Subcortical surface meshes

[effigies]

FreeSurfer's subcortical ROIs are purely volumetric. In the focus group, Greg F (Etkin Lab) pointed to FSL FIRST for surface-based parcellations of subcortical structures.

[oesteban]

Once FreeSurfer is run, it is possible to generate surfaces from subcortical structures. I have some old code here: https://github.com/oesteban/RegSeg/blob/master/Scripts/pyacwereg/workflows/surfaces.py#L30

That would save us from adding FSL FIRST on top of FreeSurfer.

[effigies]

Cool, thanks for the reference. Also, this may have been a point of information more than a direct feature request, so we should make sure that subcortical surface meshes are things people want before spending too much time on it.

[gfonzo]

Thanks, guys, for looking into this! It would be great to have the subcortical surface meshes for shape analyses, but I agree that there should be a quorum for including it. Otherwise the user can just run FSL FIRST separately.