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