[Freesurfer] Co-registration in FS

Hi FSers,

I am new to freesurfer. now start to use it for looking at struc-func relationship. Normally, in fsl, I employ bet for both example_func and highresh anat. it means that the func_brain and anat_brain are fed into flirt to estimate the co-registration.

here, i try to use reg_feat2anat to do this. but in this new version (4.5), it told me the betfunc command can not be found. thus I just used the version without --bet. the results in tksurfer looked not good. I am guessing it was caused by the highres with large neck areas. MY QUESTION is

how can I trigger reg_feat2anat (or whatever other commands) to take skull-stripped highres for the co-registration (in fact, the brainmask.mgz already there)? Or I was wrong, reg_feat2anat did this consideration?

Any suggestions would be appreciated!