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ENH: Use 4+ empty edge planes to detect skull-stripped images #233

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effigies
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@effigies effigies commented Nov 9, 2020

This proposes a relaxed heuristic for detecting skull-stripped images, detecting each empty edge plane, rather than all edge planes at once. If four planes are empty, we consider it skull-stripped.

This accounts for acquisitions where the brain is cut off on one or two edges.

An alternative we could look at is the actual edges, rather than edge planes. These should be pretty reliably 0 if the image is skullstripped.

Ref: #232 (comment)

@effigies effigies force-pushed the enh/skull_stripping_heuristic branch from eea65e7 to e220db5 Compare November 9, 2020 13:37
@effigies effigies changed the base branch from master to maint/0.7.x November 9, 2020 13:38
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codecov bot commented Nov 9, 2020

Codecov Report

Merging #233 (e220db5) into maint/0.7.x (904c027) will decrease coverage by 0.74%.
The diff coverage is 46.15%.

Impacted file tree graph

@@               Coverage Diff               @@
##           maint/0.7.x     #233      +/-   ##
===============================================
- Coverage        71.05%   70.31%   -0.75%     
===============================================
  Files               16       18       +2     
  Lines             1071     1088      +17     
  Branches           155      159       +4     
===============================================
+ Hits               761      765       +4     
- Misses             258      270      +12     
- Partials            52       53       +1     
Flag Coverage Δ
ds005 59.77% <26.92%> (-1.05%) ⬇️
ds054 49.72% <26.92%> (-0.89%) ⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
smriprep/cli/check_skullstrip.py 27.77% <27.77%> (ø)
smriprep/workflows/anatomical.py 67.12% <50.00%> (-1.51%) ⬇️
smriprep/utils/images.py 100.00% <100.00%> (ø)

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@effigies effigies closed this Jul 14, 2022
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