Repair 3dQwarp workflow #454
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## master #454 +/- ##
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+ Coverage 76.40% 76.46% +0.06%
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Files 32 32
Lines 2814 2830 +16
Branches 376 378 +2
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+ Hits 2150 2164 +14
- Misses 597 598 +1
- Partials 67 68 +1 ☔ View full report in Codecov by Sentry. |
| @@ -107,7 +107,7 @@ jobs: | |||
| pip install datalad datalad-osf | |||
| - name: Install fsl | |||
| run: | | |||
| conda install fsl-fugue fsl-topup | |||
| conda install fsl-fugue fsl-topup fsl-bet2 | |||
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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
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@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. |
Co-authored-by: Chris Markiewicz <effigies@gmail.com>
Co-authored-by: Chris Markiewicz <effigies@gmail.com>
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uh oh, seems like I may have messed things up with that force push? |
Closes #441
This repairs the 3dQwarp workflow. As before,
3dQwarpis 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_refis in general not what one would get by reconstructing the fieldmap fromfmap_coeffand unwarping the reference image inin_data.