afni.nimh.nih.gov

That's just a question of how the viewer shows the slices,
and I don't know the answer. But I do know that slice #0
does not imply slice index 0. The only way to be sure which
slice is #0 is via 3dinfo.

Note that afni is just trying to show images in an expected
manner (sagittal, axial, coronal), not how they are stored
on disk.

So basically, don't worry about it, as long as 3dinfo shows
what you expect. :)

- rick