Hi all,<br><br>Is Freesurfer going to generate all surfaces properly if I feed in a skull stripped brain to begin with starting from stage 1. In other words, is there going to be a problem if the orig.mgz is skull stripped. I checked the results after autorecon1 and the 
brainmask.mgz had a decent contrast. The xfm was also accurate.<br><br>The brain had poor contrast(and a format that Freesurfer wouldn&#39;t recognize) so I had AFNI do the skull strip and intensity correction and then fed in that brain to recon-all. 
<br><br>Thanks,<br><br>Anil.<br><br><br>