Fixing freesurfer-abcd brain masking

[birajstha]

Fixes

Fixes #2269 by @birajstha

Description

Freesurfer-ABCD brain masking strategy is improved to create a mask that resembles one created in original DCAN script.
This produces a better masked brain without residual skull and cropping.

Technical details

Removed pipeline-fs_xfm resource. Then modified the mask generation nodeblock to use desc-restore_T1w instead of desc-preproc_T1w as per the original script.

Tests

Tested with few oblique and non-oblique T1w s. Everything works perfect.
With oblique T1w, need to enable [warp] instead of [refit] as below.

anatomical_preproc:
  run: On
  deoblique: [warp]

Screenshots

Before

After

Checklist

• My pull request has a descriptive title (not a vague title like Update index.md).
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• My code follows the established code style of the repository.
• I added tests for the changes I made (if applicable).
• I updated the changelog.
• I added or updated documentation (if applicable).
• I tried running the project locally and verified that there are no visible errors.

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[codecov]

Codecov Report

❌ Patch coverage is 66.66667% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 33.9%. Comparing base (1d39110) to head (54bab39).
⚠️ Report is 9 commits behind head on develop.

Files with missing lines	Patch %	Lines
CPAC/anat_preproc/utils.py	0.0%	2 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##           develop   #2268   +/-   ##
=======================================
  Coverage     33.9%   33.9%           
=======================================
  Files          233     233           
  Lines        26354   26344   -10     
  Branches      4135    4134    -1     
=======================================
- Hits          8941    8940    -1     
+ Misses       16684   16675    -9     
  Partials       729     729           

Files with missing lines	Coverage Δ
CPAC/anat_preproc/anat_preproc.py	39.4% <100.0%> (+0.4%)	⬆️
CPAC/pipeline/engine.py	55.0% <ø> (-0.1%)	⬇️
CPAC/anat_preproc/utils.py	19.8% <0.0%> (ø)

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[shnizzedy]

Is this related to #2248 / #2256?

[birajstha]

Is this related to #2248 / #2256?

Nope, It just refines the already existing desc-preproc_T1w which had skull in it.