Hello,
There are a lot of details missing about the registration components you choose to use for this registration.
You may find the turn-key solutions available in Elastix easier to use. The just announce SimpleITK 3.0.0 beta 1 experimental includes the SimpleElastix interface as part of it’s binary distributions. You can find the original documentation for this interface here: Hello World — SimpleElastix 0.1 documentation and some updated emerging documentation here: SimpleElastix Registration — SimpleITK 2.4.0 documentation
You can find other interfaces to Elastix along with additional information here: https://elastix.dev