RMSE in Landmarks Registration

Hello everyone,
I’m trying to register two volumes using “Fiducial Registration Wizard” module. My goal is to find the minimum number of fiducial points that give me best result in the alignment.
What I observe when I increase the number of landmarks is that RMSE increases but visual alignment seems better in axial, coronal and sagittal views.
If I want to quantify registration with respect to the number of fiducials is it fair to consider RMSE or is there another way?

It is a somewhat unintuitive but but a well proven fact that fiducial registration (residual error shown as RMSE) is different from target registration error (accuracy of aligning important target positions).

You need minimum 3 points for a rigid registration, but the more points you add, the higher the chances that you reduce the effect of random errors in your imaging and point marking. However, the more points you add, the more time it takes, you may become less careful when placing the points, and you may only find lower-quality landmark points (that you are not so sure about or are farther from the region of interest), which may not improve the end result.

Most often you would end up using 6-8 high-quality landmarks, placed carefully.

If you don’t have this many good landmarks then there are alternative methods. For example, you can collect a large number of surface points using a tracked stylus or surface scanner and use points to surface registration.