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.