what do you plan to do with your template? How did you create the template? There does not look to be good alignment for cortex which is causes those big pockets.

Hi Freesurfer Experts,

I had generated my own template and want to register my subjects into this template. Before the registration, I had run recon-all on my template

Once I opened it in freeview, I get something like this. I definitely need to correct these surfaces. Could you give me some suggestions about the areas I pointed out? I am really get lost about them. Thanks a lot.

If there has more information about using own template, please send them to me. I am really appreciate your help. 

Best wishes,

Ting

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