High-Resolution Quantitative Imaging



These magnets have advanced technology from GE Healthcare with 32-Channel receiver system, multi-nuclear spectroscopy, high speed / high volume data pipeline, and high performance gradients.


Wrist Coils

  • Mayo Coil Transmit/Receive Quadrature
  • 8-Channel (In-Vivo Corporation, Gainesville, FL)

Knee Coils

  • 8-Channel T/R Knee Coil (In-Vivo Corporation, Gainesville, FL)
  • Pfizer Coil (quadrature) upgraded to 14.0
  • IGC Medical Systems (GE) Quadknee (Quadrature)

Spine Coils

  • 4-Channel Spine Coil
  • 8-Channel Spine Coil (USA Instruments, Aurora, OH)

Hip Coil

  • 8-Channel Cardia Coil used for Hip (GE Healthcare, Milwaukee, WI)

Neck Coil

  • 8-Channel Neck Coil (GE Healthcare, Milwaukee, WI)

Torso Coil

  • 8-Channel Torso Coil (USA Instruments, Aurora, OH)

Foot Coil

  • 8-Channel Foot Coil (In-Vivo Coorporation, Gainesville, FL)

Shoulder Coil

  • 4-Channel Shoulder Coil (GE Healthcare, Milwaukee, WI)



The 7T system is one of a handful of research systems constructed by GE Healthcare for collaborative development with academic partners. Research collaborations include multiple UCSF departments, industry, and other academic research institutions, investigating human disease and therapeutic interventions in brain, prostate, musculoskeletal, and neurological systems.


  • 28-Channel phase-array knee coil (QED, Mayfield Village, OH)
  • 32-Channel phase-array head coil

Sagittal Knee FSE using the 7Tesla MRI

Sagittal Knee SPGR using the 7Tesla MRI


7T Small Animal MRI

The 7T Small Animal MRI facility at China Basin Landing is a compelling in-vivo imaging solution for rodents and other small mammals. We provide high quality anatomic and functional imaging services, using our 7T 300 MHz Horizontal Bore Varian MR System.  Complete with ancillary tools and monitoring equipment, the facility is equipped with full-time support staff capable of addressing all of your imaging needs. More information can be found at:​.


  • Varian 7T 300MHz Horizontal Bore MRI System
  • 20G/cm 205mm High Duty Cycle Gradient Coil
  • 40G/cm 120mm High Duty Cycle Gradient Coil
  • Linear and Quadrature RF Coils, diameters ranging from 1.5-8cm
  • SA Instruments Animal Monitoring System, complete with heating and respiratory + cardiac gating capabilities
  • Capability for X-nuclei imaging and spectroscopy (13C, 19F, 23Na and 31P) 



Pulse Sequence Development and Image Processing


  • T1 Rho and T2 MAPS: UCSF's Department of Radiology and Biomedical Imaging has developed novel MRI T1 Rho quantification sequences in cartilage. In particular, the 3D Tip Quantification Sequences (Magnetization-prepared Angle-modulated Partitioned-k-space Spoiled Gradient-Echo Snapshots, MAPS) have been disseminated to several other research institutes through GE Healthcare and will be used in TOQIO for knee and hip cartilage imaging.
  • High-Resolution Trabecular Bone Imaging Using MRI : A general framework for Steady State Spin Echo (SSSE) pulse sequences was developed by Krug, et al. introducing the concept of fully balanced SSSE (bSSSE), non-balanced SSSE (nbSSSE), and RF Spoiled SSSE. It was found that bSSSE outperforms all other SSSE versions in terms of SNR. Both gradient-echo and spin-echo based approaches have been successfully implemented and optimized in our laboratory for imaging the trabecular network. Both implementations were done using generalized autocalibrating partially parallel acquisitions (GRAPPA).
  • Imaging Quality Control and Cross-Validation : The Department of Radiology and Biomedical Imaging's Imaging Center uses highly stringent and reproducible daily QA tests based on GE Healthcare's System Performance Test (SPT) including SNR, geometric distortion, radiofrequency (RF) power, and zisocenter. During the course of the proposed TOQIO, the IDAC will perform additional stringent quality control on cartilage and bone imaging and quantification, and cross-validation of cartilage and bone quantification between three 3T GE MR scanners at China Basin, QB3 and the Orthopaedic Institute.
  • Quantitative Image Processing
    • All the image processing and image analysis techniques that will be required in this proposal have been integrated in a package using MATLAB (The MathWorks Inc., Natick, MA). Formal training and written SOPs will be provided to facilitate the training of users and to standardize the processing.
    • Cartilage Segmentation:  The MRI group at UCSF is in the process of validating a new semi-automatic segmentation technique which has 4 main components: local thickness measures, edge-detection, lineprofiling, and Bezier splines.
    • Laminar Analysis: Cartilage segmentations will be divided into  layers, usually 2, to minimize partial volume effects. In addition to the analysis of individual layers, we will also examine the differences between each of these layers.
    • Texture analysis:  Cartilage segmentations will be overiaid on relaxation time maps by using patient coordinates and texture analysis will be performed using gray-level co-occurrence matrices (GLCM). A total of 9 parameters that result from processing the tabulations mentioned above will be computed with 5 offsets and 4 different orientations. GLCM parameters will include three from the contrast group: contrast, dissimilarity, and homogeneity; three from the orderiiness group: angular second moment (ASM), energy, and entropy; and three from the stats group: mean, variance, and correlafion. The orientations will include 0°(180°), 45°(225°), 90°(270°), and 135°(315°).
    • Registration:  3D multi-resolution image registration tools were developed and integrated into the processing software that are capable of correcting patient motion between scans.
    • Trabecular Bone Mean Intercept Length Mean Intercept Length (MIL): Analysis of trabecular bone will be performed on a slice-by-slice basis, however the segmentation of trabecular bone will be performed in three dimensions. ROIs will be placed in the high-spatial resolution images to include only trabecular bone and marrow. ROIs will be segmented using Bone-Enhancement Fuzzy C-Means (BE-FCM) clustering to compute a fuzzy Bone Volume Fraction map (f-BVF) as previously developed in our group.
    • Trabecular Bone Geodesic Topological Analysis (GTA):  A trabecular bone analysis technique that quantifies the trabecular bone network in terms of its junctions. GTA provides composite measures of scale, topology, and anisotropy.
    • Automatic Placement of Volumes of Interest:  Our group is also developing tools for automatic placement of volumes of interest (VOIs) to analyze trabecular bone at identical anatomic regions in the proximal femur in different subjects. The technique is based on Free-Form Deformations (FFDs).


