Clinical Neuroscience Research Unit
MRI Facility Resources
MRI Research Magnet: The primary research instrument is a Philips 16 Channel 3T Achieva X- series full body magnet. It utilizes Dual Quasar gradients that perform at /80mt (40x2)/m peak, 200mt/m/ms slew rate. For brain imaging, an 8 Channel phased-array SENSE Head Coil is utilized. The facility has an onsite full-time MR clinical scientist (MR physicist) and is managed and operated by two dedicated research MR technologists.
The UVM MRI Center for Biomedical Imaging was established and supported in part by funding from the U.S. Department of Energy. Initial funding for the UVM MRI Center was received in 2006. The magnet was installed in April 2007 and operation began in July 2007. The federal grant was renewed in 2008 and again in 2010. In February 2009, the UVM MRI Center was selected by Philips for the first installation in North America of the Achieva 3.0T TX (multitransmit) magnet, one of four such magnets in the world at the time. The MRI Center is owned and operated by the University of Vermont for research purposes and is located in Fletcher Allen Health Care's McClure building and is utilized by a broad range of UVM/Fletcher Allen faculty and departments for both basic science and clinical research projects that focus on understanding more about disease and wellness, evaluating new treatments and therapies, and developing new techniques for diagnosis and treatment. More than 50 UVM research studies currently utilize the MRI Center for Biomedical Imaging.
In addition to the standard MRI instrumentation, there are additional elements necessary to deliver experimental stimuli, acquire subject responses and functional images, store images, and provide initial image analysis capability. This instrumentation includes both hardware and software.
We have two experimental stimuli/subject response systems:
The Eloquence system by Invivo includes an EMC shielded console that houses dual computers with software for experimental control, subject management and functional analysis. The computers generate, present, and archive functional fMRI experiments while maintaining millisecond level experiment control. One computer controls the magnet, triggering the magnet at the appropriate time, and captures images. The second computer is yoked to the first one and allows control of subject stimuli (both visual and auditory). This is a system which contains the components for experimental control as well as visual and auditory stimulus delivery systems. Eloquence contains a comprehensive and fully integrated set of hardware and software tools that provides the user with presentation, behavioral data collection and analysis for functional MRI (fMRI) assessment. This system utilizes E-Prime software for fMRI applications to program fMRI experiments including motor, language, memory, emotion, and decision tasks in block and/or event-related paradigms as well as experimental control software. The In-Magnet Module includes a Patient Video Display Hood which consists of a 15” diagonal LCD, 1024 X 768 resolution w/mount to Phased Array Head Coil, subject headphones consisting of electrostatic stereo headphones embedded in passive noise reduction earphones, 10 key Button Response Unit, radio frequency (RF) detector and console enabled TTL trigger for pulse-based synchronization, subject microphone, and set of MR -compatible, corrective lenses for subjects (± 1-7 diopter), and a fiber optic joystick.
The second system developed by Psychology Software Tools (PST) consists of several components: a MRI Digital Projection System includes a high resolution (1024x768) DLP Projector with RF filtered enclosure, custom lens assembly, digital video (DVI) over fiber, high flow fans, and internal thermal sensor. The system includes a high resolution lenticular pitch rear projection screen. Additional components include a magnet compatible projector stand, mirror stand, and rear projection screen stand as well as right and left Hand (5 Button) Fiber Optic MR Response Pads, Interface Console, and MRI compatible auditory stimulus presentation system.
While the Eloquence system is more integrated and easier to program and interface, the software interface is restricted to Eprime. The PST system is more flexible and allows attachment and integration of virtually any type of stimulus delivery or task software (Windows based such as Eprime, Presentation, or MATLAB) or Macintosh (e.g. HyperCard).
