Hi Joel,

Well, I see that running 3dresample on the dataset throws out
the warp data (which makes some sense). So unfortunately, you
cannot use 3dresample to go from RAS back to RAI before using
adwarp.

So applying adwarp with that as the parent will not actually
warp the data, it will effectively just be resampled to match
the grid of the apar dataset.

In any case, I'm not sure why you are expecting adwarp to work
the same after a tlrc dataset gets changed from RAI to RAS
orientation. Putting acpc and tlrc datasets in RAI orientation
and having the transformations rely on it sounds like a solid
design decision to me, not a bug. The slow part was that I was
not sure enough to say that it must be RAI, up front. I only
suspected and suggested as much.

So it seems that the clear way to go is using the afni-created
tlrc dataset as the parent for warping the functional data.
Please let me know if that does not work out for you.

- rick