Perelman School of Medicine at the University of Pennsylvania

Center for Magnetic Resonance & Optical Imaging

Resources


A list of resources for CMROI are available below.

MRI-NMR Resources

NMR/MRI Research Facilities

The primary instrument of the Resource is a 7 Tesla whole-body Siemens MRI scanner is located in the basement of the Stellar Chance Building on the School of Medicine campus. It is dedicated to 100% multi-nuclear MRI research. The system is capable of performing imaging and spectroscopy studies on a variety of NMR visible nuclei, including 1H, 31P, 13C, 23Na, 19F, 17O, 7Li, 14N, 15N, 129Xe, and 3He. The pulse-programming environment allows for development of sophisticated pulse sequences. The 7T system is equipped with a 32-channel head coil. This system also includes RF coils for 31P and 13C NMR spectroscopy and a custom hybrid head/neck coil for arterial spin labeling. A parallel transmission system is also available and can be used in conjunction with an 8-channel transmit/receive array. An outboard GPU processor has been interfaced with the 3T and 7T systems to allow rapid image reconstruction for multiband EPI and other high-throughput imaging. Sequences performed at the Resource have included T1ρMRI, Sodium MRI, multiple quantum spectroscopy and imaging, MR elastography, localized spectroscopy, and perfusion imaging.

Additionally, the Department of Radiology currently houses Siemens Sonata and Symphony scanners operating at 1.5 Tesla and 3.0 Tesla. The research scanners operated by the Center for Advanced Magnetic Resonance Imaging and Spectroscopy are located within the Hospital of the University of Pennsylvania and are staffed with MRI technologists skilled in imaging research protocols. The scanners are equipped with full physiological monitoring capabilities, crash carts, and are accessible to Hospital code teams. All scanners are capable of parallel imaging and equipped with a variety of RF array coils. An on-site engineer is available to maintain the scanners in the event of technical malfunction.

A Siemens Magnetom Trio 3T whole-body MRI system is managed by the Center for Functional Neuroimaging exclusively for neuroscience neuroimaging and includes a 32-channel head receiver array. Extensive ancillary instrumentation is available on this system for fMRI, including projection systems, audio systems, video monitoring, pupillometry and eye tracking, button/joystick, trackball interface, and noise cancelling microphones.

A second neuroscience dedicated 3T MRI (Siemens Prisma) system has been installed in the basement of the Stellar Chance Building in an unoccupied bay in CMROI adjacent to our 7 Tesla whole-body system. This system has a 64-channel head/neck receiver and “connectome” gradients.

Mock MRI Scanner. A full-sized mock MRI scanner fabricated from the shell of a decommissioned 1.5T GE Signa MRI system is located in the CfN/NNC, approximately 2 minutes from the real MRI scanners and is equipped for fMRI stimulus delivery, synthetic scan sounds, and real-time inertial head movement monitoring.

MRI Compatible EEG System. BrainAmp MR Plus system (Brain Products, Gilching, Germany) for recording EEG signal in the MR scanner simultaneously with fMRI acquisition. The hardware of this system consists of a MR compatible amplifier, two MR compatible power supplies, four 32-channel MR-compatible caps, and three 14-channel MR-compatible caps specifically designed for sleep study. This system also includes a complete set of softwares, including the Recorder for multifunctional EEG signal recording, the Recview for real time data analysis, and the Analyze 2 for offline data analysis.

MRI Compatible TMS System. A MagVenture MRI compatible system configuration based on the MagPro X100 with MagOption magnetic stimulator and the MRi-B91 coil is on order for use with our new 3T MRI system. This device provides the flexibility to do up to 100 pps (100Hz) stimulation rates. Besides the Biphasic waveform, it also offers capabilities to do Monophasic, Half Sine and Biphasic Burst (Theta Burst) waveform by simple selection from the screen menu, offers versatile trigger in/out capabilities to ensure easy interface with EEG, EMG and EP equipment, monitoring and read out of the realized output values (di/dt), storing and transferring stimulation/ system status data for each and every pulse in any given protocol. Within the user interface users can design and store up to 27 different protocols which can be easily recalled by simply push of a button.

MRI Compatible tDCS System. The neuroConn DC-STIMULATOR PLUS is a micro-processor-controlled constant current source. It features multistage monitoring of the current path and by continuously monitoring electrode impedance it can detect insufficient contact with the skin and automatically terminate stimulation. A remote mode enables external control by a voltage supply source and filter boxes and cables are available for operation within an fMRI scanner. The fMRI module module allows artifact-free MR images even during EPI sequences and has been tested for 1.5 and 3 Tesla scanners.

