Except that I get identical results with this command line:
align_epi_anat.py -giant_move -AddEdge -epi2anat -anat_has_skull no -anat refvol.lpcreg+orig -epi movvol.lpcreg+orig -epi_base 0
as I do when I add these options:
-Allineate_opts -warp shift_rotate
-Allineate_opts -warp shift_rotate_scale
All three commands generate "12 free parameters" in their terminal output, and the final registration matrix looks to be at least 9, and the 3dAllineate command in the terminal output does not have a -warp option, so I'm wondering if the warp option gets passed to 3dAllineate?
thanks
doug