Re: [Freesurfer] Surface edits: Cortex that extends into the putamen + Missing gray matter

can you tar and gzip the entire subject and upload it to our ftp site with coordinates of the problem areas? On Mon, 3 Jul 2017, Vincent Koppelmans wrote: Hi Bruce, Thank you for your reply.  The aseg seems to be okay: https://www.dropbox.com/s/j1ac0ftxw8iiv34/Putamen.png?dl=0  Do you

Re: [Freesurfer] Surface edits: Cortex that extends into the putamen + Missing gray matter

Hi Bruce, Thank you for your reply. The aseg seems to be okay: https://www.dropbox.com/s/j1ac0ftxw8iiv34/Putamen.png?dl=0 Do you have any other suggestions? Here is an extra image of the cortical ribbon. Maybe this helps:

Re: [Freesurfer] Surface edits: Cortex that extends into the putamen + Missing gray matter

Hi Vincent the putamen error probably means that the aseg is wrong, and if so, you can correct the aseg and rerun autorecon2-wm and autorecon3 I believe. For the medial ttemporal lobe issue is that really cortex? I can't really tell from the single coronal slice. I'll cc Jean Augustinack to

[Freesurfer] Surface edits: Cortex that extends into the putamen + Missing gray matter

Hi all, I was wondering how to fix the following issues: 1) The cortical ribbon extends into the gray matter of the putamen (see the top row of this image: https://www.dropbox.com/s/x1euf9otl2nv6ff/Fix.png?dl=0). 2) Cortical gray matter is missing in the medial temporal lobes (see the bottom