To add to Rick's suggestions, the first two suggestions can be used with the "-oblique_origin" option for to3d and 3drefit. Normally in to3d, the origins are computed separately for the obliquity transformations and for the cardinal data for DICOM data. Usually these are the same anyway, but it's not clear which is more reliable for a particular manufacturer because of inconsistencies in their headers. To force the origin computed from the oblique info in the DICOM header, use the "-oblique_origin" option.

In any case, when a NIFTI dataset is created from an AFNI dataset, the oblique transformation (from the IJK_TO_DICOM_REAL attribute) and consequently the oblique origin is always used. To apply the origin from the IJK_TO_DICOM_REAL to an AFNI format dataset, use 3drefit -oblique_origin dset+orig. To remove obliquity information, use 3drefit -deoblique dset+orig.