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Facilities
The University of California at Davis established the Imaging Research Center (IRC) in 1998,
with a major expansion in 2003, to support human 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 the new 3T Siemens Trio MRI System.
A wide range of human and animal 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.
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 Debbie Tussing,
Senior MR Research Specialist John Ryan,
Computer Systems Administrator Scott Martin and
Administrative Assistant Jody Conrad.
The IRC is in a period of rapid development and growth.
Neuroimaging scientists and clinicians are being recruited at a rapid pace into major neuroscience
and neurology initiatives at the UCD Medical Center and main campus.
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 human and animal imaging research support. The IRC also includes a Neuroscan Maglink 136 channel system for simultaneous EEG/ERP recording in the 3T MRI system. Rooms are available for animal holding, preparation and recovery. 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.
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See data produced with the Siemens Trio |
The IRC operates a 3T Siemens Trio whole-body MRI system (Siemens Medical Solutions, Erlangen, Germany) which is fully equipped for advanced brain imaging. The new system is housed in a 1400 sq. ft. extension of the UC Davis Imaging Research Center (IRC) located on the UC Davis Health System Campus. This system has short-bore (2 meter length) magnet, a fast gradient system that provides high-speed brain imaging for fMRI as well as regular body imaging, a parallel data acquisition system with eight 1 MHz channels of signal reception for enhanced imaging speed and for parallel imaging (e.g. SENSE, SMASH techniques), as well as multinuclear spectroscopy (MNS) hardware including a 2nd RF transmitter for dynamic polarization studies. The Siemens Syngo operating system is used on the Windows-based host computer. The unique performance features of this MRI system provide specific advantages for brain imaging research. The short-bore magnet provides a low incidence of claustrophobia. The gradient rise time (200 mT/m/ms), peak gradient strength (40 mT/m per axis) and duty cycle (up to 25 64x64 echo-planar images per second) are the best in the industry for whole body systems. Parallel imaging technology allows EPI images to be acquired with higher temporal resolution and with less distortion, providing novel functional imaging studies to be performed. 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.
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.
The IRC operates a data analysis cluster consisting of a 4 TB RAID array and
four dual-Xeon Linux compute nodes connected by a 2 Gbps switched Fibre Channel fabric.
Two file servers provide peripheral data storage,
and all data is protected by nightly backups to a 7 TB RAID array.
All servers enjoy Gigabit network bandwidth.
Image transfers to workstations from the MRI host computers or from the satellite
MRI system workstations (Leonardo (Siemens) and Advantage Windows Workstation (GE))
are done using DICOM compatible transfer software,
derivatives of Siemens and GE research software, or FTP.
Raw data transfers are also done using remote copy or FTP.
Software for post-processing includes custom programs written at UC Davis (BrainMRI, MRIView),
and third-party software packages (e.g. SPM2, FSL, MedX, AFNI).
Pulse sequence development takes place on Pentium 4 Windows workstations for the Siemens MRI system
and SGI and Sun computers for the GE MRI system.
A computer lab houses Pentium 4 Windows PCs for use by visitors and students.
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.
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.
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.
Two computers, one dedicated to each MRI system, provide for acquisition of MRI system events,
as well as acquisition of human 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.
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 human subjects for the MRI scanning sessions can be acclimated
to and trained for the fMRI studies.
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