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ENH: Add a new Binarize interface using nibabel #402

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merged 2 commits into from
Sep 25, 2019

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This PR includes a very simplistic binarization interface using nibabel
to replace FSL's Threshold and others in the context of
nipreps/mriqc#803.

The PR also updates AFNI's skull-stripping workflow to use it (removing
the dependency on FSL).

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codecov bot commented Sep 24, 2019

Codecov Report

Merging #402 into master will decrease coverage by 3.74%.
The diff coverage is 96.96%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #402      +/-   ##
==========================================
- Coverage   56.82%   53.08%   -3.75%     
==========================================
  Files          44       45       +1     
  Lines        4915     4945      +30     
  Branches      676      676              
==========================================
- Hits         2793     2625     -168     
- Misses       2020     2201     +181     
- Partials      102      119      +17
Flag Coverage Δ
#masks ?
Impacted Files Coverage Δ
niworkflows/interfaces/nibabel.py 100% <100%> (ø)
niworkflows/anat/skullstrip.py 30% <80%> (+7.77%) ⬆️
niworkflows/func/util.py 24.65% <0%> (-53.43%) ⬇️
niworkflows/interfaces/fixes.py 41.17% <0%> (-45.1%) ⬇️
niworkflows/engine/workflows.py 26.31% <0%> (-15.79%) ⬇️
niworkflows/interfaces/registration.py 51.93% <0%> (-10.31%) ⬇️
niworkflows/interfaces/utils.py 38.24% <0%> (-9.98%) ⬇️
niworkflows/viz/utils.py 73.31% <0%> (-8.04%) ⬇️
niworkflows/interfaces/ants.py 63.74% <0%> (-7.02%) ⬇️
niworkflows/interfaces/images.py 45.37% <0%> (-5.61%) ⬇️
... and 2 more

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This PR includes a very simplistic binarization interface using nibabel
to replace FSL's ``Threshold`` and others in the context of
nipreps/mriqc#803.

The PR also updates AFNI's skull-stripping workflow to use it (removing
the dependency on FSL).
@oesteban oesteban merged commit c4ceb2e into nipreps:master Sep 25, 2019
@oesteban oesteban deleted the enh/skullstrip-wf-no-fsl branch September 25, 2019 15:34
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