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FEAT: Option to normalize CSF prior to template registration #419

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merged 6 commits into from
Dec 13, 2024

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@mgxd mgxd commented Dec 12, 2024

Adds new parser option --norm-csf, which will normalize the voxels within the CSF mask (max of either the median value or original value) prior to template registration.

This is experimental and should only be used carefully.

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codecov bot commented Dec 12, 2024

Codecov Report

Attention: Patch coverage is 85.89744% with 11 lines in your changes missing coverage. Please review.

Project coverage is 56.23%. Comparing base (9476035) to head (8981735).
Report is 7 commits behind head on master.

Files with missing lines Patch % Lines
nibabies/workflows/anatomical/fit.py 23.07% 8 Missing and 2 partials ⚠️
nibabies/workflows/anatomical/preproc.py 96.15% 0 Missing and 1 partial ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##           master     #419      +/-   ##
==========================================
+ Coverage   55.88%   56.23%   +0.35%     
==========================================
  Files          68       69       +1     
  Lines        6476     6553      +77     
  Branches      809      816       +7     
==========================================
+ Hits         3619     3685      +66     
- Misses       2658     2666       +8     
- Partials      199      202       +3     

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@mgxd mgxd marked this pull request as ready for review December 12, 2024 23:37
@mgxd mgxd merged commit b9efa6f into nipreps:master Dec 13, 2024
16 checks passed
@mgxd mgxd deleted the enh/spatial-norm branch December 13, 2024 00:19
@mgxd mgxd restored the enh/spatial-norm branch December 13, 2024 02:01
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