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

ENH: insert gradunwarp in bold workflow #3064

Draft
wants to merge 3 commits into
base: master
Choose a base branch
from

Conversation

bpinsard
Copy link
Collaborator

@bpinsard bpinsard commented Aug 2, 2023

Changes proposed in this pull request

The goal of that PR is to integrate gradient unwarping to the BOLD preprocessing workflows (and to anat workflows through update of smriprep).
See #1550.
Relies on an updated version of the gradunwarp https://github.com/bpinsard/gradunwarp/tree/fix/mem_leaks.

Unwarping is applied on the initial ref (to use a single volume, it mainly takes into account the matrix size and affine rather than image content).
Warp-field is then passed to the bold_bold, bold_T1w, bold_std one-step resamplings.

Still a WIP: inserting gradient unwarping seems more challenging for BOLD than for anatomical images. I need to check how that integrates with sdcflows.

Necessary PRs:
nipreps/smriprep#355
nipreps/niworkflows#819

Documentation that should be reviewed

TODO: document the option to pass a gradient coeff file.

@codecov
Copy link

codecov bot commented Aug 2, 2023

Codecov Report

Patch coverage: 36.36% and project coverage change: -0.14% ⚠️

Comparison is base (e1c4bac) 49.29% compared to head (71845e5) 49.15%.
Report is 8 commits behind head on master.

Additional details and impacted files
@@            Coverage Diff             @@
##           master    #3064      +/-   ##
==========================================
- Coverage   49.29%   49.15%   -0.14%     
==========================================
  Files          46       46              
  Lines        3593     3609      +16     
==========================================
+ Hits         1771     1774       +3     
- Misses       1822     1835      +13     
Files Changed Coverage Δ
fmriprep/workflows/base.py 10.00% <ø> (-0.26%) ⬇️
fmriprep/workflows/bold/base.py 19.84% <0.00%> (-0.71%) ⬇️
fmriprep/workflows/bold/registration.py 10.63% <ø> (ø)
fmriprep/workflows/bold/resampling.py 11.20% <ø> (ø)
fmriprep/cli/parser.py 82.74% <100.00%> (+0.07%) ⬆️
fmriprep/config.py 82.08% <100.00%> (+0.08%) ⬆️

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

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.

1 participant