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@mgxd mgxd commented Jan 23, 2025

For FreeSurfer / InfantFS, we have passed in the anatomical template - not the preprocessed anatomical - as the input. However, MCRIBS is different, since we are bypassing some of the early preprocessing in the pipeline (conforming, n4, etc). However, due to the intensity clipping, it was reported that the white matter white surface may have been hitting the upper bounds, potentially leading to a decrease in cortical thickness.

This PR restructures the MCRIBS pipeline in the following ways:

  • Pass in the anatomical template T2w (a single volume that has gone through DenoiseImage)
  • Run N4BiasCorrection prior to MCRIBS injection, making sure to pass in a mask to enable rescale_intensities to actually run (it is disabled without a mask present).

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codecov bot commented Jan 23, 2025

Codecov Report

Attention: Patch coverage is 78.33333% with 13 lines in your changes missing coverage. Please review.

Project coverage is 56.47%. Comparing base (ffc69a8) to head (c2cd283).
Report is 28 commits behind head on master.

Files with missing lines Patch % Lines
nibabies/interfaces/mcribs.py 56.25% 4 Missing and 3 partials ⚠️
nibabies/workflows/anatomical/surfaces.py 25.00% 6 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##           master     #436      +/-   ##
==========================================
+ Coverage   55.89%   56.47%   +0.57%     
==========================================
  Files          69       70       +1     
  Lines        6689     6715      +26     
  Branches      832      828       -4     
==========================================
+ Hits         3739     3792      +53     
+ Misses       2745     2714      -31     
- Partials      205      209       +4     

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@mgxd mgxd marked this pull request as ready for review January 24, 2025 04:45
@mgxd mgxd merged commit a95c8bd into nipreps:master Jan 24, 2025
16 checks passed
@mgxd mgxd deleted the fix/mcribs-clipping branch January 24, 2025 05:20
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