By default, the coordinate display in the upper left corner of the AFNI window is Right, Anterior, and Inferior = negative (RAI coordinate order). However, you can flip that to the SPM/FSL convention (LPI) by right-clicking in this coordinate sub-window, and then choosing the appropriate menu option from the hidden popup menu.
As an aside, you can tell if a location in the AFNI GUI has a hidden right-click popup menu when the cursor changes shape (a little). Move the mouse cursor around a little and you should get the idea.