I have looked at this, and there are more subtleties. Basically, the param files between 3dvolreg and 3dAllineate are not appropriate for passing between the programs. Besides the column order, there are appear to be negatives between the shifts. Also, 3dvolreg uses the center of the volume for rotations, while 3dAllineate uses xyz = (0,0,0) for its center. So the sets of rotations/shifts will not equate, even if they are "properly" rearranged and signed.
This brings up why both programs have -1Dmatrix_save options. The matrices translate better than the parameters. I will compare those, too...
- rick