Research Directions

The Mission of MQIR is to pursue research and teaching in quantitative tissue characterization focused on the musculoskeletal system by building collaborations between basic scientists, clinical scientists, and physicians and thus establishing a strong resource for musculoskeletal imaging-based research at UCSF. MQIR strengthens and nurtures partnership not only within the Department of Radiology and Biomedical Imaging, but also between the Departments of Orthopaedic Surgery, Medicine and Bioengineering at UCSF and UC Berkeley.

Research Areas and Project Summary 

Degenerative Disk Disease

degenerative disk diseaseThe process of disc degeneration is characterized by a loss of cellularity; degradation of the extracellular matrix; and as a result, alterations in physiochemical properties. The current gold-standard to isolate painful discs appropriate for treatment is physical examination and provocative discography. However, discography is an invasive, painful procedure with low specificity. Our goal is to establish non-invasive markers of disc degeneration and a comprehensive set of biomarkers for characterizing lower back pain, using magnetic resonance (MR) imaging methods such as T2 and T1rho, diffusion and spectroscopy.


diabetesBeing a major, increasingly prevalent metabolic disease, diabetes has been found to be associated with a higher risk of fragility fractures. However, diabetes is associated with higher BMD values and it is challenging to measure risk of these fractures in diabetic patients using standard bone mineral density based techniques. Our group develops new imaging techniques focusing on bone marrow adiposity using MR spectroscopy and cortical macro-porosity using high resolution peripheral QCT to better understand the risk of fragility fractures in diabetes.


Musculoskeletal CT Imaging Research Group develop and employ quantitative imaging methods to better understand the human biology of the musculoskeletal system.



Mineralization Abnormalities

mineralizationOur program encompasses tissue-level characterization of bone mineral and matrix properties, including tissue mineral density evaluation by micro computed tomography (µCT) and mineral and matrix composition by Fourier transform infrared (FTIR) spectroscopy.


osteoarthritisOsteoarthritis, characterized by progressive loss of hyaline cartilage, also affects other tissues in the joint, including bone and meniscus. Our long-term research goal is to develop advanced imaging techniques to detect early degenerative changes within the joint. Current major research efforts include developing quantitative MRI (such as T1rho) to detect early cartilage degeneration, examining interaction between cartilage, bone and meniscus in osteoarthritic joints, and exploring relationship between imaging measures and biochemical and molecular changes of osteoarthritic tissues.


osteoporosisPreventing osteoporotic fractures and understanding effects of new anti-osteoporosis medications requires sophisticated diagnostic imaging techniques, that do not simply assess bone structure but also its function. This has been termed as bone quality by the National Institutes of Health and one of the major foci of our research group is to develop and optimize novel non-invasive imaging techniques to understand bone quality.


pathomechanicsThe purpose of these studies are to use a multi-modal approach including quantitative MRI, kinematic MRI, and motion analysis to evaluate biomechanics associated with lower extremity injuries. Examples include determining the effects of meniscectomy surgery on tibiofemoral contact kinematics, and exploring the relationships between loading mechanics during athletic tasks and articular cartilage relaxation times.

Sports Injuries 

sports injuryPrevious large cohort studies have shown that joints with sports injuries, such as anterior cruciate ligament (ACL) rupture and meniscal tear, have a high risk of developing post-traumatic osteoarthritis. Using advanced imaging techniques developed in our group, our research goal is to detect early degeneration in such joints, and to explore the potential relationship between altered joint biomechanics and cartilage degeneration.

Research Directions

-Identify biomarkers for degeneration in bone, cartilage, and inter-vertebral disc, and diseases such as osteoporosis, spinal disorders, and osteoarthritis.

-Improve musculoskeletal health by using Computed Tomography (CT), High Resolution Peripheral Quantitative CT (HR-pQCT) and Positron Emission Tomography (PET)/CT imaging to study risk factors for age-related fractures, to quantify deterioration of bone structure and strength as result of aging and disease, and to analyze the anatomy and function of skeletal muscle in relation to mobility loss.

  • Effects of reduced weight-bearing on skeletal geometry, micro-structure, and strength.
  • Effects of exercise on bone quality in HIV positive individuals.
  • Mechanisms of increased cortical porosity in the peripheral skeleton.
  • Use of advanced image analysis techniques such as finite element modeling and voxel based morphometry to study age-related bone loss and to predict hip fracture.
  • Use of CT to study muscle mass and fat infiltration as risk factors for hip fracture.
  • Development of acquisition and analysis methods to standardize scanning and analytic methods for multicenter studies in osteoporosis and sarcopenia.
  • Development of PET/CT to study protein synthesis in skeletal muscle.

-Characterize muscle and bone in diabetes, HIV disease, and other diseases using Magnetic Resonance (MR) Imaging and Spectroscopy.

  • Bone marrow fat quantification in the proximal femur and spine using high-resolution water-fat imaging, and the relationship of marrow adiposity to bone quantity and quality.
  • Fat infiltration in the rotator cuff muscles as a predictor of surgical outcome.

-Detect early joint degeneration using quantitative metrics (T1r and T2), and radiological grading methods in osteoarthritis of the knee and hip and correlate these with biomechanical function, biochemical changes, clinical findings and function.

  • Contact mechanics, neuromuscular control, and cartilage composition in knee OA.
  • Changes in knee contact mechanics and cartilage composition following meniscectomy.
  • Characterization of cartilage using magnetic resonance imaging and kinematics in hip osteoarthritis.
  • Running biomechanics and overuse injuries of the lower extremity.
  • Development of osteoarthritis in anterior cruciate ligament (ACL)-injured and reconstructed knees.
  • Investigating the impact of physical activity, obesity, weight loss and gain on longitudinal development of cartilage and meniscal degeneration.

-Perform In vivo MR imaging in the presence of metal implants.

-Determine MRI temperature measurements of bone during MR-guided ultrasound.

-Apply multimodality imaging (MRI and HR-pQCT) and hyperpolarized 13C MRI to investigate rheumatoid arthritis.

-Reduce radiation dose in computed tomography (CT).