Oregon NeuroInformatics Center (NIC)

Allen D. Malony Don Tucker

Department of Computer and Department of Psychology

Information Science Electrical Geodesics, Inc.
University of Oregon University of Oregon
Experimental Methodology and Tool Integration
16x256
bits per
millisecond CT / MRI
(30MB/m)
EEG segmented
tissues
NetStation
BrainVoyager
processed
mesh generation
EEG
source localization
constrained to
cortical surface

Interpolator 3D EMSE
BESA
NeuroInformatics Center (NIC)
 Application of computational science methods to
cognitive neuroscience problems
 Understand functional activity of the brain
 Help to diagnosis brain-related disorders
 Utilize high-performance computing and simulation
 Support large-scale data analysis and visualization
 Advance techniques for integrated neuroimaging
 Address multiple domains of application
 Allow alternative experimental paradigms and methods
 Couple tools of different imaging modalities
 Build grid environments for tool interoperation
NIC Organization
 Allen D. Malony, Director
 Professor, Computer and Information Science
 Don M. Tucker, Associate Director
 Professor, Psychology; CEO, EGI
 Kevin Glass, Computational Scientist
 Ph.D., Computer Science; B.S., Physics
 Sergei Turovets, Computational Physicist
 Ph.D., Computer Science; B.S., Physics
 Sameer S. Shende, Computer Scientist
 Ph.D., Computer Science; parallel computing specialist
 Bob Frank, Mathematician
 M.S., Mathematics
Funding Support
 BBMI federal appropriation
 DoD Telemedicine Advanced Technology Research
Command (TATRC)
 Budget
 Approximately $750K for 1.5 years
 Start date: Oct. 1, 2002
 New proposals
 NSF Major Research Instrumentation (MRI)
 awarded, $1.1M with $950K for computer infrastructure
 highest ranked in NSF Social, Behavioral, and Economic
Sciences (SBE) directorate competition
 NIH Human Brain Project Neuroinformatics
NIC Approaches
 Optimize spatial resolution
 MRI structural information
 Measurement of skull conductivity
 Convergence / co-recording with MEG and fMRI
 Optimize temporal resolution
 Use EEG/MEG time course for fMRI signal extraction
 Decomposition of component analysis (ICA, PCA)
 Single-trial analysis
 Computational brain models
 BEM, FDM, and FEM brain models
 Brain information databases and atlases
Source Localization
 Mapping of scalp potentials to cortical generators
 Single time sample and time series
 Requirements
 Accurate head model and physics
 High-resolution 3D structural geometry
 Precise tissue identification and segmentation
 Correct tissue conductivity assessment
 Computational head model formulation
 Finite element model (FEM)
 Finite difference model (FDM)
 Forward problem calculation
 Dipole search strategy
Building Finite Element Brain Models
scalp
 MRI segmentation of brain tissues
 Conductivity model
 Measure head tissue conductivity
 Electrical impedance tomography CSF
 small currents are injected
between electrode pair
 resulting potential measured
at remaining electrodes skull
 Finite element forward solution
 Source inverse modeling cortex
 Explicit and implicit methods
 Bayesian methodology
Applying ICA for EEG Blink Removal
 Blinks are a major source of noise in EEG data
 Blink signals are separable from cognitive responses
 Apply Independent Component Analysis (ICA)
 Blink removal workflow
Raw EEG EEG ICA Identify blinks
Formatting preprocessing Analysis and remove
Event info Bad channel removal ICA algorithm Blink templates
Time markers Baseline correction - binICA Reconstitute EEG
Blink events Etc. - fastICA w/out blink data
- laICA (parICA)
ICA components

ERP
Analysis
NIC Relationships

Utah OHSU LANL Argonne

/ OGI
UCSD Internet2 Sandia NCSA
USC
Academic Labs / Centers 

UO Departments Intel IBM

NIC EGI
Psychology
BDL BEL Industry 

CIS Physics UO Centers/Institutes

CSI CDSI
BBMI
CNI NSI
NIC Computational Cluster (“Neuronic” Cluster)
 Dell computational cluster
 16 dual-processor nodes
 2.8MHz Pentium Xeon
 4 Gbyte memory
 36 Gbyte disk (576 Gbyte total)
 Dual Gigabit ethernet adaptors

 Master node (same specs)

 2 Gigabit ethernet switches
 Brain model development
 ICA development
NSF MRI Proposal
 Major Research Instrumentation (MRI)
 “Acquisition of the Oregon ICONIC Grid for
Integrated COgnitive Neuroscience Informatics and
Computation”
 PIs
 Computer Science: Malony, Conery
 Psychology: Tucker, Posner, Nunnally
 Senior personnel
 Computer Science: Douglas, Cuny
 Psychology: Neville, Awh, White
 Approximately $1.1M over three years
ICONIC Grid
 NSF Major Research Instrumentation (MRI) grant
graphics interactive campus
workstations visualization clusters

Gbit Campus Backbone Internet 2

NIC CIS CNI

Shared SMP Distributed

Memory Server Memory

SAN Storage System

Cognitive Neuroscience and ICONIC Grid
 Common questions to be explored
 Identifying brain networks
 Critical periods during normal development
 Network involvement in psychopathologies
 Training interventions in network development
 Research areas
 Development of attentional networks
 Brain plasticity in normal development and deprived
 Attention and emotion regulation
 Spatial working memory and selective attention
 Attention and psychopathology
EEG/ERP Methodology
 Electroencephalogram (EEG)
 Event-Related Potential (ERP)
 Stimulus-locked measures of brain dynamics
 Generated from subject- and trial-based analysis
 Raw EEG datasets processed and analyzed
 Segmentation to time series waveforms
 Blink removal and other cleaning
 ERP analysis
 Averaging for increasing signal to noise
 Characterization with respect to trial conditions
 Results visualization
 Source localization
EEG/ERP Experiment Management System
 Support EEG-based cognitive neuroscience research
 Based on experiment model
 Experiment type
 Subjects measured for trial types
 Management of experiment data
 Raw and processed datasets and derived statistics
 Per experiment/subject/trial database
 Secure protection and storage with selective access
 Analysis tools and workflows
 Generation of results (across experimental variables)
 Analysis processes with multi-tool workflows
 EEG/ERP Experiment Analysis Environment

processed datasets
raw analysis workflow / derived results

… …

virtual
services

storage
resources

compute resources
Posters
 “The FastICA Algorithm”
 R. Frank,, J. Dien, G. Frishkoff, C. Davey, K. Glass
 “Blind Separation of Blinks from EEG Data:
Evaluation of Infomax and FastICA Algorithms ”
 G. Frishkoff, R. Frank, C. Davey, J. Dien, K. Glass
 “Finite Difference and Finite Element Human Head
Modeling: Forward Problem”
 S. Turovets, K. Glass, A. Malony, V. Volkov
 “ICA Code Development and Performance Analysis”
 K. Glass, R. Frank, A. Malony