Musculoskeletal Magnetic Resonance Imaging Lab (Krug Lab)

The Musculoskeletal Magnetic Resonance Imaging Lab's main research interest relates to the assessment (MRI) and treatment (MR guided Focused UltraSound FUS) of lower back pain.  Furthermore, we assess bone and bone marrow health, obesity and whole body composition, and osteoarthritis in various patient populations. In particular, we develop methods to assess:

  • Lower Back Pain (Biochemical Assessment of the Spinal Endplate using UTE, Intervertebral Disc T1rho, and Bone Marrow using Dixon).
  • Whole Body Composition (Visceral Adipose Tissue, Subcutaneous Adipose Tissue, Intramuscular Adipose Tissue, Muscle Volumes).
  • Osteoporosis (Bone and Bone Marrow Quality in Hip, Wrist, Ankle, and Knee).
  • Bone Hydration and Porosity.
  • High-Intensity Focused Ultra-sound (HIFU) for the Treatment of Lower Back Pain.
  • Osteoarthritis (Assessment of the Calcified Cartilage Layer in the Knee).

Latest News:

  • The Krug Lab receives several NIH grants (>$30M) to study low back pain and opioid addiction (UCSF News)
    Dr. Krug is the imaging director of the Core Center for Patient-centric Mechanistic Phenotyping in Chronic Low Back Pain ( at UCSF (U19) as well as PI on a technogloy center (UH2/3).
  • The Krug Lab's work is featured on the Cover of JMRI (October 2019 edition)
    Krug R et al. Associations between vertebral body fat fraction and intervertebral disc biochemical composition as assessed by quantitative MRI. JMRI 2019 Oct;50(4):1219-1226.



Celebration of 15 years at UCSF with Department Chair and Dean

Musculoskeletal Magnetic Resonance Imaging Lab (Krug Lab)

Oral Presentations and Podium Talks

  •   ISMRM 2019 workshop on Obesity Singapore (Invited Talk)
  •   ISTU/EFUS 2019 in Barcelona. SI Joint pain ablation using MRgFUS. (Krug et al.)
  •   ORS 2018 in New Orleans. Quantitative MRI in patients with lower back pain (Krug et al.)
  •   ISMRM 2018 in Paris. Relationship of vertebral fat, and disc health in patients. (Krug et al.)
  •   ASBMR 2018 in Montreal, Canada. Bone Marrow Fat and its Associations with Bone Quality in the Proximal Femur. (Krug et al.)
  •   FUS Foundation 2018 in Virginia. MRgFUS for back pain. (Rieke, ..., Krug)

Featured on the Cover of QIMS (Feb 2018 edition)

G.J. Kazakia, J. Carballido-Gamio, A. Lai, L. Nardo, L. Facchetti, C. Pasco, C.A. Zhang, M. Han, A. Hutton Parrott, P. Tien, R. Krug. "Trabecular Bone Microstructure is Impaired in the Proximal Femur of HIV-Infected Men with Normal Bone Mineral Density"


Oral Presentation at the ORS 2018 in New Orleans

Krug et al.: Associations between Disc Biochemical Composition and Vertebral Body Fat Fraction using Quantitative MRI. 

Research on Hip Osteoporosis featured on the title page of JMRI (May 2015 edition)

Han M, Chiba K, Banerjee S, Carballido-Gamio J, Krug R. "Variable flip angle three-dimensional fast spin-echo sequence combined with outer volume suppression for imaging trabecular bone structure of the proximal femur"

