If your original data are in DICOM, I would suggest doing all the steps in Slicer (including the 3D model generation).
- You can import the DICOMs
- If the 3D images of two dicoms sets do not occupy the same space (i.e., they do not overlap), do a a rigid registration via Elastix extensions.
- Confirm the results of your registration.
- Then proceed with segmentation and model building and derive your statistics.