Hi, Cesar-
Well, align_epi_anat.py will build you a 3dAllineate command and run it. If you look at the history in the HEAD file of the output data sets after using align_epi_anat.py, you will see it. It is a wrapper in that sense-- it will include some default choices you might find useful.
I will quote the top of the 3dAllineate help:
NOTES: For most 3D image registration purposes, we now recommend that you
===== use Daniel Glen's script align_epi_anat.py (which, despite its name,
can do many more registration problems than EPI-to-T1-weighted).
-->> In particular, using 3dAllineate with the 'lpc' cost functional
(to align EPI and T1-weighted volumes) requires using a '-weight'
volume to get good results, and the align_epi_anat.py script will
automagically generate such a weight dataset that works well for
EPI-to-structural alignment.
-->> This script can also be used for other alignment purposes, such
as T1-weighted alignment between field strengths using the
'-lpa' cost functional. Investigate align_epi_anat.py to
see if it will do what you need -- you might make your life
a little easier and nicer and happier and more tranquil.
-->> Also, if/when you ask for registration help on the AFNI
message board, we'll probably start by recommending that you
try align_epi_anat.py if you haven't already done so.
So, whichever way you go, the '-lpa' cost function is likely a good place to start; to minimize smoothing when applying the warp, you might also want to look at including '-final wsinc5'
--pt