The align_epi_anat.py program should give you an output 3D/4D dataset and 1D files for the affine transformations too. In this case, you are asking for the output to be the aligned anatomical dataset, so you should find that single volume dataset called something like "anatal_junk+orig.HEAD/BRIK" in the output. The AFNI format is used for the output instead of NIFTI. You can convert that to NIFTI with 3dcopy. Note the anatomical to EPI transformation is the default and the first one computed. If you really want the reverse, then use "-epi2anat" instead of "-anat2epi".
