Thank you! However, there is one small note regarding the cost function.
I've encountered errors using nmi as a cost function; see the errors here (adjunct_deob_around_origin didn't work? or not really an oblique problem? - #10 by yc0181). I tried a couple of times during the weekend, using the previous MRI to T1 template and this CT data to T1 template, but I always get similar errors.
But maybe if I inverted T1 as you suggested, the nmi error would disappear?