MR Kinematics

Tibio-Femoral Kinematics: We have the ability to calculate accurate translatory and rotatory motion between the tibia and the femur from images acquired with the knee extended and flexed to various degrees. 

Meniscus Kinematics: We have implemented novel techniques for quantification of multiple parameters related to the movement of the menisci between the femur and the tibia with knee flexion and with knee loading.

Contact Kinematics: We are able to quantify the movement of the centroid, which allows us to capture the change in contact patterns at the knee with knee flexion or with knee loading.


Clinical Morphological Analysis

Hip Osteoarthritis MRI Scoring: The UCSF-modified Hip Osteoarthritis MRI Scoring System (mHOAMS) is a semi-quantitative MRI-based scoring system (HOAMS) of hip osteoarthritis. Cartilage is assessed separately for femur and acetabulum in five different sub-regions: superior-lateral, superior-medial, anterior, posterior, and inferior. Cartilage lesions are evaluated for both type (partial vs. full-thickness defect) and size (recorded in cm). Presence of bone marrow edema pattern and subchondral cysts is assessed in the same sub-regions. Bone marrow edema pattern is graded according to its extent as grade 0, 1, 2 and 3 if it extends for less than 5 mm, 5 to 15 mm, or more than 15 mm, respectively. Subchondral cysts are recorded as present or not present. The labrum is assessed in four different sub-regions: anterior-superior, superior-lateral, anterior-inferior and posterior-inferior. In each sub-region it is scored as grade 0, 1, 2, 3, 4 or 5, which corresponds to normal, hypoplasia/aplasia, fraying, simple tear, complex tear, and maceration.

Additional features incorporated in this scoring system are synovitis, effusion, loose bodies, paralabral cysts, and synovial herniation pits. They are all scored as present or not-present.

Whole-Organ Magnetic Resonance Imaging Score (WORMS) : Published by Peterfy, et al. assesses both depth and size of the cartilage lesions using an eight-point scale: grade 1 lesions have a normal thickness but abnormal signal; grade 2.0 lesions are partial-thickness focal defects, which are smaller than 1 cm in the greatest width; grade 2.5 are full-thickness focal defects smaller than 1 cm in greatest width; grade 3 lesions are defined as multiple areas of partial-thickness (Grade 2.0) defects intermixed with areas of normal thickness, or a Grade 2.0 defect wider than 1 cm but affecting <75% of the region; grade 4 lesions are diffuse partial-thickness lesions affecting more than 75% of the region); grade 5 lesions show multiple areas of full-thickness cartilage loss (grade 2.5) or a grade 2.5 lesion wider than 1 cm but <75% of the region and finally grade 6 lesions demonstrate full-thickness cartilage loss in more than 75% of the region.

WORMS scoring for the knee for cartilage lesions


Statistical Analysis


  • The biostatistical and data management portion of IDAC has three primary sets of responsibilities, which are the three sub-aims:
    • Statistical design of experiments
    • Data analysis
    • Data management
  • The IDAC will be available to investigators of the projects for:
    • Consultation on the design of experiments, including power and sample size choice, efficient designs for various questions, and sampling strategies
    • Formulation of scientific hypotheses, including choice of endpoints, predictors and confounders and framing in ways amenable to formal statistical analysis
    • Recommendations for statistical analysis strategies
    • Model specification, including variable inclusion, predictor selection methods, and validation methods
    • Conduct of statistical analyses including methods to deal with the longitudinal nature of OAI and the clustered nature of the images collected on participants (regions of interest clustered within knee, clustered within person
    • Managing and checking the flow of information into the database resource
    • Assembling datasets for statistical analysis and support for projects.
  • Data analysis includes biostatistical data analysis, data cleaning, quality assurance, monitoring patient recruitment and retention, and assistance with preparation of interim reports.