ENH: Include realignment matrices in TOPUP outputs

[mwaskom]

FSL's topup binary has two undocumented options: --dfout and --rbmout (see here). The Nipype interface exposes the former but not the latter, which writes out transformation matrices that encode the rigid realignment from each frame to the first frame of the input file. These matrices are necessary to properly apply the warpfields to the input images. This PR extends the currently existing logic for --dfout to --rbmout.

[codecov-io]

Codecov Report

Merging #2084 into master will decrease coverage by <.01%.
The diff coverage is 66.66%.

@@            Coverage Diff             @@
##           master    #2084      +/-   ##
==========================================
- Coverage   72.13%   72.13%   -0.01%     
==========================================
  Files        1138     1138              
  Lines       57268    57271       +3     
  Branches     8206     8207       +1     
==========================================
  Hits        41313    41313              
- Misses      14663    14665       +2     
- Partials     1292     1293       +1

Flag	Coverage Δ
#smoketests	72.13% <66.66%> (-0.01%)	⬇️
#unittests	69.75% <66.66%> (-0.01%)	⬇️

Impacted Files	Coverage Δ
nipype/interfaces/fsl/tests/test_auto_TOPUP.py	85.71% <ø> (ø)	⬆️
nipype/interfaces/fsl/epi.py	65.67% <66.66%> (ø)	⬆️
nipype/interfaces/base.py	83.62% <0%> (-0.19%)	⬇️

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[effigies]

Looks reasonable. Assume you've actually used it and the file names work out correctly?

[mwaskom]

Yep I have a workflow that needed this functionality and things look good:

_0x14aebc8e5c8129a8e4e41d37ffd1cedc.json  se_func_sess01_encfile.txt
command.txt                               se_func_sess01_field.nii.gz
_inputs.pklz                              se_func_sess01_topup.log
jac_01.nii.gz                             warpfield_01.nii.gz
jac_02.nii.gz                             warpfield_02.nii.gz
jac_03.nii.gz                             warpfield_03.nii.gz
jac_04.nii.gz                             warpfield_04.nii.gz
jac_05.nii.gz                             warpfield_05.nii.gz
jac_06.nii.gz                             warpfield_06.nii.gz
_node.pklz                                xfm_01.mat
_report/                                  xfm_02.mat
result_estimate_distortions.pklz          xfm_03.mat
se_func_sess01_base_fieldcoef.nii.gz      xfm_04.mat
se_func_sess01_base_movpar.txt            xfm_05.mat
se_func_sess01_corrected.nii.gz           xfm_06.mat