Neuroinformatics, the ICONIC Grid, and GEMINI

Allen D. Malony

University of Oregon

ProfessorDepartment of Computerand Information Science

DirectorNeuroInformatics Center

Computational Science Institute

Sun February 2005Neuroinformatics, the ICONIC Grid, and GEMINI

UO Brain, Biology, and Machine Initiative

University of Oregon interdisciplinary research in cognitive neuroscience, biology, computer science

Human neuroscience focus Understanding of cognition and behavior Relation to anatomy and neural mechanisms Linking with molecular analysis and genetics

Enhancement and integration of neuroimaging facilities Magnetic Resonance Imaging (MRI) systems Dense-array EEG system Computation clusters for high-end analysis

Establish and support UO institutional centers

Sun February 2005Neuroinformatics, the ICONIC Grid, and GEMINI

NeuroInformatics Center (NIC) at UO Application of computational science methods to

human neuroscience problems Tools to help understand dynamic brain function Tools to help diagnosis brain-related disorders HPC simulation, large-scale data analysis, visualization

Integration of neuroimaging methods and technology Need for coupled modeling (EEG/ERP, MR analysis) Apply advanced statistical signal analysis (PCA, ICA) Develop computational brain models (FDM, FEM) Build source localization models (dipole, linear inverse) Optimize temporal and spatial resolution

Internet-based capabilities for brain analysis services, data archiving, and data mining

Sun February 2005Neuroinformatics, the ICONIC Grid, and GEMINI

Neuroinformatics for Brainwave Research

Electroencephalogram (EEG)

EEG time series analysis Event-related potentials (ERP)

average to increase SNR link brain activity to sensory–motor, cognitive functions

Signal cleaning and decomposition Neural source localization

Sun February 2005Neuroinformatics, the ICONIC Grid, and GEMINI

256 channels

EEG Dense-Array Methodology

Electrical Geodesics, Inc.

Sun February 2005Neuroinformatics, the ICONIC Grid, and GEMINI

Dipole Sources in the Cortex

Scalp EEG is generated in the cortex

Interested in dipole location, orientation, and magnitude Cortical sheet gives

possible dipole locations Orientation is normal to

cortical surface Need to capture convoluted

geometry in 3D mesh From segmented MRI/CT

Linear superposition

Sun February 2005Neuroinformatics, the ICONIC Grid, and GEMINI

Building Computational Brain Models

MRI segmentation of brain tissues Conductivity model

Measure head tissue conductivity Electrical impedance tomography

small currents are injectedbetween electrode pair

resulting potential measuredat remaining electrodes

Finite element forward solution Source inverse modeling

Explicit and implicit methods Bayesian methodology

Sun February 2005Neuroinformatics, the ICONIC Grid, and GEMINI

Computational Implementation on ICONIC Grid

Designed as a conductivity search problem Master launches new inverse problems with guesses Inverse solvers run iterative

forward calculations Parallelization

Search Inverse solve Hybrid

mastercontroller

inversesolver

inversesolver

conductivityguesses

forwardsolver

forwardsolver

conductivitysolution and error

conductivityvalues

solutionpotentialsand error

measuredscalp potentials

…

A. Salman, S. Turovets, A. Malony, J. Eriksen, D. Tucker, “Computational Modeling of Human Head Conductivity,” ICCS 2005, May 2005. (awarded best paper)

Sun February 2005Neuroinformatics, the ICONIC Grid, and GEMINI

UO ICONIC Grid

NSF Major Research Instrumentation (MRI) proposal “Acquisition of the Oregon ICONIC Grid for Integrated

COgnitive Neuroscience Informatics and Computation” PIs

Computer Science: A. Malony, J. Conery Psychology: D. Tucker, M. Posner, R. Nunnally

Senior personnel Computer Science: S. Douglas, J. Cuny Psychology: H. Neville, E. Awh, P. White

Computational, storage, and visualization infrastructure

Sun February 2005Neuroinformatics, the ICONIC Grid, and GEMINI

ICONIC Grid

SMPServerIBM p655

GraphicsSMP

SGI Prism

Shared Storage System

Gbit Campus Backbone

NIC CIS CIS

Internet 2

SharedMemory

IBM p690

DistributedMemory

IBM JS20

CNI

DistributedMemory

Dell Pentium Xeon

NIC4x8 16 16 2x8 2x16

graphics workstations interactive, immersive viz other campus clusters

40 TerabytesTape

Backup112 totalprocessors

Sun February 2005Neuroinformatics, the ICONIC Grid, and GEMINI

Computational Integrated Neuroimaging System

… …

raw

storageresources

virtualservices

compute resources

Sun February 2005Neuroinformatics, the ICONIC Grid, and GEMINI

GEMINI Project

“GEMINI: Grid-based Electromagnetic Integrated Neuroimaging” NIH NIBIB proposal PIs and institutions

A. Malony and D. Tucker, University of Oregon P. Papadopoulos, San Diego Supercomputing Center C. Johnson and S. Parker, University of Utah

Under review by NIH Biomedical Imaging panel Dynamic neuroimaging algorithms and visualization Grid-based integration (processing and data sharing) High-end tool integration and environments Neuroinformatics data ontologies

Sun February 2005Neuroinformatics, the ICONIC Grid, and GEMINI

GEMINI Architecture

Sun February 2005Neuroinformatics, the ICONIC Grid, and GEMINI

Leveraging Internet, HPC, and Grid Computing

Telemedicine imaging and neurology Distributed EEG and MRI measurement and analysis Neurological medical services Shared brain data repositories Remote and rural imaging capabilities

Build on emerging web services and grid technology Leverage HPC compute and data centers Create institutional and industry partnerships

Electrical Geodesics, Inc. Cerebral Data Systems (UO partnership with EGI) Looking for other industrial partnerships