ENH: Resample BOLD data to any surface template space using the Connectome Workbench #3461
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…ectome workbench.
…nd init_wb_surf_surf_wf.
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #3461 +/- ##
==========================================
- Coverage 73.50% 0.43% -73.08%
==========================================
Files 60 59 -1
Lines 4582 4611 +29
Branches 585 591 +6
==========================================
- Hits 3368 20 -3348
- Misses 1085 4591 +3506
+ Partials 129 0 -129 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
|
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Changes proposed in this pull request
Currently in fMRIPrep the Connectome Workbench is used to resample BOLD data to fsLR spaces, as part of the CIFTI workflow.
This PR allows resampling BOLD data to any surface template space with a similar workflow, as long as (a) the "space-fsLR" spheres exist for the template (e.g., "tpl-onavg_space-fsLR_hemi-R_den-41k_sphere.surf.gii") or (b) the template is "fsLR".
In the long run, we might want to generate alternative generic workflows, e.g., (a) using the SurfaceTransform class of nitransforms by @Shotgunosine and me, and (b) using FreeSurfer's resampling workflow.
This PR depends on a recent PR of smriprep and updating TemplateFlow's files on AWS S3.
Currently the wrong subfolder on S3 was updated for some unknown reason.
This generic resampling workflow might serve as the first step for the generic CIFTI workflow.
Documentation that should be reviewed
I've updated the workflows' docstrings accordingly, but feel free to make suggestions/edits.
@effigies @oesteban