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What does 3dinfo say about the dataset (maybe 25 lines)?
3dinfo DATASET | head -25
I suspect that your dataset is really on the 0.5 grid, but maybe
your Underlay in the afni GUI is on the integer grid (meaning
that the Overlay is warped on demand to the grid of the
Underlay).
Anyway, the 3dinfo command should show what to expect.