Hi Rumana, have you gone through the troubleshooting steps that we describe on our wiki?
doug
Rumana Chowdhury wrote:
Dear all
I put a T1w image through the recon-all process and it completed without errors, but the segmentation output (aparc.a2009s+aseg) does not line up with the subjects own brain.mgz or orig.mgz. I have had a similar problem with other T1w images that I've used. Any ideas why this might be and how to correct?
Many thanks for your help Rumana