We propose the extraction of musculoskeletal structures (bones, muscles) from the lower limb, following three main objectives: development of an MRI protocol, processing and labelling of the image data, and the exploitation of multi-channel data during the segmentation of individual muscles. We propose an MR acquisition protocol that generates seamless, high-resolution images of thigh and calf. We present a method to identify air and muscle tissue in the image and massively parallel version of the approach. To identify the individual muscles, we align a muscle template which is modified with our deformable model framework under the influence of image forces to match the actual anatomy. This iterative process uses multi-channel image data to find relevant image features. We propose coupled multi-resolution deformable models that allow working on different resolutions in parallel. This work is aimed at helping the understanding of diseases by providing personalised anatomical models.