Try viewing these in the afni GUI instead. The obliquity is handled differently in the GUI than in some other packages, and that may confusing you. Also consider using the -epi2anat option on align_epi_anat.py to invert and apply the transformation. The rigid_body option is rarely used, so that's surprising to see here. Usually we try to take care of some distortion with the full affine transformation. The rigid body parameters here limit the alignment to only translation and rotation, and not shearing or scaling. That's fine if you want it, but just be aware of what it is. These parameters are also not the rigid equivalent transformation parameters computed using the full affine transformation, but extracting only the rigid part of that transformation, perhaps a subtle but important difference.