Brain Imaging Core
The Brain Imaging Core (BIC) provides technical and scientific support for multimodal brain imaging (including MR, PET, microPET and electrophysiologic imaging) for IDDRC Research Affiliates who wish to use neuroimaging methods to address research questions pertinent to intellectual and developmental disabilities (IDD). The overall goal of the Core is to train and assist affiliates in conducting research using a variety of advanced imaging modalities. The Core is organized into four highly interrelated components: (1) technical support and development; (2) image analysis; (3) human electrophysiology; and (4) small animal imaging. All components of the Core are organized to inform CHDD affiliates of the advantages (and pitfalls) of useful technologies and to provide expert technical guidance for both investigators inexperienced in imaging techniques as well as experienced neuroscientists. To maximize resources in this highly complex field, the Brain Imaging Core operates in collaboration with the MR Research laboratory and the Integrated Brain Imaging Center (IBIC) which are part of the Department of Radiology.
The Brain Imaging Core provides affiliates with assistance in all aspects of study design, implementation, and support using several modern brain imaging techniques that are capable of evaluating brain structure and function. Specifically, the Core provides: (a) expert technical guidance in study design, such as development of optimal imaging parameters, pulse sequence development, computer generated EEG source imaging methods, and appropriate functional brain imaging task design; (b) expert technical assistance and support for image acquisition, storage, and transfer; (c) training in multiple image analysis techniques; (d) assistance in preparing research subjects for scanning; (e) development of specialized custom techniques and equipment; (f) assistance in developing experimental animal imaging protocols; (g) training of affiliates and their graduate students and postdocs in safe use of the MR and EEG/ERP imaging equipment; (h) opportunities for information sharing among affiliates interested in brain imaging research to promote collaboration; and (i) limited financial support for pilot projects involving these Core facilities.
The Technical Support and Development Component specific services:
- To help design, implement, and test advanced MR methods for application to address unique neuroscience questions.
- To build novel MR pulse sequence designs needed to address specific experiment designs.
- To design and build unique new RF receiver coils for optimizing imaging and spectroscopy applications in the CNS. Some experiments would be difficult or impossible to successfully carry out without fabrication of these new RF coils.
- To provide consultation and expert support in physics, medical applications, and technical implementation to promote the use of neuroimaging in neuroscience research relevant to neurodevelopmental and neurodegenerative disorders.
- To provide access to neuroimaging equipment and imaging support for pilot studies in order to promote innovative new ideas and help provide seed data necessary for applying for grant funding to conduct a larger formal study.
- To introduce young neuroscience researchers to neuroimaging methods and train them in proper use and application of these methods for addressing their research hypotheses.
- To disseminate our neuroimaging advances through presentations at meetings and peer-reviewed publications so others may apply similar techniques and to provide shared information and opportunities to investigators in other IDDRCs.
The Image Analysis Component specific services:
- In collaboration with IDDRC-supported staff and scientists from the Integrated Brain Imaging Center and MR Research Lab, provide affiliates with expert technical guidance in study design. This includes development of fMRI tasks, multimodal image integration, measurement methods for structural MRI, and general help with research methodology.
- Assist affiliates in acquisition of quality neuroimaging data. This includes training and assistance in the use of the mock scanner and acquisition of neurophysiological measures during scanning.
- In conjunction with the Technical Support and Development component, train and assist affiliates in efficient and user-friendly methods for data transfer and storage. This includes use of the “XNAT” system for data transfer and storage, transforming new 3T imaging data formats to formats usable by software programs, and development of scripts and software solutions to address specific imaging problems (e.g., corrupted data, images with residual motion, susceptibility, etc.)
- Train and assist affiliates in using the most appropriate data analysis techniques. This includes development of new analysis techniques as well as providing group training sessions and individual consultation to solve analysis problems specific to individual investigators. It also includes training in the use of IBIC-supported image processing workflows using IBIC servers.
- Assist with proposal development and dissemination of findings. This includes image creation for publications, writing and reviewing sections of grant proposals relevant to neuroimaging, assisting in budget development for grant proposals, and assistance with IRB applications.
- Provide opportunities for information sharing among affiliates interested in brain imaging research. These include formal didactic sessions, invited speakers, and informal sessions to promote collaboration among affiliates, as well as regular meetings of IBIC Scientific Interest Groups and web-based tutorials that are also available to brain imaging researchers outside of CHDD.
The Human Electrophysiology Component specific services:
- Provide and maintain a state-of-the-art electrophysiology laboratory for Research Affiliates that can be used for piloting, testing, and designing studies. Methods made available in the laboratory include both electrophysiology and autonomic measures, such as heart rate and electrodermal responses.
