Hi Anna

it's tough to tell anything from the surface rendering. You need to go back through your volumes and see why a chunk of the surface is missing. The two most likely candidates are the skull stripping (in which case the brainmask.mgz would be missing this part of the brain) or the topology fixing (in which case the wm.mgz would contain white matter in this region, but the rh.orig would not).

cheers Bruce

On Fri, 15 Apr 2016, Anna Zubik wrote:

Dear Experts,

I'm an absolute beginner in using FreeSurfer.   After I performed recon-all I had a problem. I used T1 SPGR scans to did the reconstruction.

Left hemisphere is done well but right one has some deficits. I attached some print screens bellow.

What can I do to solve my problem?

Best regards,

Anna