ENH: added Apply VDM functionality to FieldMap SPM interface

[fabioboh]

This pull request substitutes an old one:

ENH/WIP: added Apply VDM functionality to FieldMap SPM interface #2879

I only adapted what was done there to the present nipype version.

This allows to apply a VDM directly to functional images to correct for inhomogeneities of the magnetic field. At the moment this could be performed by the realign&unwarp spm interface, which also corrects for artefacts derived by interactions between subject movement and inhomogeneities of the magnetic field. However, if one wishes to perform slice timing and realign correction in one step, using the SpaceTimeRealigner nipy module, this requires the field map correction to be executed independently from the realignment.

This was also a TODO item for issue:
[ENH/WIP] Add SPM Fieldmap Tool wrapper #1905

Acknowledgment

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

[codecov]

Codecov Report

Merging #3394 (4575810) into master (bb3c312) will decrease coverage by 0.01%.
The diff coverage is 42.55%.

@@            Coverage Diff             @@
##           master    #3394      +/-   ##
==========================================
- Coverage   65.21%   65.20%   -0.02%     
==========================================
  Files         307      307              
  Lines       40413    40457      +44     
  Branches     5344     5350       +6     
==========================================
+ Hits        26356    26379      +23     
- Misses      12982    13003      +21     
  Partials     1075     1075              

Flag	Coverage Δ
unittests	64.92% <42.55%> (-0.03%)	⬇️

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Impacted Files	Coverage Δ
nipype/interfaces/spm/__init__.py	100.00% <ø> (ø)
nipype/sphinxext/plot_workflow.py	14.95% <ø> (ø)
nipype/interfaces/spm/preprocess.py	50.23% <42.55%> (-0.21%)	⬇️
nipype/info.py	92.18% <0.00%> (+4.68%)	⬆️

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[fabioboh]

Since this is an old, tiny pull request and it already fell into oblivion once, since it seems to me that all tests are passed, I would be grateful if it could be considered quickly.

[effigies]

It looks like many unrelated files got changed. You may need to update black in your environment.

[fabioboh]

Sorry about that, I do not know how it happened but I am trying to revert the changes. Il giorno mar 19 ott 2021 alle ore 17:14 Chris Markiewicz < ***@***.***> ha scritto:

…

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[fabioboh]

So after reverting some changes and rerunning the tests I think my commit is ready to be accepted.

[effigies]

Had a quick look, and I think we need to make this a new interface, not an update to the existing one. This changes its behavior too much, disabling mandatory inputs and making new inputs mandatory. You could do some fancy things with making inputs conditionally mandatory, but it would probably be simpler to just make it an ApplyVDM interface.

[fabioboh]

I implemented the nipype class as an interface to the FieldMap SPM toolbox, which performs
both the calculation of the VDM and its application to MRI images because I thought this would be more intuitive to the end user. However, what would you suggest precisely:
1- have two interfaces, CalculateVDM and ApplyVDM. (but people around the world will have errors when updating to the new version)

2- have two interfaces, FieldMap and ApplyVDM. Leave FieldMap as it was (except removing the jobtype argument) and add ApplyVDM

?

[fabioboh]

This commit implements solution 2 above.

[effigies]

Overall looks good. Thanks for pushing ahead with option 2, that would have been my suggestion.

[fabioboh]

I have implemented the suggestions above and edited the init file, so from my side all is ready for acceptance.

[effigies]

Looks good! Thanks for your patience.