ENH: Merge T2w images and coregister to T1w template

[effigies]

The approach taken here is to merge the T2w images in exactly the same way as T1w images (N4 -> mri_robust_template) and then bbregister. This is the approach taken by recon-all, and seems the safest way to do this without running brain extraction first. Therefore this is only available if FreeSurfer is run.

Closes #69.

We could probably throw in #13 at the same time and pass the merged T2w image to FreeSurfer...

[codecov-commenter]

Codecov Report

Base: 70.29% // Head: 66.58% // Decreases project coverage by -3.71% ⚠️

Coverage data is based on head (b41116b) compared to base (270762f).
Patch coverage: 20.83% of modified lines in pull request are covered.

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Additional details and impacted files

@@            Coverage Diff             @@
##           master     #319      +/-   ##
==========================================
- Coverage   70.29%   66.58%   -3.71%     
==========================================
  Files          17       18       +1     
  Lines        1168     1185      +17     
  Branches      200      202       +2     
==========================================
- Hits          821      789      -32     
- Misses        284      338      +54     
+ Partials       63       58       -5     

Flag	Coverage Δ
ds005	56.96% <20.83%> (-3.83%)	⬇️
ds054	48.86% <20.83%> (-0.37%)	⬇️

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

Impacted Files	Coverage Δ
smriprep/workflows/base.py	80.00% <ø> (ø)
smriprep/workflows/outputs.py	63.75% <0.00%> (-2.06%)	⬇️
smriprep/workflows/anatomical.py	51.23% <26.31%> (-2.37%)	⬇️
smriprep/interfaces/surf.py	32.00% <0.00%> (-38.00%)	⬇️
smriprep/interfaces/freesurfer.py	56.43% <0.00%> (-10.90%)	⬇️
smriprep/interfaces/reports.py	86.07% <0.00%> (-6.33%)	⬇️
smriprep/cli/run.py	76.99% <0.00%> (-0.47%)	⬇️
smriprep/__init__.py	100.00% <0.00%> (ø)

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[effigies]

Raw

Preprocessed

[mgxd]

Looks good, now that we are double dipping with some workflows, it may be time to change the parameters/inputs/outputs to reflect this generalization

[effigies]

Tests verifying that this doesn't break for no T2w images, and I've rerun locally with T2 and gotten the same result. Merging.