recon-all will copy the brainmask.auto.mgz to the brainmask.mgz so they should be the same. Allison
On Tue, 2 Dec 2008, Barkay, Gavriel wrote:
Hi, I ran recon-all -all crashed for reasons unrelated to FreeSurfer. I re-ran the analysis without -clean. Is the new skull stripped volume stored in brainmask.auto.mgz instead of brainmask.mgz? Thanks, Gabi