If the segmentation datasets share the same sform/qform codes in their NIFTI header information, then the same "3dWarp -card2oblique" command will apply the equivalent transformation to those datasets. You can see the actual combined transformation used with the "-verb" option to 3dWarp. The align_epi_anat.py script calls "3dWarp -card2oblique" and extracts that transformation in order to combine it with the affine transformation to align anatomical and EPI datasets. The -child options for that script allow applying the same transformation to datasets that start aligned with each other. Using the "-ex_mode dry_run" option with align_epi_anat.py is useful for showing the steps the script would use.