3D Post processed CT Images - Co Registration

I am writing to see if somebody can help me / lead me to deal with a research project I am involved in. I am working on co-registration of post processed CT images (I can send the images if somebody needs those: Sample see the post processed image1 and 2 in the attachment - consider that CT of an animal (as in human protocols) has been done and we got 2 post processed 3D images giving different information).

I would like to see these 2 post processed images co -registered precisely so that I can see if any change if it is happening at one particular location has correlation with other image at the same location.

How to make them correlate? Do I have to do anything at the start of the post processing of images so that the spatial information is retained. And how to integrate?