A method for 3-D longitudinal cephalometric analysis of a patient, the method executed at least in part on a computer processor and comprising: acquiring a first cone beam computed tomographic (CBCT) volume data from a computed tomographic scan of a patient's head; acquiring a first surface model (S104, S106, S108) of a plurality of teeth of the patient's head; performing a first 3-D longitudinal cephalometric analysis regarding dental and skeletal relationships for the patient's head based on said first CBCT volume data; displaying one or more computed cephalometric parameters characterizing the patient's head shape and structure from the first cephalometric analysis; acquiring a second surface model of the plurality of teeth of the patient's head from an optical scan of the patient, the second surface model being a mesh model; finding changes of teeth position and orientation between said first surface model and said second mesh model; applying the changes of teeth position and orientation to said first CBCT volume data to obtain a second volume data, said second volume data being a virtual CBCT volume data that is obtained without additional x-ray exposure; performing a second 3-D longitudinal cephalometric analysis regarding dental and skeletal relationships for the patient's head based on the second virtual CBCT volume data; and displaying one or more computed cephalometric parameters from the second cephalometric analysis; wherein the one or more cephalometric parameters include coordinate information that is provided (S106; S220) directly by reference mark entry for particular features of the patient's head by an operator and information on various measurable characteristics of the anatomy of a patient's head that are not directly entered as coordinate or geometric structures but are derived from the coordinate information. acquiring a first cone beam computed tomographic (CBCT) volume data from a computed tomographic scan of a patient's head; acquiring a first surface model (S104, S106, S108) of a plurality of teeth of the patient's head; performing a first 3-D longitudinal cephalometric analysis regarding dental and skeletal relationships for the patient's head based on said first CBCT volume data; displaying one or more computed cephalometric parameters characterizing the patient's head shape and structure from the first cephalometric analysis; acquiring a second surface model of the plurality of teeth of the patient's head from an optical scan of the patient, the second surface model being a mesh model; finding changes of teeth position and orientation between said first surface model and said second mesh model; applying the changes of teeth position and orientation to said first CBCT volume data to obtain a second volume data, said second volume data being a virtual CBCT volume data that is obtained without additional x-ray exposure; performing a second 3-D longitudinal cephalometric analysis regarding dental and skeletal relationships for the patient's head based on the second virtual CBCT volume data; and displaying one or more computed cephalometric parameters from the second cephalometric analysis; wherein the one or more cephalometric parameters include coordinate information that is provided (S106; S220) directly by reference mark entry for particular features of the patient's head by an operator and information on various measurable characteristics of the anatomy of a patient's head that are not directly entered as coordinate or geometric structures but are derived from the coordinate information.