A method for jointly evaluating multi-phase magnetic resonance bone marrow images includes receiving a plurality of magnetic resonance (MR) image sequences of bones acquired using different protocols, each sequence comprising a plurality of images, each image comprising a plurality of intensities corresponding to a domain of points on a 2-dimensional grid, analyzing an image sequence to determine the MR protocol of said sequence, segmenting the bone marrow region in each image of said plurality of MR image sequences, and registering each MR image sequence to every other image sequence in said plurality of sequences wherein each point in each image of each of said plurality of image sequences is registered, wherein said registered image sequences are adapted to being analyzed synchronously.