Registration using transform slider is certainly very hard. Fortunately, there are several other registration tools in Slicer that can be applicable. For example:
- Segment registration module (in Segment registration extension): Fully automatic registration between two segments. Supports both rigid and deformable transforms.
- Fiducial registration wizard (in SlicerIGT extension): Landmark-based registration (you need to manually identify corresponding landmarks in the images).
- Model registration (in SlicerIGT extension): Iterative closest point (ICP) based fully automatic rigid registration. You need to export segments to models (using Segmentations module), as this module expects model nodes as input. ICP can stuck into local minimum, so this method requires the segments to be already somewhat aligned when you start the registration.