ENH: Updates interface for FSL's eddy command

[josephmje]

Summary

Adds a new interface for Mrtrix3's mrresize command and updates inputs and outputs for FSL's eddy command

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

• MRResize added
• Mrtrix3 tests updated after MRTrix3BaseInputSpec modified to take either grad_file or grad_fsl
• Eddy
  • field now requires a file instead of string
  • add additional options to inputspec for outlier replacement, intra-volume motion correction and susceptibility-by-movement correction
  • add additional output files to outputspec (EddyQuad fails to provide outlier metrics if outlier maps are missing)

Acknowledgment

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

[josephmje]

TO DO

For mrresize, voxel_size and scale_factor are able to accept a single number if rescaling to isotropic voxels. I'm not sure how to incorporate this into nipype.

For eddy the outputs change depending on the FSL version used. How should this be accounted for?

[codecov]

Codecov Report

Merging #3008 into master will decrease coverage by 0.52%.
The diff coverage is 66.15%.

@@            Coverage Diff             @@
##           master    #3008      +/-   ##
==========================================
- Coverage    67.5%   66.97%   -0.53%     
==========================================
  Files         344      343       -1     
  Lines       44039    44105      +66     
  Branches     5554     5560       +6     
==========================================
- Hits        29727    29541     -186     
- Misses      13560    13806     +246     
- Partials      752      758       +6

Flag	Coverage Δ
#smoketests	50.4% <57.69%> (-0.01%)	⬇️
#unittests	64.16% <66.15%> (-0.79%)	⬇️

Impacted Files	Coverage Δ
nipype/interfaces/mrtrix3/__init__.py	100% <ø> (ø)	⬆️
nipype/interfaces/mrtrix3/utils.py	83.7% <100%> (+1.28%)	⬆️
nipype/interfaces/fsl/epi.py	62.23% <57.69%> (-1%)	⬇️
nipype/interfaces/nilearn.py	40% <0%> (-56.67%)	⬇️
nipype/testing/fixtures.py	77.33% <0%> (-21.34%)	⬇️
nipype/interfaces/freesurfer/base.py	61.01% <0%> (-19.5%)	⬇️
nipype/workflows/smri/freesurfer/autorecon2.py	65.9% <0%> (-9.2%)	⬇️
nipype/workflows/smri/freesurfer/ba_maps.py	91.66% <0%> (-8.34%)	⬇️
nipype/workflows/smri/freesurfer/recon.py	66.66% <0%> (-7.81%)	⬇️
nipype/workflows/smri/freesurfer/autorecon3.py	68.4% <0%> (-6.95%)	⬇️
... and 12 more

---

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[codecov]

Codecov Report

Merging #3008 into master will increase coverage by 0.69%.
The diff coverage is 66.66%.

@@            Coverage Diff             @@
##           master    #3008      +/-   ##
==========================================
+ Coverage    67.5%   68.19%   +0.69%     
==========================================
  Files         344      344              
  Lines       44039    46004    +1965     
  Branches     5554     6199     +645     
==========================================
+ Hits        29727    31374    +1647     
- Misses      13560    13827     +267     
- Partials      752      803      +51

Flag	Coverage Δ
#smoketests	50.4% <58.49%> (-0.01%)	⬇️
#unittests	65.88% <66.66%> (+0.93%)	⬆️

Impacted Files	Coverage Δ
nipype/interfaces/mrtrix3/__init__.py	100% <ø> (ø)	⬆️
nipype/interfaces/mrtrix3/utils.py	83.7% <100%> (+1.28%)	⬆️
nipype/interfaces/fsl/epi.py	62.23% <58.49%> (-1%)	⬇️
nipype/info.py	90.09% <0%> (-4.27%)	⬇️
nipype/utils/filemanip.py	78.85% <0%> (-0.87%)	⬇️
nipype/interfaces/afni/preprocess.py	81.59% <0%> (-0.43%)	⬇️
nipype/interfaces/io.py	54.94% <0%> (ø)	⬆️
nipype/interfaces/freesurfer/preprocess.py	66.11% <0%> (ø)	⬆️
nipype/interfaces/dynamic_slicer.py	17.47% <0%> (ø)	⬆️
nipype/interfaces/nipy/preprocess.py	45.79% <0%> (ø)	⬆️
... and 6 more

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[oesteban]

Hi @josephmje sorry for duplicating requests, hopefully git is making it easy for you.

Could you split this PR in two? One for the changes in eddy and the other for the new interface? That will make review and investigation of regressions much easier.