This work addresses the patient-specific characterisation of the morphology and pathologies of muscle–skeletal districts (e.g., wrist, spine) to support diagnostic activities and follow-up exams through the integration of morphological and tissue information. We propose different methods for the integration of morphological information, retrieved from the geometrical analysis of 3D surface models, with tissue information extracted from volume images. For the qualitative and quantitative validation, we discuss the localisation of bone erosion sites on the wrists to monitor rheumatic diseases and the characterisation of the three functional regions of the spinal vertebrae to study the presence of osteoporotic fractures. The proposed approach supports the quantitative and visual evaluation of possible damages, surgery planning, and early diagnosis or follow-up studies. Finally, our analysis is general enough to be applied to different districts.