Repair 3dQwarp workflow

[psadil]

Closes #441

This repairs the 3dQwarp workflow. As before, 3dQwarp is used to generate a displacement field and correct the reference image.

As per discussion with @effigies during Brainhack 2024, the repairs were done so that the workflow now matches the topup workflow in terms of outputs and inputs. The repaired workflow now also returns an estimated fieldmap and the coefficients for a bspline fit to the fieldmap. Note that this means that the unwarped image returned in fmap_ref is in general not what one would get by reconstructing the fieldmap from fmap_coeff and unwarping the reference image in in_data.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 76.46%. Comparing base (08e198f) to head (dd5f251).

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #454      +/-   ##
==========================================
+ Coverage   76.40%   76.46%   +0.06%     
==========================================
  Files          32       32              
  Lines        2814     2830      +16     
  Branches      376      378       +2     
==========================================
+ Hits         2150     2164      +14     
- Misses        597      598       +1     
- Partials       67       68       +1     

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[effigies]

I'm sorry, I had this collection of review comments queued up but didn't finish the review.

[effigies]

Are you using BET anywhere?

[psadil]

The pipeline still uses init_enhance_and_skullstrip_bold_wf, which depends on BET: https://github.com/nipreps/niworkflows/blob/1f9a0cf6d5b74e1aadf544841a0adaee19cc63b0/niworkflows/func/util.py#L391-L393

[effigies]

@psadil Sorry about the long delay. I'm marking this as draft just so I know that it's waiting on you. Please feel free to mark as ready again whenever you get back to this.

[psadil]

@psadil Sorry about the long delay. I'm marking this as draft just so I know that it's waiting on you. Please feel free to mark as ready again whenever you get back to this.

Sorry it's taking me so long to respond to your review! I'm aiming to be able to get to this by the end of next week.

[psadil]

uh oh, seems like I may have messed things up with that force push?