- Assist in the design of experiments, and the design, creation, and delivery of stimuli for electrophysiology studies. This often includes creating novel experimental paradigms and stimuli (e.g., moving targets for studies of attention, talking faces for studies of auditory-visual linguistic processing).
- Provide access and training to use MR-compatible EEG acquisition system for concurrent recording of EEG/ERP in MRI scanner, including consultation on design of MR acquisition protocols optimized for MR artifact removal.
- Train investigators and their assistants in all phases of conducting electrophysiology studies, including net and sensor application, data recording, artifact editing, and analysis.
- Provide consultation regarding co-registration of ERP and MRI, source localization, and the advantages and disadvantages of different ERP analysis methods. Consultation often includes development of new methods for ERP analysis (e.g., wavelet analysis, gamma analysis) to address new areas of interest by investigators.
- Provide consultation on the purchase of new equipment and software for CHDD investigators who have their own electrophysiology laboratories, including researching, reviewing, and writing specifications for new equipment and software related to all aspects of observational and/or electrophysiology studies.
- Trouble-shoot all aspects of technical problems arising in developing, piloting, and implementing studies using electrophysiological methods, both at the Core's laboratory, as well as investigators' laboratories.
- Offer seminars on new equipment, experimental designs, and analytic techniques.
The Small Animal Imaging Component specific services:
- Provide access to equipment and expertise needed to perform in vivo radiological assessments of small animals (rodents to primates).
- Provide support to enable studies using standard (3T) and high 7T and 14T energy MRI, nuclear imaging by positron emission tomographay (PET) or single photon emission computed tomography (SPECT) and near infrared (indocyanine green or ICG) optical imaging.
- Assist investigators with experimental design, IACUC protocol development, imaging processing and quantitative analysis as well as histological confirmation/registration of novel tracking methodologies.
Faculty & Staff
|Technical Support and Development Component
Ken Maravilla, M.D.
Director, Brain Imaging Core
Director, Technical Support and Development Component
Chris Gatenby, Ph.D.
|Image Analysis Component
Thomas Grabowski, M.D. Director, Image Analysis Component
Julia Owen, Ph.D.
Research Scientist, Image Analysis Specialist
|Human Electrophysiology Component
Neva Corrigan, Ph.D.
Director, Human Electrophysiology Component
Mark Pettet, Ph.D.
|Small Animal Imaging Component
Donghoon Lee, Ph.D.
Co-Director, Small Animal Imaging Component
Robert Miyaoka, Ph.D.
Co-Director, Small Animal Imaging Component
Gregory G. Garwin, M.S.
To Use Our Services
Investigators who are interested in using brain imaging in their projects are invited to read about the equipment and services we provide, then email a one-paragraph description of your project so the Brain Imaging Core can direct you to the proper personnel and provide pre-project consulting:
- For Technical Support and Development information, contact Dr. Ken Maravilla (email@example.com, 206-685-0457).
- For Image Analysis information, contact Dr. Tom Grabowski (firstname.lastname@example.org, 206-685-0457).
- For Human Electrophysiology information, contact, contact Dr. Neva Corrigan (email@example.com, 206 685-7044).
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Philips 3T MRI Scanner System | Inveon Small Animal PET/CT system | Bruker 4.7
T | Small Vertical Bore Magnet | Small Bore 14 T | Mock
Scanner | Image Analysis | Electrophysiology Laboratory
Magnetic Resonance Equipment
Philips 3T MRI Scanner System
The two MR systems (Phillips Achieva) consist of an actively shielded, compact, super-conducting magnet, with a field strength of 3 Tesla (157 cm in length, 60cm bore size). They have extremely high performance gradient systems consisting of Quasar Dual high performance gradients that are actively shielded gradients with 80mT/m peak amplitude and up to 200mT/m/ms slew rate, 100% duty cycle.
The RF systems are equipped with quadrature body and head coils, 32 channel SENSE head array coil and 16 channel SENSE neurovascular coil. There are presently 32 parallel RF receiver channels in the systems that will support 4, 8, 16 and 32 channel phased array coils. The systems are also equipped with multinuclear Spectroscopy capabilities for measurement of 31P, 13C, 23Na or 19F, among other elements. Available MRS techniques include a complete range of single voxel, 2D multi-voxel and 3D multi-slice, multi-voxel spectroscopy acquisition methods.
The South Lake Union facility operates with a stronger focus on human vascular biology imaging and small animal research studies utilizing rat and mouse models. In addition, there are also several different types of neuroscience studies performed at this South Lake Union site including BOLD functional brain imaging, diffusion tensor imaging, brain perfusion studies, and brain spectroscopy. This facility serves as an additional support site for 3T MR imaging research projects for CHDD affiliates.
