You haven't given an epi dataset with the "-epi my_epi_dset+orig". The epi_base is the sub-brick volume of the EPI dataset to use as a reference volume for the alignment with the anatomical volume and for motion correction. It's useful to select an epi_base that has little motion and good spatial contrast between CSF and tissue. Typically almost any sub-brick will be sufficient, and useful choices are the first,third and last sub-bricks, but for some high flip-angle and low TR EPI datasets, the spatial contrast is poor, and the pre-steady state TR's are better choices. Most of this is described in the help for the program (align_epi_anat.py -help / -h_view) and in the class documentation linked below:
http://afni.nimh.nih.gov/pub/dist/edu/latest/afni10_volreg_talairach/
