Cartilage loss is shown to be a risk factor for Osteoarthritis (OA) which is one of the main causes of disability in older people. This invention, consisting of methods in image segmentation, 3D reconstruction, morphological quantification, and 3D visualization, is a system for automatic mapping of articular cartilage thickness. It can be used for articular cartilage thickness measurement and full-thickness cartilage loss quantification. It facilitates the early diagnosis and progression monitoring of OA.