afni.nimh.nih.gov

align_epi_anat.py has some options for partial data that will try to avoid moving data out of plane, but that's still a difficult proposition with only four slices. It would be better to have a full coverage EPI dataset that is in alignment with the partial dataset and move the two together with the same affine transformation. In that case, the partial dataset would be a "child" dataset. In align_epi_anat.py, that would be implemented with the "-child_epi" option.