Facilities

Introduction
The UC Davis Imaging Research Center (IRC) consists of two distinct facilities. The main facility, opened for investigator-initiated research in 2003, is located on the University of California Davis Medical Center Campus in Sacramento, CA. A new satellite facility located on the UC Davis Main Campus, at 1629 Da Vinci Court in Davis, CA, named the "MRI Facility for Integrative Neurosciences", opened for investigator-initiated research on September 6, 2011.

 

Imaging Research Center in Sacramento
The University of California at Davis established the Imaging Research Center (IRC) in 1998, with a major expansion in 2003, to support imaging science research and promote the use of modern imaging methods in basic science and clinical investigations of the brain and body. The IRC is located in a 13,000 sq.ft building on the UCD Medical Center campus in Sacramento, and currently houses two research-dedicated whole-body MRI scanners — a 1.5T GE Signa MRI System and a 3T Siemens TIM Trio MRI System. A wide range of imaging studies are carried out in the IRC. The IRC supports basic science and clinical research that investigates the structure and function of the nervous system, including perceptual, motor and cognitive function using real-time functional imaging techniques, and research that investigates systemic physiology and morphology in health and disease.

 

Imaging Research Center in Davis: The MRI Facility for Integrative Neurosciences
The new MRI Facility houses a new Siemens 64-channel 3 Tesla "Skyra" MRI System (Siemens Healthcare, Erlangen, Germany). The Siemens 64-channel 3T Skyra system is fully equipped for advanced neuroimaging. This system has a fast gradient system that provides high-speed spatial encoding, a 64-channel data acquisition system with digital wireless technology to improve SNR and temporal stability, and a dual-channel RF transmitter system for reduction of dielectric effects, and more flexible RF pulse design. The gradient rise time (200 mT/m/ms), peak gradient strength (45 mT/m per axis), and duty cycle (100% using full gradient strength on all three axes) are the highest specifications in the industry for whole-body systems. Also, the gradients have a balanced geometric design that results in less acoustic noise generation. Every hardware and software option that Siemens offers for neuroimaging is installed on this MRI system. Parallel imaging capabilities in one and two-dimensions enable EPI acquisitions at higher temporal resolution and with less geometric distortion. In addition, the IRC maintains an active Master Research Agreement with Siemens Healthcare that makes available advanced "works-in-progress" pulse sequences for EPI and structural neuroimaging to deal with specific technical challenges.

 

People

The Director of the Imaging Research Center, Dr. Cameron Carter, is a senior scientist with an established imaging research program. The IRC is an independent research unit supported by the Technical Director, Professor Michael H. Buonocore, Management Services Officer Jessica Hicks, Administrative Assistant Jacqueline Smith, Senior MR Research Specialist Jerry Sonico, MR Physicist Costin Tanase, Engineer Dennis Thompson, and Systems Administrator Scott Martin. These last four full-time staff members optimize, operate and maintain the IRC MRI systems and accessory equipment, and train investigators and their laboratory personnel to use these systems and equipment. These individuals, along with IRC Technical Director and IRC Director, constitute the IRC Technical Support Team. This Team provides immediate and continuous technical support for the MRI systems and all of the accessory equipment, and works to minimize interruptions caused by equipment failures and suboptimal performance.

 

The Center

The UC Davis Imaging Research Center (IRC) is dedicated to research involving advanced imaging and image processing technologies, and serves the UC Davis Health System and Main Campus. The Center houses a whole-body 1.5T MRI system and a 3T MRI system (see below), and equipment for general imaging research support. The IRC also includes a Neuroscan Maglink 136 channel system for simultaneous EEG/ERP recording in the 3T MRI system. The IRC holds PC, Silicon Graphics, Sun and Linux workstations for MR imaging research, PC workstations for general image processing and office work, and other workstations for nuclear and x-ray imaging. In addition to visiting faculty offices, there are private offices for visiting faculty, and ample computer work areas for graduate research assistants. Imaging physics faculty and technical support personnel have offices at the IRC, and continually improve upon the research infrastructure and provide support for faculty research projects.

 

3T MRI System

      See data produced with the Siemens Trio

The IRC operates a 3T Siemens Trio Total imaging matrix (Tim) whole-body MRI system (Siemens Medical Solutions, Erlangen, Germany) which is fully equipped for advanced brain imaging. This system has a short-bore (2 m) magnet, a fast gradient system that provides high-speed structural and functional imaging, and a 32-channel data acquisition system with 32 1-MHz receiver channels for parallel imaging. The gradient rise time (200 mT/m/ms), peak gradient strength (40 mT/m per axis), and duty cycle (100% using full gradient strength on all three axes) are the best specifications in the industry for whole-body systems. Multi-dimensional parallel imaging capabilities enable EPI acquisitions at higher temporal resolution and with less geometric distortion. Three multi-channel RF head coils are available: a new Siemens 32-channel brain coil that takes full advantage of the 32 receiver channels and provides the highest signal-to-noise ratio, a new 12-channel coil that provides excellent SNR while also providing more space between the head and the coil for headphones and goggles for enhanced auditory and visual presentation, and the original In-vivo, Inc. 8-channel head coil upgraded for the Trio Tim system to allow investigators to use the same coil for ongoing research studies.