Physiologic Recording and Measurement Capabilities
Additional support equipment for research in neuroimaging has also been installed in the AA-wing lab. Physiologic monitoring systems include capabilities for monitoring a number of parameters during MR studies: (1) ECG: the ECG signal can be used for either/or both MR acquisition synchronization or for subject cardiac monitoring; (2) Respiratory rate; (3) Non-Invasive blood pressure measurement; (4) Pulse oximetry measurement; (5) End tidal CO2 measurement; and (6) Physiology display monitors in MR room and in control area.
This system provides a great deal of flexibility for experimental setup and can be extremely reliable and efficient when incorporating physiologic measurements into various imaging experiments by CHDD Research Affiliates. The system can also be configured for use with small animal imaging research that is done in the same scanner when it is not being used for human studies, i.e., during evening-hours and weekends.
Support for Image Data Storage and Transfer
The CHDD Brain Imaging Core, through collaboration with the MR Research Laboratory and the Integrated Brain Imaging Center, has implemented new systems for secure storage and retrieval of experimental research data on a high speed, large capacity redundant image storage system called XNAT system. All scan data are immediate transferred and stored in XNAT system after each scan session.
XNAT is an open-source eXtensible Neuroimaging Archive Toolkit developed by the NRG at Washington University in Saint Louis. This imaging informatics platform manages image data sets related to individual subjects and to specified research studies as well as any text-based and graphical data (such as medical histories, medication information, physiological measurements, etc.) associated with the study, and allows complete storage, integrity, data security, and HIPAA compliance of research data from the various projects. XNAT is hosted on an HP ProLiant DL 380p Generation 8 server with 20TB of storage (12.7 TB RAID 6), and located behind A Cisco Adaptive Security Appliance (ASA5520) serves as the firewall for the secured zones (as well as MRI scanner suite).
The image data are easily retrievable and can be downloaded for viewing through Web browser, or transferred to offline computers for specialized image processing or analysis using Web API. Data is organized 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 be able to access, store, manipulate or retrieve data, depending on the level of permissions granted to a given individual. Thus, this system is very powerful and is designed in such a manner as to support multicenter research projects where the central coordinating site would be located at UW. Complete data security and HIPAA compliance is assured in XNAT systems.
In addition to its storage ability, it also adds support for pipeline processing. User can choose from preloaded/customized pipelines to automate process on their study data before downloading for further processing, especially useful on data preprocessing, like artifact removal, head motion correction, etc. XNAT will store preprocessed image files together with its original image data. Please refer to Image Analysis component for customizing pipeline development.
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Siemens Inveon Small Animal PET/CT system
The system is suitable for imaging mouse, rat and avian brains.The resource is staffed by skilled imaging technologist/research scientist for study design, implementation and basic data support. A range of radio tracers are available. For more details contact Dr. Robert Miyaoka (firstname.lastname@example.org, 206-543-2084) or Dr. Steve Shoner (email@example.com, 206-598-6711). In addition to the Inveon PET/CT the lab is equipped with the following: a dose calibrator, a gamma counter, two anesthesia units and physiologic monitoring equipment.
Bruker 4.7T MR System
This system has a 35-cm-bore magnet equipped with high-speed 100 mT/m gradients and a Varian spectrometer console. It is capable of high-speed and high-resolution imaging and broadband spectroscopy. It is utilized for human limb experiments (muscle energetics, perfusion studies and physiology) and for animal studies and in vitro imaging and spectroscopy experiments.
Small Vertical Bore Magnet
The 7 T, 7.5 cm vertical bore magnet is equipped with an identical Varian console as the 4.7 T system so that software and pulse sequences developed on one system are readily transportable to the other. This system is used primarily for broadband spectroscopy and for mouse studies. It has also been fitted with special gradient and RF hardware, designed and built in the MR Laboratory, to obtain high resolution MR images with <40 μm resolution.
14T Magnetic Resonance System (@SLU N101)
This is an Advance III 14T (600) Ultrashield high resolution 89 mm vertical bore magnet from Bruker at the South Lake Union Campus of the University of Washington. This system includes state-of-the-art Bruker shimming systems, digital amplifiers and filters, and MRI/MRS probes to generate high signal to noise images/spectra from in vivo mouse, phantoms and biological tissues. The 14T MR laboratory is 410 sq. ft., including an animal preparation area. The lab is equipped with the following:
- 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.
- Actively shielded gradient assembly producing 2.5 G/cm/A (100 G/cm at 40 A).
