Hi Jamie
from the point of view of generating surfaces, we don't really care about the cerebellum. Depending on positioning it can be pretty far from isocenter and hence quite dark, so it may not be labeled as wm in the wm.mgz. In general this doesn't really matter. Do the cortical surfaces look okay? You pics look good, although a couple of places I think the control points extended a touch too far out.
cheers, Bruce On Fri, 24 Aug 2007, Jamie Hanson wrote:
Hi Fellow Freesurfers-
I am new to the world of FS and just had a quick question re: cerebellar white matter.
After some skull-stripping issues (and adjusting the watershed algorithm numerous times), I just edited a bad skull-strip with manual aux vol value cloning. I ran autorecon2 again (and again because of some need for control points). But while double-checking / looking at my wm.mgz, I found massive holes in cerebellar white matter.
Pics here: http://brainimaging.waisman.wisc.edu/~hanson/freesurf/ 001.tiff - my brainmask.mgz with some surfaces (just to show nothing wrong with those steps) 002.tiff - brainmask.mgz + aseg.mgz + surfaces 003.tiff- brainmask.mgz + surfaces (at brain-cerebellar "junction") 004.tiff- my wm.mgz + surfaces of the cerebellum in question.
My surfaces "seem" to be fine. But I have a few more subjects who show the same patterns in their wm.mgz . Any thoughts?
jamie. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer