Here are some freesurfer goodies that you might find useful:
[http://ltl.tkk.fi/wiki/images/1/18/Henriksson_fMRI09_visuquan.pdf An introduction tutorial to freesurfer by our own LindaHenriksson, of particular use to me was page 6]
[http://imaging.mrc-cbu.cam.ac.uk/imaging/FreesurferGoodies/generatefreesurferscripts A matlab function 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]