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ENH: Add ConstrainedSphericalDeconvolution interface to replace EstimateFOD for MRtrix3's dwi2fod #3176

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Merged
merged 10 commits into from
Feb 24, 2020

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Summary

This supersedes #3004 by creating the fixed interface as a new interface, avoiding the possibility of breaking existing workflows using msmt_csd. The new interface retains all of the capabilities of the original, so it isn't separating out msmt_csd and csd.

Fixes #2822.

Closes #3004.

@matteomancini WDYT?

List of changes proposed in this PR (pull-request)

Acknowledgment

  • (Mandatory) I acknowledge that this contribution will be available under the Apache 2 license.

@effigies effigies added this to the 1.5.0 milestone Feb 23, 2020
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codecov bot commented Feb 24, 2020

Codecov Report

Merging #3176 into master will decrease coverage by 2.34%.
The diff coverage is 59.89%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master    #3176      +/-   ##
==========================================
- Coverage   67.22%   64.87%   -2.35%     
==========================================
  Files         343      299      -44     
  Lines       44823    39499    -5324     
  Branches     5609     5219     -390     
==========================================
- Hits        30131    25624    -4507     
+ Misses      13936    12826    -1110     
- Partials      756     1049     +293
Flag Coverage Δ
#smoketests ?
#unittests 64.87% <59.89%> (+0.56%) ⬆️
Impacted Files Coverage Δ
nipype/interfaces/afni/__init__.py 100% <ø> (ø) ⬆️
nipype/interfaces/ants/base.py 60% <ø> (-1.71%) ⬇️
nipype/interfaces/ants/__init__.py 100% <ø> (ø) ⬆️
nipype/interfaces/afni/model.py 86.93% <ø> (+4.97%) ⬆️
nipype/interfaces/base/core.py 83.85% <ø> (-3.14%) ⬇️
nipype/info.py 92.3% <ø> (+6.89%) ⬆️
nipype/interfaces/afni/preprocess.py 82.02% <ø> (ø) ⬆️
nipype/algorithms/modelgen.py 59.61% <ø> (-8.49%) ⬇️
nipype/interfaces/afni/svm.py 97.61% <ø> (-0.06%) ⬇️
nipype/interfaces/ants/segmentation.py 74.39% <ø> (-3.83%) ⬇️
... and 354 more

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@effigies effigies merged commit 9049156 into nipy:master Feb 24, 2020
@effigies effigies deleted the mrtrix3-usedefault-issue branch February 24, 2020 13:29
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MRtrix 3.0 dwi2fod single output error
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