With the most recent release, does the skullstripping take place with brainmask.auto.mgz  and brainmask.mgz?  After completing recon-all –autorecon-all I checked brain.mgz. I had some frontal areas missing, so ran  recon-all -skullstrip -wsthresh 30.  Brainmask.mgz looks good.  

I believe that I know the answer, but to be safe, after running –autorecon2 brain.mgz will reflect these edits?  Thanks, Cliff  


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Clifford Smith, PhD
Assistant Professor of Behavioral Sciences
Rush University Medical Center
312.942.2893