Bob:

Sorry for the ambiguity.

The problem to be solved most immediately is with the behavior we are seeing from AFNI viewer's write acpc capability.

I did mention 3drotate, misremembering the command-line version of the functionality in question, which I guess is actually in adwarp. Ultimately we do expect to use the command-line version, but for now let's focus on the viewer situation.

So, in AFNI source, I have followed the trail to discover:
-- ATLAS_ALIGNBOX_POS etc are the source of the box dimensions.
-- AFNI_make_warp( ) makes the warp specification

... but I haven't tracked down the spot where that spec is actually used to calculate an integral number of voxels for each side of the result BRIK.

Further clues appreciated.

Thanks,

Graham