fix: Use consistent skull-stripping pre- and post- SDC

[effigies]

Overall seems safe, the skullstrip_wf is extracted from the enhance_and_skullstrip_wf, skipping reruns.

Running locally now. We'll see if does address #3406.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 72.33%. Comparing base (910c232) to head (3833723).

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #3415   +/-   ##
=======================================
  Coverage   72.32%   72.33%           
=======================================
  Files          57       57           
  Lines        4268     4269    +1     
  Branches      545      545           
=======================================
+ Hits         3087     3088    +1     
  Misses       1065     1065           
  Partials      116      116           

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[mgxd]

Curious if you think sdcflows' brainextraction workflow could be an alternative

[effigies]

That's what this replaces.

[mgxd]

Ah, I missed that in the connections - perhaps we should change this directly in sdcflows then, to keep it consistent across nibabies/nirodents/etc

[effigies]

I was doing this out here because I didn't want to change that workflow and risk impacting use cases where that wishes well. Really, I think I should just go ahead and use the resampler for unwarping and get rid of the unwarp workflow altogether.