Thanks Doug! I need to do this procedure 100 times, so I have to automate it. Do you have an example C-shell script for this? Or is there a way to call mri_surf2surf inside a "for loop" of Matlab?

Thanks, Reza

not that I know of. When I have to do this, I save the data to a file, then call mri_surf2surf with a system call, then load the result back into matlab.