7 Mar
2007
7 Mar
'07
1:09 p.m.
Hi all,
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.
The brain had poor contrast(and a format that Freesurfer wouldn't recognize) so I had AFNI do the skull strip and intensity correction and then fed in that brain to recon-all.
Thanks,
Anil.