Animal MRI Scanning. The MR laboratories in the Small Animal Imaging Facility (SAIF) are located in two facilities: in the basement of the John Morgan Building in the Perelman School of Medicine and in the basement of the Founders Building of the Hospital of the University of Pennsylvania. The Morgan facility houses a state of the art Varian 9.4 Tesla horizontal bore small animal MRI system. This system is equipped with 12 and 21 cm gradient insert tubes with maximum gradient strengths of 40 and 20 G/cm and a switching time of 200 µsec (Magnex Scientific, Abingdon, UK). This system is interfaced to a multi-nuclear dual channel DirectDrive console (Agilent, Palo Alto, CA) with full gradient and RF shaping capabilities and four-channel receiver array. The receiver train of the DirectDrive console digitizes the data at the full bandwidth of the IF (20 MHz) with 14-bit resolution. The system is equipped with a variety of coils including; a 72 mm ID dynamically detunable linear birdcage, a 4 channel phase array coil suitable for rat brain imaging, a 4 channel phase array coil suitable for mouse brain imaging, a 20 mm ID circularly polarized birdcage suitable for mouse brain.

A newly constructed preclinical imaging lab located in the Smilow Center for Translational Research adjacent to the Perelman Center for Advanced Medicine now houses a 4.7 T 50 cm horizontal bore and a 9.4 T 8.9 cm vertical bore animal MRI scanners. The consoles on both systems were upgraded in 2009 and 2010 to the DirectDrive consoles. The 4.7 T system is equipped with a 39 cm ID gradient tube with a maximum gradient strength of 3 G/cm and a 12 cm ID gradient insert with a maximum gradient strength of 25 G/cm. The upgrade included a 4-channel receiver array and an assortment of M2M RF coils that include a dynamically detunable 72 mm ID linearly polarized birdcage, a 4 channel phased array suitable for mouse brains, a 4 channel phased array suitable for mouse brains, a 20 mm circularly polarized birdcage suitable for mouse brains, a 35 mm ID circularly polarized birdcage suitable for rat brains, and a 72 mm ID circularly polarized birdcage suitable for rat abdomens. A fully equipped animal surgery room is adjacent to the MR installation, with the facilities for surgery and animal preparation for MR imaging of large and small animals. A 3 Tesla Siemens Trio (clinical) system is also installed at this location for large animal MRI.

The 9.4 T vertical bore Is a three-channel Direct Drive system is equipped with 5 mm, 10 mm and 20 mm Varian and Doty double and triple tuned multinuclear high resolution probes. The system is configured with a 55 mm ID 100 gauss/cm gradient insert. A variety of resonators specifically designed for observation of tumor xenografts in mouse models have been constructed in house for use with this system. In addition, 20 mm ID and 11 mm ID resonators suitable for high resolution MR microscopic imaging and high resolution diffusion tensor imaging of fixed rat and mouse brains are available for use with this system.

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Hyperpolarized Resources

The Resource has created a laser facility for producing hyperpolarized noble gases, and imaging and spectroscopic measurements of hyperpolarized 3He and 129Xe have been performed in vivo.