- Animal monitoring system from SA instrument (Model 1024).
MR Scan Simulator (Mock Scanner)
Image Analysis component assists affiliates in preparing subjects for neuroimaging research by providing access and training in use of our MR Scan Simulator (mock scanner). The mock scanner closely resembles the current Philips Achieva 3T scanner, allows investigators to save time and money by determining which subjects will be unable to tolerate the scanning experience and/or need extra time to acclimate to the scanning environment.
The MR scan simulator features include a blank 32-channel Philips head coil and synthesized scanner noise for a range of commonly-used sequences (e.g., MRI, fMRI, and MRS sequences), a full audiovisual presentation system, functional button response system for recording accuracy of responses to stimuli, A trakSTAR tracker from Ascension Technology Corporation with a MoTrak console allows for continuous monitoring of head position and training to reduce head motion.
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Image Processing Laboratory
The Image Analysis component has full access to the computing resources of the Integrated Brain Imaging Center. These resources are available to CHDD affiliates and include the following:
Six HP Quad-core Xeon Z800 workstations (Intel® Xeon® E5530 2.40 GHz 8MB/1066 QC CPU) each with 24GB RAM, 1.5 TB of local hard disk storage, NVidia Quadro FX3800 graphics, are clustered with Sun Grid Engine as a 48-core computing cluster. The cluster supports IBIC developers and research scientists developing software and designing/scripting analysis pipelines.
Two additional HP dual Quad-core Xeon Z800 workstations (Intel® Xeon® E5630 2.53 GHz 12MB/1066 QC CPU) each with 24GB RAM, 1.5 TB of local hard disk storage, NVidia Quadro FX3800 graphics, are dedicated to individual developers and project groups.
One final HP dual Quad-core Xeon Z800 workstation (Intel® Xeon® E5630 2.53 GHz 12MB/1066 QC CPU) with 72GB RAM, 9.0 TB hard disk space, NVidia Quadro FX3800 graphics, is dedicated to internal development and memory-intensive processing.
All resources are linked with 1 Gb Ethernet, with 10 Gb bandwidth connectivity to two Network Attached Storage (NAS) systems through a dedicated 24 port DLink switch.
IBIC also has a virtual desktop interface (VDI) server system implementing virtualization of an interoperable image processing environment (IVAN: Interoperable and Virtualized Analysis for Neuroimaging). The hardware is comprised of three Sun FIre X4170 serving as primary and fail-over VDI brokers and thin client servers, and three Sun FIre X4270 servers (each dual quad core 16 Gb RAM) serving as VDI guests. The servers run Sun VirtualBox 3.1.0. Guests OS is typically Ubuntu Linux 10.04. The VDI is accessed via Sun Ray 270 Virtual Display ("thin") clients (Software Version 4.1) or via Secure Global Desktop from any computer. This system supports and facilitates experiment-specific workflows.
High-performance network attached storage is provided by two Sun model 7310 NAS controllers each with a J4400 SAS ARRAY of 24 X1TB 7200RPM SATA HDDs. The disk arrays are configured as Single Parity Mirrored. This NAS system has privileged bandwidth to the compute cluster (10Gbit). IBIC also has a secondary network attached storage system (Thecus N16000) providing 16 x 3TB in a RAID6 configuration. This system has 10 Gb bandwidth to the UW network. IBIC also has access to a 50 Tb capacity extensible central data repository in the Department of Radiology, University District Building, funded by an NIH S10 grant.
Network security: A Cisco Adaptive Security Appliance (ASA5520) serves as the firewall/VPN/Gateway for the secured zones (XNAT, MRI scanner suite, and the internal interfaces and management ports of the VDI server).
Drs. Thomas J. Grabowski and Julia Owen support image data analysis and statistical image processing for affiliates. IBIC workstations and the IBIC server system noted in the previous section are equipped with image analysis software available to CHDD affiliates. Dr. Owen works with a group of contributing scientists in IBIC that share software efforts and combine talents and resources to research image processing ideas, address analysis questions and problems, brainstorm solutions and engineer new code to address these. Advances are brought to the attention of CHDD Research Affiliates. Image analysis staff and related personnel also provide support and training for image processing routines for fMRI and other types of analyses. The Image Analysis component of the Core has implemented many new pre- and post-processing scripts to be used in conjunction with FMRIB’s Software Library (FSL), including scripts for motion correction, removal of scanner artifacts, improved registration, post-processing quantification, and batch processing for multiple study subjects. These scripts can be combined with others to support experiment-specific workflows for image data analysis.
