You should use
auto_warp.py to normalize your T1 to MNI space. And then use
3dNwarpApply to apply that transform to your EPI data.
There is a new tool:
@SSwarper that will take care of the skull stripping and nonlinear warping (via 3dQwarp) your T1 to MNI space, and then you can use 3dNwarpApply to apply the transformation to your EPI dataset. You'll see in the help, there are also hooks in
afni_proc.py for taking the output of @SSwarper and doing all the other processing on your EPI datasets.
-Peter