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

Allow external atlases organized as BIDS datasets #1226

Open
tsalo opened this issue Aug 8, 2024 · 0 comments · May be fixed by #1265
Open

Allow external atlases organized as BIDS datasets #1226

tsalo opened this issue Aug 8, 2024 · 0 comments · May be fixed by #1265
Assignees
Labels
enhancement New feature or request

Comments

@tsalo
Copy link
Member

tsalo commented Aug 8, 2024

Summary

Once in a while, users will request that we add a new atlas to the list of built-in atlases for XCP-D. Unfortunately, that list is growing quite long at this point. I would prefer to have a solid way to let users provide their own atlases.

The relevant BEP, BEP038: Atlas Specification, proposes adding an "Atlas" dataset type. XCP-D currently writes out its atlases in a manner that somewhat follows the BEP, so I don't think it's a massive stretch to ingress atlas datasets to be used for parcellation.

Additional details

We may need to wait until the Atlas BEP is finalized and merged before XCP-D can officially start supporting it.

Next steps

  1. Allow atlases in --atlases to be specified with the label=path structure, like how fMRIPrep handles --derivatives.
  2. Load the relevant information from the atlas dataset.
  3. In the near term, limit atlases to ones in MNI152NLin6Asym space (for nifti processing) or fsLR+MNI152NLin6Asym space (for cifti processing). In the long term, we should be able to use workflows from fMRIPost pipelines to warp to whatever space is necessary- at least for niftis.
@tsalo tsalo added the enhancement New feature or request label Aug 8, 2024
@tsalo tsalo self-assigned this Aug 8, 2024
@tsalo tsalo linked a pull request Sep 16, 2024 that will close this issue
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request
Projects
None yet
Development

Successfully merging a pull request may close this issue.

1 participant