Piecewise subcortical alignment for CIFTI mapping

[effigies]

To have a persistent link, here's the current script from DCAN: SubcorticalAlign_ROIs.sh

Note that this supersedes an older script: SubcorticalAlign_MNI_Affine.sh

[mgxd]

Checklist of wb_commands that need to be Nipype-ized.

• cifti-create-dense-from-template
• cifti-create-dense-timeseries
• cifti-dilate
• cifti-create-label
• cifti-resample
• cifti-separate
• cifti-smoothing
• volume-resample
  • Replaces deprecated volume-affine-resample
• volume-all-labels-to-rois
• volume-label-export-table
• volume-label-import

[effigies]

Going to start on volume-resample.

[effigies]

I did not quite finish volume-resample. I'm not sure why they didn't just use flirt's apply transform, tbh.

[mgxd]

The only missing interface is for -cifti-separate, which has already been converted in nipy/nipype#3306.

[effigies]

@mgxd Want to copy that one in here for now, so we don't need to wait on the review/release process in nipype?

[mgxd]

Yeah, that sounds like the fastest way forward