afni.nimh.nih.gov

All the spatially transforming programs remove the obliquity of the data, but maybe that one shouldn't, or should only match the grid and obliquity of the base dataset. In any case, to restore the oblique information, you can do something like this:

3drefit -atrcopy IJK_TO_DICOM_REAL original_dset warped_dset

To use this, the grid has to be exactly the same size, i.e. the number of rows, columns and slices are the same for both the warp and original datasets.