afni.nimh.nih.gov

That looks good. As Peter points out, the other commands you mentioned do not do any alignment at all. 3dresample just puts a dataset into another grid. 3drefit only changes the header of the dataset. To move data from one space to another, you have to use an alignment program as you did with auto_warp.py which calls @auto_tlrc and 3dQwarp to do the actual alignment. It also takes care of the resampling and setting the header attributes.