Hi Prof. Lasso, thanks a lot for your kind reply!
Yeah, the SlicerElastix extension can register the two images in one step, which is very convenient. In fact, I’m using the SlicerElastix to do the registration for PET and CT as described in https://discourse.slicer.org/t/does-slicer-support-this-kind-of-pet-ct-registration/2354. I want to do the registration with separate steps to check if we could get better results for some challenging cases.
Thanks for your suggestion! But I’m not sure if the crop step could be reasonable in my case, as I register CT1 to CT2 is to get the transformation for register PET1 to CT2.