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Center on Human Development and Disability
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Technical Support and Development Component

    Brain Imaging pictures
Swati Rane photo
Swati Rane, Ph.D.
Director, Brain Imaging Core
Director, Technical Support and Development Component

Chris Gatenby photo
Chris Gatenby, Ph.D.
MR Physicist

Donghoon Lee
Donghoon Lee, Ph.D.
High Field MRI Director
Robert Miyaoka
Robert Miyaoka, Ph.D.
Small Animal PET Imaging Director

Magnetic Resonance Imaging

The MR research facilities have been configured with support capabilities for carrying out complex structural and functional imaging experiments. The Diagnostic Imaging Sciences Center (DISC) houses the research-dedicated Philips 3T MRI magnet and provides technical support for development and implementation of study-specific imaging protocols. As indicated on the campus map, DISC is located adjacent to CHDD’s Medical Research Tower to CHDD’s behavioral phenotyping facilities in the Clinic Building (see Behavioral Evaluation Center in Resources section of Clinical Translational Core).

DISC 3T Scanning facility: The DISC scanner supports most IDDRC affiliate neuroscience imaging research. A recent upgrade for the DISC scanner was made possible by a successful S10 NIH Instrumentation Grant funding (PI: Grabowski, S10OD023454) and UW support. When the upgrade is fully complete in 2019, it will provide digital (fiber-optic) coil connection technology as well as support for simultaneous multi-slice (SMS) or multi-band imaging, which will improve image quality (higher signal to noise ratio by 10-40% depending on application) as well as reduce acquisition times by 2 to 3-fold. This is especially desirable when imaging children, especially those with IDD, where there is an increased chance of involuntary motion and related artifact. The 3T MR system is equipped with a 32 channel RF system and multinuclear spectroscopy capabilities for measurement of 31P, 13C, 23Na, or 19F elements. There is a full range of available RF coils for human brain, neurovascular, head and neck, spine, extremity, and body imaging.

Ancilliary Imaging equipment: Extensive additional support equipment is available in the imaging labs for complex neuroimaging research studies. These include physiologic monitoring systems for:

  • ECG signal monitoring
  • Respiratory rate
  • Non-Invasive blood pressure measurement
  • Pulse oximetry
  • End tidal CO2

Customized fMRI paradigm presentation and subject response hardware and software (E-Prime 2.0 Professional Suite, Psych Toolbox, Presentation, Inquisit, PsychoPy) are installed that provide high quality audio and visual presentation. Available fMRI stimulus equipment includes:

  • A computer-controlled LCD projector with a long throw lens that projects onto a back-projection screen located within the bore of the magnet for visual stimulus presentation
  • A pair of five button, two-hand fiber optically coupled response boxes
  • A pair of single button, carbon wire response boxes for use with each hand
  • Audio presentation is provided using a high performance tightly controlled amplifier (Crown D-75) with improved talkback system coupled with high dynamic range piezo-electric headphones
  • A set of pneumatically driven audio headphones is also available for less critical audio use
  • A phase canceling microphone that actively suppresses background noise from the MR gradients to better hear subject audio responses during an fMRI study
  • Two different eye tracking systems (EyeLink 1000) are in place, each available for affiliate use, depending on their preference, to provide correlation of visual focus with fMRI acquisition
  • MRI compatible eye-glasses with pre-made lenses of all diopters
  • A specially developed hand writing system that enables fMRI testing of subject written responses while in the magnet bore
  • Weighted blankets to reduce motion in small children
  • A Pearl-Tec Crania is available for children and adults. It is a subject positioning aid made of air chambers filled with polypropylene pearls and adapts to the patient’s head shape while minimizing motion artifacts, thereby improving image quality and reducing the number of exam repetitions.
  • BIOPAC( See Human Electrophysiology component)

South Lake Union 3T Scanning facility: A second research-dedicated Philips 3T MRI system is housed at the South Lake Union (SLU) facility, The SLU scanner and spectrometer were upgraded in 2017 to the 3T Ingenia System. The SLU facility operates with a stronger focus on human vascular biology imaging. It also serves as a site for additional MR neuroimaging and supports ultra-high field, high resolution mouse imaging research utilizing an 8.9cm bore 14T available for IDDRC affiliates.

Information Technology for Storage of MRI Data

Bioscribe/PACSoft. The Brain Imaging Core provides systems for secure storage and retrieval of experimental research data using a high speed, large capacity redundant DICOM image storage system called PACSoft. This system has been in use for over a decade and can handle multiple terabytes of image data that provides more than adequate storage for years of data. In addition to the PACSoft image archiving system, there is an overarching research metadata database called Bioscribe that can manage image data related to individual subjects and to specified research studies and link these together with all of the corresponding text-based and graphical data (i.e., medical histories, medication information, physiological measurements, etc.) acquired at the time of imaging. Bioscribe links processed image files with metadata and with appropriate source image files stored in PACSoft that are related to a specific experiment. Bioscribe thus allows complete storage, integrity, and security of research data from various projects. Data are stored by project, by individual experiment, and by Principal Investigator (PI), and is accessible only by the PI and his or her designated associates for a given project. Data can be shared between investigators if permission is granted by the PI in charge of a given project. The PI can designate as many associates as desired to access, store, manipulate or retrieve data, depending on the level of permissions granted. Thus, this system is very powerful and provides complete data security and HIPAA compliance.

