Hi, JR-
OK, that sounds like a plan. For discussing this more, knowing what your $template and $dset_pre variables/datasets are will be key. For example, most templates are T1w volumes, and you said you are looking at using a T2w input (is that your ${dset_pre}?). If that is the case, those dsets have opposite tissue contrast, and you would want to use a cost function appropriate for that-- such as "lpc" or some variant thereof.
I think after watching the alignment lectures, these kinds of things will be easier to discuss, so please ping back.
--pt
