afni.nimh.nih.gov

Lots of choices:

auto_warp.py (affine, nonlinear
@auto_tlrc (affine only)
align_epi_anat.py (affine only, for two anatomical datasets, use -dset1 templateset and -dset2 mydset -dset2to1)
3dQwarp (nonlinear only)
@SSwarper (MNI-2009 template only, affine, nonlinear)