Extensible Neuroimaging Archive Toolkit (XNAT). While Bioscribe has served the imaging lab well for years, it now serves as a backup system. XNAT is an open-source eXtensible Neuroimaging Archive Toolkit developed by the NRG at Washington University in Saint Louis. This imaging informatics platform provides the functionality of the combination PACSsoft and Bioscribe systems and adds support for pipeline processing. In addition, XNAT has a large and growing user community. XNAT is hosted on an HP ProLiant DL 380p Generation 8 server with 20TB of storage (12.7 TB RAID 6). The XNAT system is the successor to PACSsoft / Bioscribe and is being used for all ongoing and new studies.

These storage systems are periodically upgraded and maintained by the DISC computer system administrator from DISC and IBIC. Two computer system administrators maintain the XNAT and Bioscribe serves as well as the IBIC computer storage and image analyses platforms.

Mock Scanner:

Mock scanner photo
Mock scanner to prepare children and anxious adults for their MRI session.

Our mock scanner includes scanner bore, cowling, and table geometry that is an exact replica of the current Philips scanner. It also incorporates a 32-element head coil shell procured from Philips, and hardware that emulates table vibration, gradient switching noise, and AV task presentation identical to the Philips 3T system. It contains a head motion tracking and training system that is especially valuable for reducing head motion in scans of children. It is sited adjacent to the DISC MR Lab allowing researchers to schedule mock scanner sessions shortly prior to their 3T scan experiment. A stimulus presentation computer running E-prime, Presentation, Inquisit, and PsychoPy paradigm presentation software and attached button boxes allow experimental tasks to be transacted in the mock scanner just as they are in the 3T. A trakSTAR tracker from Ascension Technology Corporation with a MoTrak console allows for continuous monitoring of head position and training to reduce head motion.

High-field, Small Animal Imaging

In addition to the DISC 3T, a specialized, smaller bore High-Field (4.7T) and Ultra High-Field (14T) MRI units are available for small animal studies on the SLU campus. An Avance III 14T (600 Hz) Ultra-shield high-resolution 89 mm vertical bore magnet system from Bruker includes state-of-the-art Bruker shimming systems, digital amplifiers and filters, MRI/MRS radiofrequency coils, Paravision software and Topspin software to generate high signal-to-noise ratio, and high-resolution images/spectra from in vivo mouse and biological tissues. This system is equipped with physiological monitoring and gating capabilities for use in in vivo acquisitions. The 14T MR scanner is utilized for in vivo mouse brain, body, heart and skeletal muscle imaging and spectroscopy. The lab is equipped with RF coils for 1H, 31P and 23Na: 25 mm ID (inner diameter) 1H birdcage custom-built RF coil, 30 mm ID 1H/31P volume coil, 30 mm ID 1H/23Na volume coil and 20 mm 1H/31P surface coil and animal monitoring system from SA instrument (Model 1024).

Positron Emission Tomography/Computed Tomography

The PET facilities provide support for microPET/CT and primate PET imaging, as well as a near-infrared camera system for Indocyanine Green (ICG) fluorescence imaging. The Primate PET imaging operation is located in the J-wing of the Health Sciences Building, which lies in close proximity to several other facilities includes the Infant Primate Research Laboratory that works closely with the Animal Behavior Core. Small Animal PET/CT Imaging resources include a Siemens Inveon dedicated PET docked with a Siemen microCT system and supports biologic research for IDDRC affiliates. The Inveon PET/CT is a third-generation product that provides high (>5% absolute) detection efficiency; whole body mouse imaging capability (12.7 cm axial field of view); rat imaging (10 cm transverse field of view); and a full portfolio of image reconstruction tools. The system achieves ~1.5 mm image resolution at the center of its field of view using 2D filtered back projection and slightly better using 3D iterative image reconstruction methods. The combined PET/CT system provides accurate PET image quantitation and fused PET/CT image viewing to provide excellent anatomic localization of PET tracer activity. In addition to the Inveon PET/CT system, other resources available to support imaging studies are two anesthesia units; a Capintec dose calibrator; a Packard Cobra II gamma counter; physiological monitoring equipment; and two HP workstations for off-line image reconstruction and image analysis. The system is located within the newly constructed UW Animal Research and Care Facility (ARCF) and resides within a special suite of rooms constructed to support small animal imaging. Therefore, for most imaging studies the animals remain within the barrier-controlled vivarium. Further in addition to the small animal imaging resources, UW Radiology also operates a radiochemistry/cyclotron facility for generation of PET radiotracers with easy access to the ARCF.

The new UW ARCF building has helped centralize animal housing at the UW main campus. The top floor of the facility is for small animal and rodents while the bottom floor is for larger animals and primates. While not all of the imaging equipment for small animals is located within the ARCF there is ready access to the major MR facilities via connecting corridors within the ARCF, the Health Sciences Building, and the other vivariums operated by the Department of Comparative Medicine. For serial (long term) imaging studies, animals can be transported from the vivariums or the Infant Primate Research Laboratory to the various imaging facilities without having to exit the building. IACUC approved short-term holding cage rooms in the imaging facilities for MRI and primate PET are available. All imaging suites are approved for Biosafety Level 2 studies.

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University of Washington • Center on Human Development and Disability Box 357920 • Seattle WA 98195-7920 USA • 206-543-7701 • chdd@uw.edu