You can see the voxel indexes as stored on disk (versus as displayed in the image viewers) in at least two ways in the interactive AFNI GUI. The first is to open a graph window, and then look in the lower left corner, where you'll see something like the below (next to the AFNI logo)
X: 12
Y: 22
Z: 32
These are the indexes of the focus voxel as stored on disk. You are in the #0 slice when "Z: 0" is displayed.
The second way is to click on the "Define Datamode->Misc->Voxel Coords?" button, which will then replace the usual spatial coordinate display in the upper left corner of the AFNI controller window.