing at the Copenhagen meeting was the meaning of "atlas" in the BIDS context. BEP 38 (https://bids.neuroimaging.io/bep038) will propose a rigorous definition and can be debated back and forth, but there's some cleanup to do first.

When we published common derivatives an "atlas-<label>" entity and "Atlas" metadata were claimed for the quite narrow use case of "named segmentation". Melanie has put together a proposal to un-specify the atlas entity and metadata, and replace the entity with "seg-<label>", which better fits the narrow use case: https://github.com/bids-standard/bids-specification/pull/1579

Because this is a breakage of backwards compatibility, this warrants more advertisement and discussion than the usual process, so we want to get a sense of whether anybody would actually be affected by this, and (if so) whether they are willing to accept the fallout. Please let us know if this does affect your tools or data.

Best,

Chris

[Jon Clucas]

C-PAC uses "atlas-<label>", but its usage is a work-in-progress, only used within a workflow and as final outputs, so no pipeline-to-pipeline issues. bids-standard/bids-specification#1579 seems like an important clarification and worth the backwards-compatibility breaking change. We'd just include a note in our docs about the former naming once we update, so the breakage shouldn't be a big problem for us.

[Chris Markiewicz]

Hi all,

Just wanted to bug everybody once again to offer your feedback on PR 1579 (https://github.com/bids-standard/bids-specification/pull/1579). A thumbs-up (or thumbs-down) on the PR would be appreciated as a signal that you've seen it and approve (or disapprove), though any more in-depth comments are also welcome!

And thanks for the feedback, Jon.

Best,

Chris

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