Also I have a new CMTK GUI integration which may be more helpful to you. The idea was to integrate CMTK into a 3d rendering and editing environment while keep it native. Geometry, grid and transforms are directly tranlated into CMTK conventions, also data is processed as raw arrays into CMTK input so  no compatibility and naming concerns. The main idea is that you can see the same physical pose and intensities as CMTK would receive so you can make better judgment on your data and the parameters, also you can easily and interactively pre align your data with the manual transform tool. 

get it from here, windows store version is the most convinient option at the moment, but mac and ubuntu is also supported:

https://madi3d.org

It is still beta but it should be stable enough for your purposes, also the registration modul is open sourced on github so you can validate the math.