Abstract: Methods of generating three-dimensional models of musculoskeletal systems, and three-dimensional bone and soft tissue model reconstruction, and associated apparatus, are disclosed. An example method of generating a virtual 3-D patient-specific bone model may include obtaining a preliminary 3-D bone model of a first bone; obtaining a supplemental image of the first bone; registering the preliminary 3-D bone model of the first bone with the supplemental image of the first bone; extracting geometric information about the first bone from the supplemental image of the first bone; and/or generating a virtual 3-D patient-specific bone model of the first bone by refining the preliminary 3-D bone model of the first bone using the geometric information about the first bone from the supplemental image of the first bone.