JMRI Hip Osteoporosis


Most Recent Publications

  1. R. Krug, G.B. Joseph, M. Han, A. Fields, J. Cheung, M. Mundada, J. Bailey, A. Rochette, A. Ballatori, Ch. McCulloch, Z. McCormick, C. O’Neill, Th. Link, J. Lotz. Associations between Vertebral Body Fat Fraction and Intervertebral Disc Biochemical Composition as assessed by Quantitative MRI. (JMRI 2019 in press).
  2. G.J. Kazakia, J. Carballido-Gamio, A. Lai, L. Nardo, L. Facchetti, C. Pasco, C.A. Zhang, M. Han, A. Hutton Parrott, P. Tien, R. Krug. "Trabecular Bone Microstructure is Impaired in the Proximal Femur of HIV-Infected Men with Normal Bone Mineral Density"
  3. R. Krug, L. Do, V. Rieke, M.W. Wilson, M. Saeed. Evaluation of MRI Protocols for the Assessment of Lumbar Facet Joints after MR-Guided Focused Ultrasound Treatment. Journal of Therapeutic Ultrasound 6;4:14. (2017). PMCID: PMC4822243.
  4. E. Ozhinsky, M. Han, M. Bucknor, R. Krug, V. Rieke. T2-Based Temperature Monitoring in Bone Marrow for MR-guided Focused Ultrasound. Journal of Therapeutic Ultrasound (2017 in press).
  5. M. Bucknor, E. Ozhinsky, R. Shah, R. Krug, V. Rieke. The Effect of Sonication Duration and Power on Ablation Depth during MR-Guided Focused Ultrasound of Bone. JMRI (2017 in press).
  6. D. Lansdown, S. Lee, C. Sam, R. Krug, B. Feeley, C.B. Ma. A Prospective, Quantitative Evaluation of Fatty Infiltration Before and After Rotator Cuff Repair. OJSM (2017 in press).
  7. D.C. Karampinos, S. Ruschke, M. Dieckmeyer, M. Diefenbach, D. Franz, A.S. Gersing, R. Krug, Th. Baum. Quantitative magnetic resonance imaging and spectroscopy of bone marrow. JMRI (2017 in press).
  8. B. Berg-Johansen, M. Han, A.J. Fields, E.C. Liebenberg, B.J. Lim, P.E.Z. Larson, C. Gunduz-Demir, G.J. Kazakia, R. Krug, J.C. Lotz. Cartilage Endplate Thickness Variation Measured by Ultrashort Echo-Time MRI is Associated with Adjacent Disc Degeneration. Spine (2018 in press).
  9. G.J. Kazakia, J. Carballido-Gamio, A. Lai, L. Nardo, L. Facchetti, C. Pasco, C.A. Zhang, M. Han, A. Hutton Parrott, P. Tien, R. Krug. Trabecular Bone Microstructure is Impaired in the Proximal Femur of HIV-Infected Men with Normal Bone Mineral Density. QUIMS; 8(1):5-13. (2018).

See a complete list of published work in MyBibliography

Research Projects

Quantifying Temperature Changes in Bone 

We have recently published our research on temperature assessment of bone during heating. The goal of this research is to monitor temperature in bone in-vivo during high intensity focused ultrasound (HIFU) ablation.

High Resolution Assessment of Bone Marrow Fat Content

Our group has been pioneering the assessment of bone marrow fat content in the presence of trabecular bone with high spatial resolution. We have recently evaluated this technique in phantoms and compared in-vivo with MR spectroscopy:

 high-resolution MRI Fat Fraction maps
Figure shows typical in-vivo examples of high-resolution MRI images along with corresponding MRI Fat Fraction maps. The top row shows images from a young, healthy female. Image a) depicts the trabecular structure and image b) the corresponding Fat Fraction map. The high-resolution image shows a dense trabecular structure. The darker, hematopoietic bone marrow is clearly depicted and can be quantified on the Fat Fraction map b). The bottom row shows images from a postmenopausal woman who sustained a low impact fracture. The high-resolution image c) shows dense bone but the Fat Fraction map d) also reveals overall high bone marrow fat content as compared to b) where large areas of hematopoietic bone marrow are present.

Assessment of Temperature in Bone using MRI

We have recently shown for the first time that temperature changes can be measured in bone during heating using T1-UTE based MR imaging. We have presented these results at ISTU 2014 and ISMRM 2014 in oral presentations.

Bone Marrow Fat Fraction Mapping in the Proximal Femur in vivo using IDEAL

Fat Water Images
Figure: Clockwise from top left: Water only image, Fat only image, Fat Fraction Image and In-Phase image.

