The cheap way to do a "3dAPflip" would be to use 3drefit to swap the AP and LR orientations in the header, use 3dLRflip, then swap the orientations back. For example, if the dataset is reported by 3dinfo to be RAI, then something like so might do the job

3dcopy infile+orig zork
3drefit -orient ARI zork+orig
3dLRflip -prefix outfile zork+orig
3drefit -orient RAI outfile+orig
/bin/rm -f zork+orig.*

where the first two axes are swapped in 3drefit because those are the two that involve the RL and AP directions.

I haven't tried this myself, and notice that I operate on a copy ("zork") so that if something bad happens, I haven't trashed the original "infile" dataset.