In some embodiments, a method for determining a deformity in a bone surface comprises performing a scan of a healthy bone and a diseased bone; creating 3-dimensional (3D) representations of a current surface of the diseased bone; constructing an estimated healthy surface in 3D for the diseased bone based on the surface of the healthy bone; and identifying a deformity in the diseased bone by comparing the estimated healthy surface to the current surface of the diseased bone. In some embodiments, the scan is performed using high resolution peripheral quantitative computed tomography (HR-pQCT).