Hello,
Thank you all for your help. @animal_warper worked well for my T1 scans. However, 3/4 of my scans are T2. The template I am using is the NMT template, which is a T1 scan. Is there an option that I can use to make the command work for a T1 template with a T2 scan? I couldn't find anything in the command documentation for what to do.
Another problem I am having is that the skulls are not being stripped off, even when I use the -skullstrip option with a template skull stripped. Is there something else I am missing?
Thank you!
JR
