Hi, Will-

Hmm, weird. I ran this similar command (just didn't have followers and ts_shifts, but those should not affect this) and did not get the same error:

align_epi_anat.py                                                            \
    -anat         FT_anat+orig.HEAD                                          \
    -epi          pb00.FT.r01.tcat+orig.HEAD                                 \
    -anat2epi                                                                \
    -giant_move                                                              \
    -cost         lpc+                                                       \
    -epi_base     mean                                                       \
    -output_dir   ./odir                                                     \
    -save_vr                                                                 \
    -suffix       _al                                                        \
    -overwrite

And your understanding of what should be happening there is correct, yes.

Ummm, I am not sure why it would be different for you. Having a non-numeric argument after "-epi_base .." should trigger a 3dTstat command, so it shouldn't be trying to use that argument as a subbrick selector.

Just out of curiosity, what is your "afni -ver"? Also, is there more text output by the command before that failure, in case that might provide any clues? And perhaps could you run it with "-verb 5" as an extra option, and copy+paste the output text here?

thanks,
pt