Hi Kate,
Sorry to jump in a little late and without reading
all of this (maybe I will tonight). But the 3drefit
operation (before 3dTshift) should have no effect on
the result on disk (meaning "diff *.BRIK" would show
nothing) because the timing applies to the order of
slices on disk, regardless of what the HEAD file
claims I and S are.
The only affect of the 3drefit command should be to
flip the image in the afni viewer.
I think "slice 0" in the viewer might always be RAI,
and have nothing to do with the orientation on disk.
But I am not positive.
- rick