There seems to be a naming error: QmitkFiducialRegistrationWidget uses two pointsets to calculate a transform. This Filter should be called ...LandmarkFilter... since it is meant to be used for coresponding landmarks in image and patient/tracker coord.-space.
In addition we need a filter, that stores the position of several reference (fiducial) marker, that can be used to continuously compensate for movement (field generator to fiducial markers connected to patient). (Will be solved in different feature request). T2380 "Create hybrid navigation data and fiducial transformation filter" ( word "Landmark" used correctly) cannot solve this, because we will need the NavigationData to be used as input for LandmarkRegistration and no pointset.