Depending on what you want to do exactly, you can try several approaches:
3drefit -duporigin
3dresample
@Align_Centers
align_epi_anat.py
The first two are described in this recent thread:
[
afni.nimh.nih.gov]
@Align_Centers forces the centers of the datasets to the same point. align_epi_anat.py aligns data using an affine transformation of the data.