  1. GE Healthcare optical pumping 3He polarizers (x2)
    • These devices are capable of producing up to 1.2 liters of 30 – 35% polarized 3He gas in approximately 10 hours. 3He has been successfully used for regional structural and functional imaging of upper and lower airways in animals, as well as humans. 3He is however an inert gas and does not take part in any chemical or metabolic process, and therefore its application is limited to the abovementioned studies.
  2. Home-built optical pumping 3He polarizers (x2)
    • These devices are capable of producing up to 1.5 liters of 45 – 55% polarized 3He gas in approximately 12 hours. 3He has been successfully used for regional structural and functional imaging of upper and lower airways in animals, as well as humans. 3He is however an inert gas and does not take part in any chemical or metabolic process, and therefore its application is limited to the abovementioned studies.
  3. GE Healthcare parahydrogen-induced 13C polarizer
    • This device is capable of producing 5 – 15 ml of 40 – 50% polarized 13C in approximately 3 minutes. 13C has applications as contrast agents in in vivo MRI imaging in small animals. Toxicity of certain 13C compounds limits its use.
  4. Home-built parahydrogen-induced 13C polarizer
    • This device is capable of producing 4 – 10 ml of 40 – 50% polarized 13C in approximately 30 seconds. 13C has applications as contrast agents in in vivo MRI imaging in small animals. Toxicity of certain 13C compounds limits its use.
  5. Parahydrogen Production System
    • In addition to the two listed parahydrogen 13C polarizers, our hyperpolarized 13C facility includes a cryogenic parahydrogen generator and an ortho/parahydrogen measurement device. The devices are capable of polarizing suitable 13C compounds through parahydrogen-induced polarization transfer technique with substrates such as hydroxyethyl acrylate. We have successfully achieved polarization levels as high as ~90% in the “para” state.
  6. Oxford Instruments Hypersense System
    • This device is capable of polarizing a large assortment of biologically friendly molecules, including pyruvate, with a range of polarization (5 – 18%) depending on the compound. This device is limited by the sample cup size, magnetic field strength making it suitable for small animal experiments.
  7. Home-built optical pumping 129Xe polarizer
    • This device is capable of producing 20 ml/min nearly 10% polarized 129Xe gas almost continuously. 129Xe has been used for regional functional imaging of lower airways in animals.This capability can be easily extended to humans by increasing the production rate of this polarizer. 129Xe is however an inert gas and does not participate in any chemical or metabolic process in the body. Limited spectroscopic information is available from hyperpolarized 129Xe, which used for in vitro studies can elucidate certain aspects of lung function, but it is not generally applicable to metabolic processes or other organs.

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Optical Resources

  1. Diffuse Optical/Correlation Tomography Instrument (Adult Brain)
    • There are two identical (in functionality) instruments.Three laser diodes and drivers (675, 785, 830nm) with coupling optics and fibers are used as sources and the sources are further coupled to a series of fast, optical switches (two 1×4 prism switches, DiCoN). Furthermore, a high coherence length, external cavity laser (780nm) from Crysta Laser with a stable laser driver, optical isolator and coupling optics is also used. Two high sensitivity, fast avalanche photo diodes (APDs) and two large sensor area photomultiplier tubes (PMTs) all from Hammamatsu and eight high sensitivity, fast, photon counting APDs (Perkin-Elmer) are used as detectors. Extensive radio-frequency (RF) electronics (RF oscillators, I/Q demodulators, electronic attenuators, amplifiers, shielded cables) from Mini-Circuits are used to encode/decode signals. A custom-build (Correlator.Com) eight channel, multi-tau, correlator board is used to calculate auto-correlation functions of detected photons. Two A/D boards and two DIO boards (National Instruments) housed in a rack-mounted personal computer are used to control the instrument and record the data. A 20″ LCD screen displays the data and interface (Dell). Variety of custom-build probes housing series of fiber-optics are used with the instrument to couple the instrument to adult head. The portable instrument is housed on a 19″ rack-mount, medical instrumentation cart
  2. Diffuse Optical/Correlation Tomography Instrument (Rat Brain)
    • Five laser diodes and drivers (675, 785, 830, 915 nm) with coupling optics and fibers are used as sources and the sources are further coupled to a series of fast, optical switches (one 1×16 and one 1×8 prism switches, DiCoN). A high coherence, high power, diode-pumped, diode laser (SDL) working at 800nm is also used with an optical isolator, portable, stabilized optical bread-board and coupling optics. Eight high sensitivity, fast avalanche photo diodes (APDs) from Hammamatsu and nine high sensitivity, fast, photon counting APDs (Perkin-Elmer) are used as detectors. Extensive radio-frequency (RF) electronics (RF oscillators, I/Q demodulators, electronic attenuators, amplifiers, shielded cables) from Mini-Circuits are used to encode/decode signals. A custom-build (Correlator.Com) nine channel, multi-tau, correlator board is used to calculate auto-correlation functions of detected photons. Two personal computers are used to control the instrument and acquire data. Each has two A/D boards and two DIO boards (National Instruments) to interface with the instrument. The interface and data are displayed on two 14″ LCD screens. A custom-build fiber-optics probe (FiberOptic Systems) with a large number of fiber-optics are held in a grid coupled to the back of a modified SLR camera (FM2N, Nikon) is used to relay the light to and from the tissue. The instrument is portable on a custom-build rack mount set-up secured on an instrumentation cart.
  3. Laser Speckle/Optical Intrinsic Imaging Instrument
    • The source part consists of a collimated, laser diode (Hitachi, HL 785 1G, 785nm, 50mW, Thorlabs) driven by a custom-made driver and coupled to collimating/focusing optics and a white light, arc-lamp source (Oriel) coupled to optics and a fast, computer controlled filter-wheel (ASI) with a selection of filters between 400-650nm wavelength range. The data is acquired by a 12-Bit, TEC cooled CCD camera (QImaging, Retiga 1350EX) using imaging software (StreamPix, NorPix) coupled to a 60-mm lens (AF Micro-Nikkor 60mm f/2.8D, Nikon). Two personal computers (Dell) running in parallel are used to store the data and trigger various components. For triggering and high-precision timing an A/D board (DataWave Technologies) is used. The data is stored on a fast RAID array (320Gb) of hard drives working in parallel. The data and control interface is displayed on two 20″ LCD screens (Dell).
  4. Board Assembly Laboratory
    • The Penn HEP Engineering Group board assembly and test lab is a 400 square foot facility with state of the art tools for prototype board assembly and repair. The lab includes IR desoldering tools, robotic solder paste application tools, optical examination systems, and soldering ovens. This facility is capable of assembling or replacing fine pitch ball grid array and chip scale packages as well as the older TQFP and SOIC devices.
  5. System Test Laboratories
    • The Group also has to several electronics system testing laboratories available for use in verifying operation of advanced electronics. Tools include oscilloscopes (up to 1 GHz bandwidth), pulsers up to 300 MHz repetition rate and sub ns rise time, pattern generators, signal generators, power supplies, temperature and voltage measuring and logging systems, and a variety of VME based custom data acquisition systems. The Group also has an eighty pin, 400 MHz, Integrated Measurement Systems (IMS) model MSTS mixed analog/digital integrated circuit tester. The IMS tester is unlikely to be necessary for this work, but is a way to get a fast, extremely programmable pattern generator and logic analyzer attached to a recalcitrant system.

