All of the volumes, except the inner and outer boundaries, are segmentations, rather than structural volumes (as far as I know).
But you could find one of those intermediate volumes -- possibly named like hindbrain* -- and subtract that volume from the anatomical volume, and then use the volume math features to set the floor to 0. There are lots of caret_command tools for this sort of thing, not to mention FSL/AFNI tools (e.g., 3dcalc). I'm surprised Caret gets rid of the marmoset hindbrain at any resolution -- cool. On Jul 1, 2012, at 12:20 PM, Colin Reveley wrote: > 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 > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
