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Brain Imaging Core

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Overview | Location | Faculty & Staff | To Use Our Services | Services & Equipment
Dr. Maravilla

Kenneth Maravilla, M.D., Director, Brain Imaging Core
The Brain Imaging Core supports CHDD Research Affiliates conducting in vivo brain imaging research in humans and animals using a variety of modalities that include structural and functional Magnetic Resonance (MR) brain imaging, MR spectroscopy, and evoked response potentials (ERP), and provides a wide range of sophisticated image processing support. 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 objectives are:

  • 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 objectives are:

  • 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 “Bioscribe” 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 objectives are:

  • 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).
  • 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. This objective is carried out in close conjunction with the Image Analysis component of the Brain Imaging Core.
  • 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. This service is generally carried out in conjunction with staff from the Instrument Development Laboratory Core.
  • 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:

The Small Animal Imaging Center (SAIC) provides CHDD Research Affiliates with access to equipment and expertise needed to perform in vivo radiological assessments of small animals (rodents to primates). Equipment available 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.

  • • Assistance is also available for experimental design, IACUC protocol development, imaging processing and quantitative analysis as well as histological confirmation/registration of novel tracking methodologies.
  • To access the facility please contact Dr. Donna Cross ( for an initial consultation.

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south campus map     Brain Imaging locations

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Faculty & Staff

Technical Support and Development component
Image Analysis
Human Electrophysiology
Small Animal Imaging

Dr. Maravilla
Ken Maravilla, M.D.
Director, Brain Imaging Core

Director, Technical Support and Development component

Dr. Grabowski
Thomas Grabowski, M.D.

Co-Director, Image Analysis component

Dr. Aylward
Elizabeth Aylward, Ph.D.

Co-Director, Image Analysis component

Dr. Murias
Michael Murias, Ph.D.

Director, Human Electrophysiology component

Dr. Minushima     
Satoshi Minoshima, M.D., Ph.D.
Co-Director, Small Animal Imaging component

Dr. Garden
Gwenn Garden, M.D., Ph.D.
Co-Director, Small Animal Imaging component

Dr. Hayes 
Cecil Hayes, Ph.D.
M.R. Physicist

Mr. Mathis
Mark Mathis
Research Scientist

Dr. Johnson
Clark Johnson, Ph.D.
Image Analysis Specialist

Dr. Pettet
Mark Pettet, Ph.D.
Research Scientist

Dr. Cross
Donna Cross, Ph.D.
Technical Director

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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. Maravilla (, 206-543-3320).
  • For Image Analysis information, contact Dr. Grabowski (
  • For human electrophysiology information, contact Dr. Murias (, 206-616-3342).
  • For small-animal imaging information, contact, Dr. Garden (, 206-616-9402).

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Services & Equipment

Magnetic Resonance Equipment | Philips 3T MRI Scanner System | Bruker 4.7 T | Vertical Bore 7 T | Mock Scanner | Image Analysis | Electrophysiology Laboratory

Magnetic Resonance Equipment

Philips 3T MRI Scanner System

Philips T magnet

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, 8 channel SENSE head array coil and 16 channel SENSE neurovascular coil. There are presently 16 parallel RF receiver channels in the systems that will support 4, 8 and 16 channel phased array coils. An upgrade to a 32 channel RF architecture has recently been made. 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 alternative support site for 3T MR imaging research projects for CHDD affiliates.

Additional Support Equipment

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. Custom fMRI paradigm presentation/subject response hardware and software are also in place and include: (1) 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 stimulation of the subject, (2) a five button, two hand fiber optically coupled response box, (3) a single button, two hand carbon wire response button, (4) a set of high dynamic range piezo electric headphones, (5) a set of pneumatically driven audio headphones, and (6) a phase canceling microphone that actively suppresses background noise from the MR gradients to better hear subject audio responses during an fMRI exam.

New Physiologic Recording and Measurement Capabilities

A new Labview control computer has been installed and is used to monitor and record many measures that include heart rate, respiratory rate, blood pressure, pulse pressure, 02 saturation, expiratory C02, temperature. Additional hardware modules for recording of various physiologic parameters such as electrodermal response and EEG recording in the magnet are currently being evaluated and will be added shortly. This system provides a great deal of flexibility for experimental setup and can be extremely reliable and efficient when incorporating a wide variety of task stimuli or 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.

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Bruker 4.7 T 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.

