Add a --fs-reuse-base option to reuse existing freesurfer outputs from a longitudinal pipeline

[bpinsard]

For now, it is not possible to run f/sMRIPrep with existing longitudinal freesurfer output.
If I understood correctly, the current surface generation workflow:

• runs autorecon1 without skullstripping
• injects a custom (and more robust) brainmask.mgz
• resume to autorecon2/3 without any other tweaks.

Currently, when reusing existing freesurfer outputs, it is not clear to me (maybe docs should be more informative) if the injected brainmask always triggers a rerun of autorecon2/3, from the nipype interface code, I would say no. So it seems only the brainmask.mgz is overwritten, but existing surfaces are directly grabbed.

The simpler way I found to input the base/template recon-all is to use the FreeSurferSource and reconnect everything appropriately. Does that make sense, or I missed something (like registering the sMRIPrep generated average to the freesurfer one).

[pep8speaks]

Hello @bpinsard! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file smriprep/workflows/surfaces.py:

Line 247:80: E501 line too long (88 > 79 characters)
Line 249:80: E501 line too long (82 > 79 characters)
Line 250:80: E501 line too long (87 > 79 characters)
Line 261:80: E501 line too long (89 > 79 characters)
Line 263:80: E501 line too long (81 > 79 characters)

Comment last updated at 2023-10-05 17:47:57 UTC

[codecov]

Codecov Report

Attention: 12 lines in your changes are missing coverage. Please review.

Comparison is base (6995f33) 58.65% compared to head (ef41799) 57.56%.
Report is 1 commits behind head on next.

Additional details and impacted files

@@            Coverage Diff             @@
##             next     #371      +/-   ##
==========================================
- Coverage   58.65%   57.56%   -1.09%     
==========================================
  Files          26       26              
  Lines        1872     1909      +37     
  Branches      238      245       +7     
==========================================
+ Hits         1098     1099       +1     
- Misses        717      752      +35     
- Partials       57       58       +1     

Flag	Coverage Δ
ds005	∅ <ø> (∅)
ds054	46.51% <7.69%> (-0.28%)	⬇️
pytest	36.60% <0.00%> (-0.26%)	⬇️

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Files	Coverage Δ
smriprep/cli/run.py	66.80% <100.00%> (-7.08%)	⬇️
smriprep/workflows/anatomical.py	38.85% <ø> (ø)
smriprep/workflows/base.py	75.00% <ø> (ø)
smriprep/workflows/surfaces.py	21.36% <0.00%> (-1.16%)	⬇️

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[bpinsard]

I am not super familiar with the circleci-codecov setup. Should I add an upload of the coverage.xml with a different tag after running with the new option to avoid the errors in the present PR? @effigies
Thanks for your feedback.

[effigies]

Sorry, this got closed due to the merge. I would not worry about codecov at the moment. I'm not sure what you mean about failures, unless you mean the red X's. It looks like it's getting submitted, it's just hard to get good coverage from a nipype workflow.

[bpinsard]

No problem. Do you want me to reopen with base master? Or this change has been rejected?

[effigies]

Yes, please reopen with master. It just got closed because I deleted the branch.