Osteoarthritis is the most common chronic joint disease in the world. With its progression, cartilage thickness tends to diminish, which causes severe pain to human being. One way to examine the stage of osteoarthritis is to measure the cartilage thickness. When it comes to inter-subject study, however, it is not easy task to compare cartilage thickness since every human being has different cartilage structure. In this paper, we propose a method to assess cartilage defect using MRI inter-subject thickness comparison. First, we used manual segmentation method to build accurate atlas images and each segmented image was labeled as articular surface and bone-cartilage interface in order to measure the thickness. Secondly, each point in the bone-cartilage interface was assigned the measured thickness so that the thickness does not change after registration. We used affine transformation and SyGN to get deformation fields which were then applied to thickness images to have cartilage thickness atlas. In this way, it is possible to investigate pixel-by-pixel thickness comparison. Lastly, the atlas images were made according to their osteoarthritis grade which indicates the degree of its progression. The result atlas images were compared using the analysis of variance in order to verify the validity of our method. The result shows that a significant difference is existed among them with p < 0.001.