Bruker 4.7 T MR system

Vertical Bore Magnet

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 studies. It has also been fitted with special gradient and RF hardware, designed and built in the MR Laboratory, to obtain MR microscopy images with <40 μm resolution.

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 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.

Mock scanner

The MR scan simulator (designed and built by the Instrument Development Laboratory Core) features include a full audiovisual presentation system, functional button response system for recording accuracy of responses to stimuli, a head motion detection system with the option of feedback for subjects, and realistic sounds for room noise and different types of scanner noise (e.g., MRI, fMRI, and MRS sequences).

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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) with 12Gb RAM, 1 Tb hard disk space, NVidia Quadro FX3800 graphics, and dual 24 inch LCD monitors are clustered with Sun Grid Engine. The cluster supports IBIC developers and research scientists developing software and designing/scripting analysis pipelines.

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 9.4.  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.

PACSoft, a DICOM image archive, and Bioscribe, a research database, manage 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. Bioscribe allows complete storage, integrity, data security, and HIPAA compliance of research data from the various projects. The system has a 4 Tb capacity. 

A Sun model 7710 NAS (RAID J4400 SAS ARRAY FOR SUN STORAGE 7410 12X1TB 7200RPM SATA HDD) configured as RAID 5 running ZFS provides network attached storage for the workstations and the VDI.  IBIC will also have access by June 2010 to a 50 Tb capacity extensible central data repository for research studies, currently under construction for Department of Radiology. 

Network resources:  A Cisco Adaptive Security Appliance (ASA5520) serves as the firewall/VPN/Gateway for the secured zones (Pacsoft, Bioscribe, MRI scanner suite, and the internal interfaces and management ports of the VDI server).  NAS and workstation connectivity is 1Gb.

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Image Analysis

Drs. Thomas J. Grabowski and Clark Johnson 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. Johnson 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. This group, called DIGIT, meets on a biweekly basis to discuss these issues and to share interim advances made since the prior meeting. 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. In conjunction with DIGIT, 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.


FSL menu

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. Newer processing methods implemented recently include:

  • DTI: mrVISTA ( VistaLab/software.php#vista)- provides powerful visualization tools -- used in addition to the Functional MRI of the Brain—Diffusion Toolbox (FDT) tools supplied in FSL
  • GenFA.CHDD This script automates the preliminary processing of DTI data (Eddy current correction and FA map)
  • MRS: MRUI ( is a graphical interface to several programs for processing MR spectroscopy (MRS) data in the time-domain that is specially designed for dealing with in vivo MR spectra obtained in low-field clinical MR spectrometers
  • Several programs that automate the initial processing of MRS data by Todd Richards, Ph.D., (CHDD affiliate and consultant to the Brain Imaging Core). These programs provide graphical quality control output that enable the analyst to identify problems
  • Data transfer: The Phillips 3T scanner stores data in proprietary formats that have been difficult to convert into the data format used by the analysis software. Allow automated conversion of file format during image download and transfer to the Bioscribe prior to doing any image processing
  • Software for B0 correction of DTI data. These programs read the DICOM header and write correctly scaled NIFTI images as well as necessary supporting files (e.g. Bvalues and Bvectors) for use with FSL and several other processing packages
  • Coregistration: RDI (Registration Diagnostic Images) is a script that generates an image that highlights registration errors, and provides a mechanism for the analyst to explore parameters that improve registration to standard space
  • EEG—FMRI coregistration uses a script that is in early developmental stages. Utilizing RDI technology it can identify common regions of activation that are extracted from different imaging modalities such as EEG/ERP and fMRI to then overlay the common areas of activation for comparison and further analysis. Allows comparing the anatomic activation from fMRI with the temporal information obtained from ERP
  • Co-registration and source localization analysis of EEG/ERP. Source analysis software consist of BESA and the EMSE user suite, which includes software that can integrate MRI images with ERP data. A photogrammetry apparatus that consists of eleven digital cameras arranged at the nodes of a geodesic dome around the head allows for the registration of the positioning of all electrodes in a three-dimensional coordinate system (hardware). Also, Brain Voyager, an MRI visualization and fMRI analysis program, is available for investigators interested in source localization and co-registration of ERP and fMRI.
  • A MATLAB-based library of software used in advanced analysis of Event Related Potentials. Includes functions, such as jitter-analysis, continuous wavelet transformation and wavelet coherence, signal pattern detection and source analysis based on a Finite Element Method. CHDD scientists are currently developing methods and software for the processing and analysis of electrophysiological signals, such as discrete wavelet transform, bootstrapping and non-linear dynamical methods for establishing causal relations between signals from various sources.

