A method and system generate a scan model that is a mathematical model to simulate an imaging process performed by an x-ray imaging device that created a two-dimensional x-ray image of at least one tooth. The scan model uses an initial estimate of one or more parameters of the x-ray imaging device to simulate the imaging process on a three-dimensional model. The method and system generate the two-dimensional contour of the three-dimensional model based on the scan model that uses the initial estimate of the one or more parameters of the x-ray imaging device. The method and system adjust the two-dimensional contour to cause a first component of the two-dimensional contour to approximately align with a second component of the two-dimensional x-ray image. The method and system calibrate the scan model based on data obtained from adjusting the two-dimensional contour.