Also, given a volume x.nii.gz and a file y.lta, how do I obtaijn z.nii.gz as the original volume x.nii.gz transformed according to y.lta? I tried with mri_vol2vol but somehow I could not figure a way to make it work properly.

Also, given a volume containing a full head and a second volume containing a stripped skull, what is the best approach with FreeSurfer to transform the brain so that it is properly registered with the full head (using an affine transform)? I tried many different ways to get it done with mri_robust_register and also with bbregister, but somehow I could not get a satisfactory result (i.e., I could always get a much better fit by hand using freeview)....