For further information see the Integrated Brain Imaging Center

MR Research Laboratory

Support for Image Data Storage and Postprocessing

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 PACSoft. This system can handle multiple terabytes of image data. The system consists of a DICOM image archive server that is modeled on a mini PACS (Picture Archival and Communications Server) system such as those commonly used in hospital settings for storage, review, and retrieval of large volumes of clinical imaging studies. The image data are easily retrievable and can be downloaded for viewing or transferred to offline computers for specialized image processing or analysis. In addition to the PACSoft image archiving system, there is an overarching research metadata database called Bioscribe that can retrieve and manage image data sets related to individual subjects and to specified research studies and link these together with all of the text-based and graphical data (such as medical histories, medication information, physiological measurements, etc.) associated with the research experiment. Bioscribe will also link processed image files together with this data and with the appropriate source image files stored in PACSoft that are related to a specific experiment. Bioscribe is a system that allows complete storage, integrity, and security of research data from the various projects. Data is 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 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. The image archive from PACSoft is accessible through Bioscribe but only for specific project-related images. Complete data security and HIPAA compliance is thus assured in both the Bioscribe and PACSoft systems.

Electrophysiology Laboratory

The EEG/Event Related Potentials (ERP) apparatus is made by Electrical Geodesics Inc. (Eugene, OR) and utilizes the dense array electrode system that can record brain activity from up to 128 scalp sites. The lab currently has ten 128 channel nets of adult, children and infant sizes. Data collection is accomplished through an interconnected group of computers and amplifiers, running the EGI suite of software (EGI Inc.). In the operating system room, a Dell Windows-based computer is used to generate visual or auditory stimuli using E-prime. In the testing booth, stimuli are displayed on a 21”computer monitor. Simultaneously, the signal is amplified, filtered and digitized via a preamplifier system (128 Net Amps, EGI, Inc) and the EEG raw data is acquired using Netstation 4.3 (EGI Inc.), which operates on a Power Macintosh 9500 computer. Synchronization between the two computers is accomplished through a common single clock; this ensures very precise and accurate synchronization between stimulus presentation and data acquisition. A video camera can monitor behavior that can be recorded during a study, synchronized with EEG, and coded off-line.

EEG data are acquired and stored continuously for off-line processing. Post acquisition data processing (averaging, filtering, baseline correction, replacement of bad channels, etc.), as well as plotting is done using Netstation’s analysis utilities.

The Electrophysiology Laboratory also can record a wide range of autonomic measures which can be utilized in conjunction with EEG in studies of attention, stress, and emotion, among others. Measures provided include the following:

  • Impedance cardiography
  • Respiration
  • Skin conductance
  • Photoplethysmography
  • Electromyography
  • Cardiography
  • Temperature

AcqKnowledge is used for data acquisition and analysis of autonomic measures. This is an interactive, intuitive program that allows investigators to instantly view, measure analyze and transform data. They can perform complex data acquisition, stimulation, triggering and analyses using simple pull-down menus and dialogs. On-line analysis settings, filters and transformations provide real-time feedback, or investigators can choose from a wide variety of off-line analysis tools.

Computer Workstation and Lab Space

Located in two separate areas, each within close proximity to the MR laboratory in the AA-wing and the CHDD complex. There is also an adjacent lab that contains the Core’s Electrophysiology Laboratory. This system uses a 128 channel EEG computerized system to record and process brain responses during task performance in order to track brain electrical responses in real time as children perform various brain stimulus studies (see detailed description of this laboratory below).

A second area of data analysis and image processing support consists of about 800 square feet of space that lies immediately adjacent to the MR scanners in the AA-wing MR Research laboratories. This area provides 8 computer workstations for use by research scientists and members of their team. The operation is supported by several MR Research lab scientists who are experts in various aspects of image processing such as morphometric analysis, fMRI analysis, DTI analysis, to name a few. The computer support area also provides software engineering to develop new programs or to modify existing applications. Technical support personnel provide computer hardware support together with support for data manipulation, storage, and retrieval. There are also research scientists who can perform image processing tasks for various projects on a contract basis as needed.

Geodesic photorammetry structure

Subject wearing sensor net in geodesic photogrammetry structure with a camera at each intersection. With Net Station software, cameras are synchronized to take pictures simultaneously to ensure accurate head measurements.

Brain diagram at lower right shows data gathered via sensor-net.

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