3drefit is not right. It does no transformation. It only changes the header to say the name of the dataset's space is something. So if you know that the dataset is already in MNI space, and the dataset is not already identified as MNI space, then that command would be correct. 3drefit is a general purpose tool to change everything that AFNI knows about a dataset. In general, 3drefit should be used sparingly and only with good understanding.