Hi Jeffrey;
I've been talking to Rick Reynolds on a related subject on a different thread. One possibility is that we need to get you to use an updated version of pghtoafni.
Another possibility which just struck me is that FIASCO knows something about oblique slices, but AFNI doesn't like them much. If you see *something* when you do your overlay but it is in very much the wrong place, we may have to make sure the functional and structural images are coregistered and that their corner coordinates (in FIASCO form) are in the same coordinate system.
-Joel
welling@psc.edu