ENH: SPM NewSegment multi-channel segmentation

[jhuguetn]

Summary

SPM Segment supports including additional images as alternative data channels to help improving the segmentation results of the first/main channel images by providing complementary information (e.g. multimodal images) to the segmentation procedure.
However, this feature is not (yet) supported by nipype NewSegment interface (see nipype.interfaces.spm.preprocess).

This PR proposes a modification to the existing NewSegment interface to support using several data channels for SPM's segmentation procedure.

As suggested in the contribution guide, changes have been successfully tested via pytest with the following results:

 2734 passed, 230 skipped, 7 xfailed, 15 warnings in 183.65s (0:03:03) 

Related issue: #2342 (comment)

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

• refactored NewSegmentInputSpec() class to support a list of channels
• updated docstring-based examples and new T2.nii file added to testing data
• updated tests (see test_NewSegment_inputs()

Acknowledgment

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

[satra]

@jhuguetn - thank you for this.

we should maintain backwards compatibility for existing scripts/workflows using the current interface. this can be done by making the original inputs mutually exclusive with the new one. (and still supporting the original functionality).

[jhuguetn]

Thanks @satra for considering this proposal.

I see two possible alternatives,

1. support both original and new inputs in a mutually exclusive way as you suggest, however that -in my opinion- makes the code a bit messier/longer than it should originally be.
2. create a brand new Interface (e.g. MultiChannelNewSegment) with the changes proposed.

What you think?

[satra]

create a brand new Interface (e.g. MultiChannelNewSegment) with the changes proposed.

i would be fine with a new interface here.

[jhuguetn]

I've just included new changes to my original PR proposal. Now it creates a brand new Interface called MultiChannelNewSegment which supports defining multiple channels when running SPM Segment procedure.

[codecov]

Codecov Report

Merging #3162 into master will not change coverage by %.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master    #3162   +/-   ##
=======================================
  Coverage   67.61%   67.61%           
=======================================
  Files         299      299           
  Lines       39494    39494           
  Branches     5219     5219           
=======================================
  Hits        26703    26703           
  Misses      12083    12083           
  Partials      708      708           

Flag	Coverage Δ
#smoketests	53.05% <0.00%> (ø)	⬆️
#unittests	64.86% <0.00%> (ø)	⬆️

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[effigies]

Is this ready to go?

[jhuguetn]

Hi @effigies, it is from my side. Do you plan to include it in the 1.5.0 release?

[effigies]

Sounds good. Yes, we'll include it in 1.5.0. That's currently stalled as we try to find time to debug failing tutorials...

[jhuguetn]

Great, thanks