Hi,
I have tried virtually all methods available in 3D Slicer for surface registration and found the IGT fiducial registration method, a semi automatic method to be the most useful one.
However, I no longer use any 3D Slicer-based tools for registration as results are subpar and take too much time and uses the ICP registration addon in the Blender which is a fully automatic tool and works wonderfully well.
you can find this add-on in github and install it on Blender. It is very easy to use.
You can see the discussion I had on this topic, with very useful input from others at,
Colour maps
I use the model to model distance and shape population viewer in the 3D slicer to create the color maps.
measurement
What measurements you need ? If you are going to segment the structures then you can use the segment editor statistics to measure. Also there are lots of other measurement tools available but will depend on what you need to measure and using what type of data.