Additional available equipment for in-magnet room use includes:
We utilize the MR compatible BIOPAC system for monitoring vital signs. Components include the MP150 data acquisition and analysis system and AcqKnowledge software and includes hardware and software for ECG, pulse and respiration, and skin conductance. ECG: The MRI Electrocardiogram Amplifier will reliably record ECG from humans in an MR environment. The amplifier output can be switched between normal ECG output and R-wave detection. Pulse and Respiration: Pressure pad for measurement of pulse and respiration including a differential pressure transducer, sensor, and tubing. Skin Conductance: This device measures both the skin conductance level and skin conductance response as they vary with sweat gland (eccrine) activity due to stress, arousal or emotional excitement. The MRI compatible device uses a constant voltage (0.5 V) technique to measure skin conductance. The controls allow selection of absolute or relative skin conductance measurements.
Pain and Sensory Evaluation System:
Medoc Pathway MRI Compatible Pain & Sensory Evaluation System is used to deliver thermal stimulation during fMRI scanning and paradigm testing. This mobile system on a specially designed custom cart includes electronic base unit, heavy duty integrated cooling unit, analog output and TTL input & output. Additional components include a digital thermal calibration Ki, an fMRI-Compatible ATS Thermode (30X30mm), fMRI filter, and ATS Model Operating Software (for temps ranging from 0-54 C).
Additional Out of Magnet Resources Include:
The MRI Simulator provides a realistic approximation of an actual MRI scanner to allow habituation and training of participants in an environment less anxiety provoking than a real scanner. The MRI Simulator introduces the participant to the complete scanning environment permitting them to gradually become accustomed to the scanning procedure and trained to minimize movements. The simulator includes a 60 cm circular bore, realistic scanner body, mock head coil with participant view mirror, cooling fans and diffused lighting, amplified speakers with subwoofer for realistic scanner noise production and vibration, motorized participant table, MoTrak™ head motion tracking system capable of monitoring participant output based on user-defined criteria, SimFx™ software to emulate ambient scan room noises and pulse sequences, participant headphones a 15” LCD video display system with 1024x768 resolution and integrated display controls, and right and left hand button response units (5 buttons each hand).
Image/Data Storage and Archive System:
The large amount of data produced by even a single run of a subject for an fMRI experiment requires a large amount of redundant storage (approximately 700 MB per run). We utilize RAID servers (Redundant Array of Inexpensive Disks) which allows a large amount of storage with redundancy in case of disk failure. In addition, a tape backup system is utilized for archival storage of information from the RAID servers. The tape backup/archive system has nightly backups (incremental) run to LTO tapes and the Ultrium Tape Library Monday night through Friday night. Weekly backups (stored indefinitely off-site) are sent to the MagStar tape device on Sunday night. MagStar tapes are sent to the local hospital Disaster Recovery Data Center each Monday and are marked for permanent retention.
The Vermont Advanced Computing Center (VACC) supports computationally-intensive research and high performance computing (HPC) services at the University of Vermont (UVM). The VACC is a university-wide Center, managed and coordinated with priority initiatives in the Office of the Vice President of Research. At the core of VACC is a 7.1 teraflop computing cluster -- an IBM e1350 known as the Vermont BlueMoon. The IBM Bluemoon cluster has 284 nodes providing 1420 compute cores connected to an IBM DS4800 providing 50 terabytes of raw storage.
In collaboration with the BIP, the VACC has implemented cluster level computing for computationally intensive brain anatomical analyses including voxel-based morphometry (VBM) utilizing FSL and SPM and internal segmentation and parcelation of brain structures utilizing Freesurfer. Imaging data is moved smoothly from image storage servers from the hospital IT system (as well as the University system) to the BlueMoon cluster and back without firewall interference. This facilitates multi-subject analyses that would take weeks using single workstations to be completed in as little as a few hours.
We have multiple high performance (PC and Mac) analytical workstations for brain image processing, utilizing FSL and Brain Voyager for fMRI and structural analysis. We also have access to proprietary Phillips workstations for specialized applications.
fMRI Study Group: This group consists of a weekly paper review/journal club format where new literature is reviewed by the participants and experimental proposals can be informally discussed.
fMRI Users Group: This group meets monthly and consists of active investigators utilizing the Brain Imaging Core resources. This meeting will offer opportunities for group consultation regarding experimental and technical problems in functional and structural brain imaging for individual investigators as well as involving individual investigators and COBRE trainees in decisions regarding Brain Imaging Core resources, strategic planning, and administrative issues.