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