You may want to consider the overlap issues encountered by some other users recently. As Rick noted, this assumes the data matches, but the header information for one of the datasets is wrong for some reason (and you know this from the scanner acquisition parameters, for instance). For your case, you can consider the @Align_Centers script (which effectively still calls the same 3drefit command to reset the origin) but is useful for applying origins across many datasets. Alternatively, you may want to align the datasets using one of AFNI's alignment tools (like align_epi_anat.py).
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afni.nimh.nih.gov]
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afni.nimh.nih.gov]
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afni.nimh.nih.gov]
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afni.nimh.nih.gov];