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Oversight / Regulatory

All human research is performed under guidelines set by University of Pennsylvania’s Institutional Review Board (IRB) with full accreditation by the Association for the Accreditation of Human Research Protection Programs. Accreditation standards establish the highest expectations for the conduct and oversight of human research. Further oversight of all MRI-based research on the clinical scanners is provided by the Center for Advanced Magnetic Resonance Imaging and Spectroscopy (CAMRIS), located within the Department of Radiology of the Hospital of the University of Pennsylvania.  It is responsible for maintenance, safety and staffing of Siemens human research MRI systems in the Department.  Maintenance includes service, upgrades and cryogen refills.  In addition to MRI technologists skilled in imaging research protocols,  an on-call Radiologist is available and the scanners are equipped with full physiological monitoring capabilities, crash carts, and are accessible to Hospital code teams.  A local Siemens engineer is available to address malfunctions. A CAMRIS committee reviews applications for MRI research studies on the Siemens systems for safety and feasibility and provides approval.

The University of Pennsylvania has a complete ALICE-approved small animal care facility.  It is maintained by a fully licensed, NIH-approved University Laboratory Animal Resource (ULAR). Facilities provided by ULAR include boarding, routine inspection for disease, treatment, surgical facilities, and assistance from veterinarians. This facility is fully accredited by AAALAC, demonstrating compliance with NIH Guidelines. The Institutional Animal Care and Use Committee (IACUC) oversees the operation of all animal facilities and approves all protocols for animal use. The Department of Radiology provides further support and oversight through its Small Animal Imaging Facility (SAIF).  In addition to the Animal Resource Center facilities, a surgery room equipped with complete surgical facilities and monitoring equipment is available with equipment such as anesthesia equipment, animal respirator and ventilator, EKG, transducers and hemodynamic monitors are available.

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Miscellaneous Facilities

RF laboratory

A well-equipped RF laboratory with state of the art test equipment including two network analyzers (10 MHz to 1.3 GHz), a vector impedance meter (1-100 MHz), a sweep generator (1-400 MHz), a spectral analyzer (1-400 MHz), two 500 MHz oscilloscopes, two frequency synthesizers (0-160 and 0-500 MHz) and a function generator. The facility also includes all necessary equipment for constructing coils and customized circuits.

Machine shop

A fully equipped machine shop is available for fabrication and repair of devices for MR research including phantoms, probes, coils, perfusion apparatus and animal positioners.

Animal Surgery Room

A fully equipped animal surgery room, an analytical biochemistry laboratory, tissue culture laboratory, and a synthetic organic chemistry laboratory are available for use.

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