Hi Matt,

I think this is because the extreme capsule is lost so it looks like the putamen borders cortical gray matter. We prevent the surface from deforming once it's adjacent to a subcortical structure to stop it from doing strange things. They editing the aseg.mgz and the wm.mgz so that there is white matter between cortex and putamen then rerun autorecon2-wm.

cheers, Bruce

On Tue, 30 Oct 2007, Matt Colvin wrote:

Dear Freesurfer gurus,

Hello, my name is Matt Colvin, with the Conte Center at Washington University in St. Louis. I came across a problem with a particular brain where the wm and pial lines cut out a chunk of white and grey matter. I have not come across a problem quite like this one so I was wondering if anybody had a suggestion as to how to fix it? I believe it is in the insula of the left hemi of this brain, though I am not certain (the region gets labeled as "unknown" in the parcellation). I have attached two screen caps which show the problem area. Thanks for any help anyone could offer.

--Matt Colvin