Hopefully you are using afni_proc.py for this work? If so, what is the afni_proc.py command that you are using?

And when you say "problems", what do you mean? There are some help options for this, such as adjusting the cost function, and maybe needing the "ginormous move" or "giant move" option because the origins are far away (sigh... data). These two options can be added into the alignment block in afni_proc.py with something like:

-align_opts_aea -cost lpc+ZZ -ginormous_move

Again, this all depends on the details of what the current commands being used are, and the current ways in which the data processing is going awry, so the above are just exemplar suggestions.

But if you aren't using afni_proc.py for processing, I would strongly consider using that to reduce numerous headaches and to allow testing of different options easily in a pipeline.

--pt