afni.nimh.nih.gov

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.