3dNwarp (Calc and Apply) are works in progress, and not for the faint-of-heart at this time. They have yet to be polished up for spaces and stuff like that. I'm glad to get feedback, and in fact I'm working on a better nonlinear registration algorithm now -- seems to work OK on my first try, but there's some peculiar bug I'm having trouble figuring out.
I'm sorry you've run into a rough spot here, and someday I hope to smooth these things over. But first I want to get a good registration method working, something that my mother would be proud of.
