Hi Doug,
Thanks!
I manually tweaked the registration of the PET to T1 on a number of subjects to bring the mincost down to < 0.5. After saving the pet2free volume in Freeview, I noticed that a new .lta is produced in the same directory (i.e. pet2free_fsl.mgz.lta).
Will the option --regheader tell the subsequent commands (i.e. mri_vol2surf) to use the updated registration .lta instead of the original .dat that was produced via bbregister?
Best Wishes, Elijah