Thank you! I actually meant 3drefit, rather than Regrid, but there had been some local discussion about these options that infected my email, so I'm glad to know we're already doing what you would suggest.

I'm enjoying the file_tool utility- thank you. But it's adding a bit to my confusion. Craig Stark sent us the following advice, "Personally, all I do is to grab the EPIs and the structurals at the same oblique angles. That way, it's just as if the person's head were tilted, so tell AFNI that they're standard non-obliques." Thus, we treat our obliques, which are almost axial, as axials,
but the file_tool output is making me wonder if this is really OK.

It seems that the zcoordinates reported by file_tool would be scanner space, and not on an axis orthogonal to slice plane since they're oblique, so seems to make sense why they'd be closer together on the z projection. The extents we used came from an SPM recon, which seems to get the geometry ok. The z-slab it reports does indeed correspond to 15 slices 5 mm thick, which is how we prescribe then at the scanner.

I'll continue on unless you followup with other suggestions, which I'll keep alert for. We are struggling a bit with the origin question as well, but I'll dive into teh documentation abit before asking about that!
Many thanks for your help with this!
Alison