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nipreps / sdcflows

Susceptibility Distortion Correction (SDC) workflows for EPI MR schemes
https://www.nipreps.org/sdcflows
Apache License 2.0
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Repair 3dQwarp workflow #454

Open psadil opened 4 months ago

psadil commented 4 months ago

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[bot] commented 4 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

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

Additional details and impacted files ```diff @@ 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 commented 1 month ago

@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 commented 1 month ago

@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 commented 1 month ago

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