With the support of IBIC, we continue to develop state-of-the art methods for the complex analysis of data from multiple imaging modalities, including structural MRI, fMRI, DTI (diffusion tensor imaging), MRS (magnetic resonance spectroscopy), EEG/ERP, and other psychophysiological measures. Methods are also being designed for the integration of data from these different modalities (e.g., coregistering a timecourse movie of source-localized ERP signal over an fMRI image that shows an average blood flow change in response to the same stimuli; comparing white matter integrity as assessed by DTI with the neurochemical characteristics of specific brain regions using MRS). Methodology for integration of behavioral data with imaging data is also been a strong focus of the Image Analysis Component (e.g., determining which areas of brain activation during an fMRI study of emotional face processing are associated with measures of social anxiety in autism.) Finally, efforts are made to introduce affiliates to the potential of neuroimaging research for their particular area of study, to facilitate networking and collaborations among new and experienced neuroimaging researchers, and to ensure dissemination of information regarding the latest software and hardware advances available to them.
CHDD scientists continue to survey solutions as new analysis programs become available and they have recently shifted segments of the image analysis pipeline to incorporate newer software solutions that are felt to best suit our needs. Multiple specialized software packages have been installed in IBIC workstations to create an integrated neuroimaging analysis environment. This operating system and application software platform is also available to IDDRC Brain Imaging Core Research Affiliates. Some processing methods implemented include:
- Afni: Analysis of Functional Neuroimages: A set of programs for process, analyzing, and displaying functional MRI data.
- AIR: Automated Image Registration of 3D (and 2D) images within and across subjects and within and sometimes across imaging modalities.
- Diffusion Toolkit (DTK): Diffusion Toolkit is a set of command-line tools with a GUI frontend that performs data reconstruction and fiber tracking on diffusion MR images. Basically, it does the preparation work for Trackvis.
- TrackVis: TrackVis is a software tools that can visualize and analyze fiber track data from diffusion MR imaging tractography.
- Dicom3tools: DICOM and other image format conversion and manipulation tools.
- And many more...for complete list of packages.
For further information see the Integrated Brain Imaging Center http://www.ibic.washington.edu.
High-density EEG and Event-Related Potentials (ERP) are collected using a Geodesic EEG System 300 (GES-300) manufactured by Electrical Geodesics Inc. (EGI). The lab has several 128-channel geodesic sensor nets and hydrocell nets sized to fit adults, children and infants. EGI's proprietary NetStation 4.5 acquisition software runs on a dedicated Mac workstation connected to the NetAmps amplification module. A dedicated Windows-PC workstation integrated into the recording system hosts a variety of stimulus delivery software applications, including E-Prime, Presentation, and Matlab's PsychToolbox. Stimulus delivery protocols implemented in any of these are equipped to deliver synchronized stimulus markers directly into NetStation recordings. The acquisition system also includes a video camera to monitor participants and deliver a video stream into the EEG/ERP recording for off-line behavioral coding. When a study requires source estimation of EEG/ERP signals, investigators use the lab's Geodesic Photogrammetry System (GPS) to determine sensor location coordinates on the participant's head. Offline data analysis tasks using NetStation are performed on either the Mac workstation in the lab (when available) or a shared Mac laptop.
Psychophysiological data are collected using the lab's BIOPAC MP-150 acquisition system, which includes modules for measuring electrocardiograms, impedance cardiograms, respiration, electrodermal responses, photoplethysmograms, electromyograms, and temperature. The acquisition system can be equipped to receive synchronized markers from stimulus delivery applications, as described above. BIOPAC's AcqKnowledge software acquires all the data, and can also be used for a variety of analysis tasks. An extensive library of Matlab software has been developed by core staff to facilitate artifact screening and coregistration of pyscho-physiological measures with behavioral coding data obtained from videos recorded concurrently during experiments.
EEG/ERP can also be recorded in the MRI scanner using the BrainAmp MR acquisition system from BrainProducts. This system receives two signals from MRI scanning hardware to facilitate removal of scanning artifacts from the EEG recording: 1) a clock signal to synchronize the EEG sampling rate with the MRI system; and 2) a digital trigger marking the precise onset of fMRI scan pulses. Using these two sources of information, the EEG system constructs a precise estimate of the scan pulse artifact and then subtracts the artifact from the EEG signal each time it occurs during the imaging pulse sequence. The EEG acquisition unit is specially shielded against RF interference from the scanner, and the EEG electrodes are designed to resist heating during scanning. The lab is stocked with BrainCap MR electrode caps with 32 and 64-channel montages for collection and analysis of whole-head scalp potential topography. The BrainAmp MR acquisition components are portable, allowing for more convenient testing of EEG/ERP protocols outside of the MRI scanner.
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