align_epi_anat.py is a wrapper for 3dAllineate.-- that is, when you run align_epi_anat.py, it actually just puts together a command with specific options present for 3dAllineate.

In the AFNI_history part of the 3dinfo output for a file, you can see both. Here is an example from the afni_proc.py Bootcamp example:

[ptaylor@eomer: Mon May 20 12:23:00 2019] align_epi_anat.py -anat2epi -anat FT_anat_ns+orig -suffix  _al_junk -epi vr_base_min_outlier+orig -epi_base 0 -epi_strip 3dAutomask  -anat_has_skull no -check_flip -volreg off -tshift off

... translates to ->

[ptaylor@eomer: Mon May 20 12:21:46 2019] {AFNI_19.1.09:linux_ubuntu_12_64} 3dAllineate -lpc -wtprefix ./FT_anat_ns_unflipped_al_junk_wtal -weight ./vr_base_min_outlier_ts_rs_ns_wt+orig -source ./FT_anat_ns_unflipped+orig -prefix ./FT_anat_ns_al_junk -base ./vr_base_min_outlier_ts_rs_ns+orig -nocmass -1Dmatrix_save ./FT_anat_ns_al_junk_mat.aff12.1D -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass

So, there are some other things set. If you want to go the align_epi_anat.py route (perhaps you are using afni_proc.py yourself with this?) then you can provide some other defaults/settings. For example, you would twopass on, instead of onepass: "-Allineate_opts -twopass". It is also possible that the maxrot and maxshf would need to be increased-- in 3dAllineate's defaults, the help says:

-maxrot dd    = Allow maximum rotation of 'dd' degrees.  Equivalent
                 to '-parang 4 -dd dd -parang 5 -dd dd -parang 6 -dd dd'
                 [Default=30 degrees]

 -maxshf dd    = Allow maximum shift of 'dd' millimeters.  Equivalent
                 to '-parang 1 -dd dd -parang 2 -dd dd -parang 3 -dd dd'
                 [Default=32% of the size of the base image]
         **N.B.: This max shift setting is relative to the center-of-mass
                 shift, if the '-cmass' option is used.

So, in the end, you might want to add something like this to your align_epi_anat.py command:

"-Allineate_opts -twopass -maxrot 30 -maxshf 40"

(almost like using -giant_move, but you *don't* want the -cmass behavior, because you have a partial dataset)

-pt