Depending on exactly what you want to do, the typical and simple method is to do what you have said and move all ROIs at the same time. You can input CSF/Ventricles/White matter as input ROIs for afni_proc.py. Brainstem and cerebellum are often more difficult to align across subjects while still trying to align the cerebrum at the same time. You can do these as separate alignments if that's important to you.The SUIT cerebellum atlas and template have their own template you can use for that purpose.
