ENH: Add new flags to MRtrix/preprocess.py (DWI2Tensor, MRtransform)

[alexandreroutier]

Summary

This PR adds some new flags to MRtrix commands.

Please let me known if anything is missing.

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

• Add -mask flag for dwi2tensor command
• Add -linear flag for mrtransform command

Acknowledgment

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

[codecov]

Codecov Report

Merging #3365 (a1d56ab) into master (7080ef9) will decrease coverage by 0.27%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master    #3365      +/-   ##
==========================================
- Coverage   65.11%   64.83%   -0.28%     
==========================================
  Files         307      307              
  Lines       40373    40366       -7     
  Branches     5326     5326              
==========================================
- Hits        26288    26171     -117     
- Misses      13014    13103      +89     
- Partials     1071     1092      +21     

Flag	Coverage Δ
unittests	64.83% <100.00%> (-0.01%)	⬇️

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

Impacted Files	Coverage Δ
nipype/interfaces/mrtrix/preprocess.py	64.10% <100.00%> (+0.23%)	⬆️
nipype/interfaces/r.py	45.83% <0.00%> (-37.51%)	⬇️
nipype/interfaces/nipy/base.py	80.00% <0.00%> (-20.00%)	⬇️
nipype/testing/utils.py	70.90% <0.00%> (-18.19%)	⬇️
nipype/workflows/__init__.py	88.23% <0.00%> (-11.77%)	⬇️
nipype/interfaces/freesurfer/base.py	65.32% <0.00%> (-11.30%)	⬇️
nipype/info.py	78.12% <0.00%> (-9.38%)	⬇️
nipype/__init__.py	46.80% <0.00%> (-6.39%)	⬇️
nipype/pkg_info.py	75.00% <0.00%> (-6.25%)	⬇️
nipype/interfaces/fsl/base.py	77.65% <0.00%> (-3.20%)	⬇️
... and 28 more

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[alexandreroutier]

Hello,

I was wondering if anybody had the chance to look at this PR? :)

I would like to create another PR with some extra flags for other tools and I would like to be sure that I followed correctly the guidelines.

Best,
Alexandre

[effigies]

LGTM. Apologies for the slow response.

[effigies]

I'm confused as to why all of these are position=1, but I don't think it can hurt for another one to be.