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Hi Bruce,
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 [image: Screen Shot 2018-10-27 at 5.28.33 PM.png]
[image: Screen Shot 2018-10-30 at 11.44.05 AM.png]