RF: dcm2niix interface

[mgxd]

Summary

This PR fixes the convoluted approach used for gathering dcm2niix outputs.

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

• Checks the output prefix for possible suffixes, instead of assuming outputs based off stdout switches.

Acknowledgment

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

[mgxd]

@neurolabusc not that we were catching it before, but am I missing any output formats?

[neurolabusc]

The recent release (v1.0.20190410) includes ".nrrd" (-e y -z n) and ". nhdr"/".raw.gz" (-e y -z y). This was added for the Slicer team and so you may or may not want to support NRRD format export. There is also a deprecated text output ".txt" (-t y) which predates BIDS.

[codecov-io]

Codecov Report

Merging #2936 into master will decrease coverage by 3.31%.
The diff coverage is 18.18%.

@@            Coverage Diff            @@
##           master   #2936      +/-   ##
=========================================
- Coverage   67.51%   64.2%   -3.32%     
=========================================
  Files         344     342       -2     
  Lines       44094   44030      -64     
  Branches     5556    5552       -4     
=========================================
- Hits        29772   28270    -1502     
- Misses      13576   14642    +1066     
- Partials      746    1118     +372

Flag	Coverage Δ
#smoketests	?
#unittests	64.2% <18.18%> (-0.78%)	⬇️

Impacted Files	Coverage Δ
nipype/info.py	88.73% <ø> (-5.64%)	⬇️
nipype/interfaces/dcm2nii.py	50.23% <18.18%> (+2.1%)	⬆️
nipype/interfaces/nilearn.py	40% <0%> (-56.67%)	⬇️
nipype/utils/spm_docs.py	25.92% <0%> (-44.45%)	⬇️
nipype/interfaces/freesurfer/base.py	50% <0%> (-30.51%)	⬇️
nipype/utils/logger.py	59.7% <0%> (-29.86%)	⬇️
nipype/algorithms/rapidart.py	35% <0%> (-29.42%)	⬇️
nipype/interfaces/spm/base.py	57.94% <0%> (-29.14%)	⬇️
nipype/utils/provenance.py	55.73% <0%> (-28.35%)	⬇️
nipype/interfaces/fsl/model.py	55.26% <0%> (-25.35%)	⬇️
... and 41 more

---

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[effigies]

@mgxd Any chance of a test? This is pretty tough to evaluate without seeing the code paths exercised.

[mgxd]

we already have a regression test

nipype/nipype/interfaces/tests/test_extra_dcm2nii.py

Line 27 in 704b97d

def test_dcm2niix_dwi(tmpdir):

though I'm not sure it's actually being hit in the current testing. I'll fix this up for the next release

[oesteban]

CircleCI (both py36 and py27):

[gw1] [ 87%] SKIPPED ../src/nipype/interfaces/tests/test_extra_dcm2nii.py::test_dcm2niix_dwi 

Travis (py37):

interfaces/tests/test_extra_dcm2nii.py::test_dcm2niix_dwi 
[gw1] [ 87%] SKIPPED interfaces/tests/test_extra_dcm2nii.py::test_dcm2niix_dwi 

[mgxd]

looks like we never got around to adding it to testing in #2498 - looks like the original problem (#2498 (comment)) was fixed so I'll add that change here.

[effigies]

@mgxd I think you need to merge/rebase master to fix the Docker builds.

[effigies]

@mgxd What's the status of this one?

[mgxd]

ready for review!

[effigies]

Looks reasonable, and the tests are passing. Codecov is flaking out, so unclear what the coverage is. :-/