Thanks for your reply to ask me to check lh.pial and rh.pial. I checked and they look good to me as attached picture. Another information is that cortical layers that I generated from the freesurfer recon-all look good as well. So it seems like the problem is only on cortical parcellation? Do you have any other suggestions on what I can check or is there any parameters that I can tune to make cortical parcellation better?

Best regards,

Yixin