I agree that a WM and PIAL from freesurfer is the way to go with marmoset. For what it's worth, if you calls it a galago (in caret) and uses a 300um MTR you can get a halfway decent surface (not really that good, but it works).
at 300um caret successfully get's rid of the hindbrain. If I could get access to a volume either of the hidbrain, or of everything else with hindbrain removed, that would save me a huge amount of work. First, experience tells me that with no hidbrain caret will make a surface from 150um data. second, I'll need to remove the hindbrain by hand before I try to do this with Freesurfer. Caret spits out many volumes as it runs segmentation and surface construction. are any of these a sturctural volume with hindbrain removed? I could upsample that and use as a mask for hindbrain removal. best, Colin
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