(D. Karampinos, R. Krug)

There is some evidence that osteoporosis is associated with increased marrow fat content as well as a conversion from red marrow to yellow (fatty) marrow with age. In this project, we investigate the marrow fat composition in the proximal femur in vivo using a method based on Iterative Decomposition of water and fat with Echo Asymmetry and Least-Squares Estimation (IDEAL). Three-point IDEAL FGRE hip images of six healthy subjects were acquired and water-fat separation was performed using multi-peak IDEAL. The average fat fraction and standard deviation were determined in three different regions of interest (femoral head, trochanter and neck). Significant differences in marrow fat content were identified between the three regions for all subjects.  

spectraFigure 1:  Comparison of single-voxel PRESS MR spectra from the trochanteric region (left) and the neck region (right). Note the enhanced water peak on the right spectrum.

Advanced Image Analysis Techniques of New High-resolution Images of the Proximal Femur in the Presence of Red and Yellow Bone Marrow using Local Bone Enhancement Fuzzy Clustering

(J. Folkesson, R. Krug)

Using advanced MR hardware and pulse sequences technique, we have been able to image the small trabecular structure of deeper sited seated regions like the proximal femur with very high spatial resolution in a clinically feasible scan time. We have developed and employed a novel partial membership bone segmentation technique (BE-FCM) that enhances bone segmentation compared to an established dual thresholding method in the presence of signal variations due to different marrow types. The new image acquisition and analysis framework enables trabecular bone analysis in the deeply situated femoral head, something which has been previously unfeasible in vivo.

HipFigure 2:  High-resolution in vivo image of the proximal femur. Hemopoietic or red marrow is composed of ~40% water (longer T1) and appears dark (femoral head, neck and shaft). The more prevalent yellow marrow is more fatty and yields a brighter MR signal.

FuzzyFigure 3:  Top images: ROI defined in the femoral head. Bottom image (left):  Trabecular bone segmentation of the ROI using the advanced BE-FCM technique. Bottom image (right): The same ROI segmented using an established dual thresholding technique.


Post-doctoral Opportunities

The Krug lab is currently seeking exceptional candidates for a postdoctoral appointment focusing on developing and applying quantitative MRI methods for the assessment of lower back pain, osteoporosis and osteoarthritis. The ideal candidate should have a PhD or equivalent in biomedical engineering, and a background in magnetic resonance imaging acquisition, processing, and advanced techniques.
Interested candidates should contact Dr. Krug directly and provide a copy of their CV and references at [email protected]



Jiamin Zhou, MS
Research Associate 
[email protected]

Jiamin received her B.A. (Hons) in Natural Sciences from the University of Cambridge and M.S. in Biomedical Imaging from University of California San Francisco. She is interested in the applications of advanced tools such as machine learning in further characterizing clinical diseases and conditions, including chronic lower back pain and HIV/AIDS, in order to improve diagnoses, treatment, and management. In her free time, she enjoys traveling, trying new food, and making music.

Ravi Chachad, MS
Research Associate
[email protected]

Ravi received his B.S. in Biochemistry and Cell Biology from University of California San Diego and M.S. in Biomedical Imaging from University of California San Francisco. He is interested in studying backpain using MR-guided focused ultrasound. He enjoys hiking with his dog, going to hockey games, and trying new food.


Rukayah Abdolcader
Administrative Assistant
[email protected]

Stephanie Taylor
Research Coordinator
[email protected]

Susan Lin
Financial Analyst
[email protected]


Misung Han
Assistant Researcher
[email protected]

Sonia Lee
Nuclear medicine fellow
[email protected]

Lorenzo Nardo
Nuclear medicine fellow
[email protected]

Andrew Lai
Undergraduate Student Researcher (UC Berkeley)
[email protected]

Christina Gee
Undergraduate Student Researcher (UC Berkeley)
[email protected]

Christopher Schuppert
MD student Heidelberg
[email protected]

Jennifer Nguyen
Undergraduate Student Researcher (UC Berkeley)
[email protected]

Candice Marquez
Undergraduate Student Researcher (UC Berkeley)
[email protected]

Charles Fang
Undergraduate Student Researcher
Bioengineering, UC Berkeley
[email protected]

 Musculoskeletal Magnetic Resonance Imaging Lab Director

Associate Professor
Asst. Professor in Residence