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: Break up surface workflows for easier mix-and-match in fMRIPrep #360

Merged
merged 18 commits into from
Aug 28, 2023

Conversation

effigies
Copy link
Member

Should have no effect on current outputs, but:

  1. Moves midthickness check/creation back into surface_recon_wf, which then needs a sync function to ensure that downstream nodes don't try to extract surfaces before midthickness is present.
  2. Split surface and morphometric translation to GIFTI into their own workflows, as these are independent.
  3. Pass the selected surfaces and morphometry files as arguments.

Does not need immediate merge. Will probably do more.

@codecov
Copy link

codecov bot commented Aug 27, 2023

Codecov Report

Patch coverage: 9.45% and project coverage change: -9.00% ⚠️

Comparison is base (311328c) 53.65% compared to head (9425caa) 44.65%.

Additional details and impacted files
@@            Coverage Diff             @@
##             next     #360      +/-   ##
==========================================
- Coverage   53.65%   44.65%   -9.00%     
==========================================
  Files          22       22              
  Lines        1627     1666      +39     
  Branches      214      225      +11     
==========================================
- Hits          873      744     -129     
- Misses        686      853     +167     
- Partials       68       69       +1     
Flag Coverage Δ
ds005 ?
ds054 44.65% <9.45%> (-0.77%) ⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files Changed Coverage Δ
smriprep/interfaces/surf.py 0.00% <0.00%> (-46.16%) ⬇️
smriprep/workflows/anatomical.py 45.07% <0.00%> (-0.35%) ⬇️
smriprep/workflows/base.py 75.00% <ø> (ø)
smriprep/workflows/outputs.py 54.70% <8.33%> (-1.06%) ⬇️
smriprep/workflows/surfaces.py 12.09% <10.63%> (-0.08%) ⬇️
smriprep/cli/run.py 73.30% <100.00%> (+0.12%) ⬆️

... and 8 files with indirect coverage changes

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

@effigies effigies force-pushed the rf/split_surface_workflows branch 3 times, most recently from c8d6cee to 7c82f55 Compare August 28, 2023 00:42
@effigies
Copy link
Member Author

This is ready for review.

Copy link
Collaborator

@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.

A few little things, but overall a nice housecleaning on surfaces - will have to port over the MSM sulc stuff once that's in

smriprep/workflows/surfaces.py Show resolved Hide resolved
smriprep/workflows/surfaces.py Show resolved Hide resolved
smriprep/cli/run.py Show resolved Hide resolved
smriprep/interfaces/surf.py Outdated Show resolved Hide resolved
@effigies
Copy link
Member Author

will have to port over the MSM sulc stuff once that's in

I think it should be pretty straightforward.

@effigies effigies merged commit 8bdd2ce into nipreps:next Aug 28, 2023
0 of 2 checks passed
@effigies effigies deleted the rf/split_surface_workflows branch August 28, 2023 17:15
@effigies effigies added the next label Oct 11, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants