Here are some freesurfer goodies that you might find useful:
[http://imaging.mrc-cbu.cam.ac.uk/imaging/FreesurferGoodies/generatefreesurferscripts A Method for semi-automated batch recon-all]
[http://imaging.mrc-cbu.cam.ac.uk/imaging/FreesurferGoodies/batchcreateRegistrationFiles Creating the register.dat and the v2r.dat that are needed for the transformation from freeSurfer RAS space to your subject native space]