The UC Davis IRC recently upgraded their 8-channel 3T Trio System with the Trio Tim system discussed above. This upgrade enables improvements in the brain imaging protocols originally developed on the Trio system. For EPI sequences used in fMRI, signal loss due to underlying B0 inhomogeneity, for example in the orbital frontal cortex (OFC), is greatly reduced by reducing the effective echo time (TE), echo spacing (ESP) and by increasing the k-space acquisition matrix size, using parallel imaging. Another benefit resulting from increased spatial and temporal SNR is reduced total exam time. Studies with children and patients with anxiety generally are higher quality when the time in the scanner is less. The gradients of the Trio Tim system create significantly less noise pressure than the gradients of the Trio system. Siemens reports that acoustic noise pressure from the gradient pulses in the Trio Tim system is just 10% of the noise pressure produced by the same gradient pulses in the Trio system. Many participants, particularly children and patients with anxiety disorders, complain about the acoustic noise of the scanner. Reduction in acoustic noise is expected to substantially increase the percentage of adults and children that are able to complete their scanning sessions.

Early experience with the Trio Tim system confirms that this upgraded system has significantly better performance compared to the original Trio system. Test images show the following improvements:

  1. Reduction in signal drift in EPI timeseries for fMRI,
  2. Increases in temporal SNR in EPI timeseries for fMRI,
  3. Increases in single image SNR for improved contrast in structural MRI,
  4. Decreases in image ghost intensity on EPI and diffusion weighted images,
  5. Reduction in image distortion caused by non-linear gradients.
These results are consistent with the experiences of University of Minnesota (Bryon Mueller, Kelvin Lim), University of Southern California (Jiancheng Zhuang), Northwestern University (Todd Parrish), and UC San Francisco (Vibhas Deshpande, PhD of Siemens Healthcare).

The MNS option provides spectroscopic imaging and spectral analysis of Na-23, P-31, C-13, O-17, Xe-129, Li-7, He-3 and others. The Siemens multinuclear spectroscopy analysis package performs water suppression, phase correction, apodization, zero filling, spectral transformation, base line correction, automatic and manual phase correction, curve fitting and peak labeling, and computation of relative metabolite concentration, with customizable settings.

 

1.5T MRI System

The IRC also operates a 1.5T, whole-body, neuro-optimized GE Signa Horizon LX NV/I MRI system (GE Medical Systems, Waukesha, WI). The 1.5T system has enhanced gradient performance (150 mT/m/ms rise time, 40 mT/m peak) for functional brain imaging. The high gradient strength and rise time provides single image acquisition in under 25 ms using EPI or spiral pulse sequences. Pulse sequences for blood oxygenation level dependent (BOLD) imaging, arterial spin-tagging, diffusion tensor imaging, single-voxel spectroscopy, and all clinical imaging scans are available. The system uses the LX operating system (Version 84M4), an SGI Octane workstation with enhanced reconstruction capabilities (approximately 100 images/sec), and a Sun Ultra (Sun Microsystems, Inc. Mountain View, CA) for real-time interactive control of functional (fMRI) image acquisition, scan parameter selection, image visualization, and image processing. An Advantage Windows Workstation (AWW, GE Medical Systems) can also be used for advanced image processing and analysis of images obtained using fMRI, MR angiography, gated cardiac imaging, velocity encoded phase imaging, and first-pass contrast enhanced imaging.

 

Data and Image Processing

The UC Davis Imaging Research Center (IRC) operates a data analysis cluster consisting of eight Xeon-based Linux compute nodes accessing 60 terabytes of file server space. All data is protected by nightly backups to a network of off-site file servers. Software for post-processing includes custom programs written at UC Davis (BrainMRI, MRIView), and third-party software packages (e.g. SPM, FSL, AFNI, FreeSurfer). Pulse sequence development takes place on Windows workstations for the Siemens MRI systems. A computer lab houses both Windows and Linux workstations for use by visitors and students.

