It might expect the inverse of the transformation. And there should not be any actual alignment happening (so you can remove -autoweight -cmass -twobest MAX).
You also might compare with what afni_proc.py does when applying an aea.py xform matrix, as in
s15.proc.FT.uber. Note that it uses "cat_matvec AEAMAT -I" to extract the inverse of that matrix before passing it to 3dAllineate to apply.
- rick