 

Visual and Auditory Presentation Systems
Visual System: The visual projection system for the Siemens Trio 3T scanner has been designed to present high resolution in-bore images with tightly controlled timing necessary for recording event-related potentials (ERP) simultaneously with fMRI data acquisition. The heart of the system is the Digital Projection Mercury 5000HD projector. The three-chip DLP technology of this projector allows for 1200:1 black/white transitions within 5 ms with no raster delay anywhere in the image. The simultaneous presentation of all image pixels and the total lack of image flicker create images that appear more stable than those of CRTs and allows for management of stimulus durations that are not possible with CRT displays. The lens assembly for projection within the bore of the magnet consists of a custom 18 foot focal-length long-throw Navitar-Buhl projection lens mounted in front of the projector on an adjustable Edmund optical bench. The lens can project a 7-inch, 1280 pixel wide image at 17 feet permitting a stimulus of visual 30 degree visual angle for the observer. The projector and lens assembly is vibration stabilized by an Model NT57-167 optical vibration isolation platform (Edmund Optics, Barrington, NJ 08007-1380). The whole assembly is located on a sturdy height-adjustable table from Baker Industries. The custom in-bore screen made by Ben Krasnow (Mag Design and Engineering, Inc. Sunnyvale, CA 94086) mounts to the phase-array head coil using non-magnetic hardware. The projector is located outside of the MRI scan room and projection occurs into the magnet room though a dedicated wave-guide.
Auditory System: Auditory stimuli are presented during scanning via a high-fidelity system designed for the MR environment (MR confon GmbH, 39118 Magdeburg, Germany). The headphones contain electrodynamic transducers for a broad, flat frequency response and construction-grade Peltor earmuffs for passive damping of gradient noise. By using electrodynamic rather than pneumatic transduction, this system produces sound quality comparable to a home stereo, with 88dB signal-to-noise ratio (SNR) and high channel separation. During a functional MRI scanning session, sounds can be presented at detection-threshold levels between "sparse" acquisitions or at conversational levels (approx. 75-80 dB) during continuous scanning. Active Noise Cancellation (ANC) in the headphones will further reduce the gradient noise and create a quieter environment for subjects. ANC is under final pre-release testing at MR-Confon, and the UC Davis IRC will be one of the first centers to use ANC in fMRI research. For communication from the subject, the subject's voice is transmitted to the scan operator via Phone-OR, an MR-compatible, optical microphone mounted on the headphones (Magmedix, Inc., Fitchburg, MA, 01420). This microphone system suppresses gradient noise from the transmitted audio signal, using both simple subtraction and advanced algorithms based on speech-recognition. Combined with the MR confon system, extremely clear bidirectional (subject to/from operator) communication is possible during scanning to provide excellent audio SNR for voice-key applications.

 

Eye-Movement Monitoring Equipment
For the 3T MRI system, the eye-tracking system is the Applied Science Laboratories (ASL, Inc. Bedford, MA) Model 504 with long-range optics. It includes the series 5000 control unit with long-range remote optics and multi-speed camera with telephoto lens needed for the MRI environment, two 9 inch black and white monitors, one 5 inch LCD monitor for the MRI scan room, and the EYEPOS package for real-time conversion of the eye movements into numerical pupil position and diameter data streams. The system includes a custom PC with two frame grabbers, one capable of supporting 240 Hz eye imaging, and the other capable of recording to disk the entire image of the eye during the MRI scan.

 

Stimulus Presentation and Button Response Recording Equipment
On both the 3T and 1.5T MRI systems, investigators use a Windows XP MRI system to deliver visual paradigms. Stimulus presentation and button press response acquisition is controlled by the e-Prime (Psychology Software Tools, Inc.) or Presentation software system (Neurobehavioral Systems, Inc.). Subjects respond with button presses obtained with specially constructed 5-finger MR-compatible fiber-optic devices held in both left and right hands (Photon Control Inc.). The metal-free keypads are connected via fiber optic cable to an optoelectronic controller unit.

 

Physiological Monitoring and System Diagnostics Equipment
Two computers, one dedicated to each MRI system, provide for acquisition of MRI system events, as well as acquisition of physiological waveforms from the subject being scanned. Each computer has three data acquisition boards and the National Instruments Labview Professional Development software for creating virtual instruments to automate the acquisition of diagnostic or physiological data. These computers have been programmed using Labview to collect and analyze waveforms of the MRI system events during a pulse sequence simultaneously with cardiac, respiratory, galvanic skin response, and other physiological signals from the subject. For the 3T system, the Siemens Measurement Acquisition and Test Environment (MATE) software tool, which is built into the MRI system, also provides detection of heart rate, breathing, and peripheral pulse with 10 to 20 ms resolution.

 

Mock MRI System
The simulated environment of an MRI system, consisting of a wood mock-up of an MRI system, non-functioning RF coils, and including a built in speaker system for playing back recordings of the pulse sequence sounds (purchased in 2001 from Psychology Software Tools, Inc.) is located in Room 1121 of the IRC. This environment also includes the visual and auditory stimulus presentation system, and an ASL eye-tracking system (see above), that are also used in the actual MRI environment. Using the mock MRI system, potential subjects for the MRI scanning sessions can be acclimated to and trained for the fMRI studies.