Jorge Jovicich, Ph.D.Massachusetts General Hospital - Harvard Medical School

Biomedical Informatics Research Network

• Overview• Testbeds

• Morphometry BIRN• Function BIRN• Mouse BIRN• Coordinating Center

fMRI

Clinical Query

Integrated View

Receptor Density

Web

Other Databases

Structure

Clinical

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ARIP - 20MG ARIP - 30MG RISP - 06MG PLACEBOTreatment Group

MediatorMediator

BIRN in 1 slide

• Creating infrastructure that facilitates distributed collaborations in biomedical science• Initial focus in brain imaging of neurological disorders (human and mice) • 15 Universities, 22 Research Groups, connected through Internet2• Established in Oct. 2001

http://www.nbirn.net/

http://abilene.internet2.edu/10 Gbps (goal 100 Gbps)

Clinical Measures

GenotypeData

Local Storage

StandardizedAcquisition

MRI Protocol

DataProtection

INSTITUTION A

BIRN Rack

SRBMCAT

HID

INSTITUTION BBIRN Rack

SRBMCAT

HID

PortalMediator

INSTITUTION C

Calibration& Analysis

Tools

Grid

Workflow Control:- Queries - Statistical Analysis- Download data >Visualization > More Statistics > More Processing- Interoperable Queries (literature, homology, other databases, etc.)

Data Flow Overview

Federation: distributed DB, autonomous, access integrated resourcesMediator: translates heterogeneous data sources to consistent representation

Testbeds Overview

BIRN Testbeds:

• Morphometry BIRN

• Function BIRN

• Mouse BIRN

• BIRN Coordinating Center

Review:

• Common scientific goal: Biomarkers

• Testbed goals & methods

• Available tools

Scientific Goal

Methods• Support multi-site structural MRI clinical studies or trials• Multi-site MRI calibration, acquisition and analysis• Integrate advanced image analysis and visualization tools

Sites (9) MGH, BWH, Duke, UCLA, UCSD, UCI, JHU, Wash U, MIT

Morphometry BIRN

human neuroanatomical data clinical datacorrelates

Diseases: Unipolar Depression, Alzheimer’s, Mild Cognitive Impairment

Multi-site MRI

Calibration

Integrate Analysis &

Visualization Tools

Data Management

Processing Workflows

Morphometry BIRN

Application Caseshttp://nbirn.net/Publications/Brochures/index.htm

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BWH/MGH and UCSD Data

• fBIRN• Mouse BIRN• BIRN CC

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CVLT Discriminability Score

Morphometry BIRN Tools

Contact: Jorge Jovicich (jovicich@nmr.mgh.harvard.edu)

Structural MRI acquisition protocols Public multi-site MRI dataset Analysis & Visualization tools

• Gradient unwarping (MRI distortion correction, MGH)• 3DSlicer (visualization, BWH)• Freesurfer (cortical segmentation, MGH)• LDDMM (shape analysis, JHU)• LONI (processing pipeline, UCLA)

Future goals: • Calibration recommendations for diffusion MRI• Analysis Tools: De-facing tool; Sub-cortical segmentation• Databasing schemas

(available later this summer)

Function BIRN

Scientific goal

Method• Develop a multi-site fMRI protocol to study regional brain

dysfunction related to the progression & treatment of schizophrenia

Sites (11)

UCI, UCLA, UCSD, MGH, BWH, Stanford, Yale, UMn, UI, UNM, Duke/UNC

human neurofunctional data clinical datacorrelates

Disease: Schizophrenia

Statistical Mapsuperimposed on

anatomical MRI image

~2s

Functional images

Time

Condition 1

Condition 2 ...

~ 5 min

Develop Method for Multi-site fMRI

Region of interest (ROI)

Calibrate multi-site fMRI experiments

Statistical analysis of multi-site neuroimaging data

Extend Morphometry BIRN technology Into 4D (time)

Validate tasks for calibration and disease biomarkers

Initial disease application is schizophrenia

fMRI acquisition, QA and stimulation protocols Human Imaging Database

• Extensible to new clinical assessments • Extensible to new imaging methods

Public multi-site fMRI dataset (available later this summer)

Analysis & visualization tools• 3DSlicer (visualization and fMRI processing, BWH)

• SPM XML toolbox (already on the SPM Plug-in page)

• Functional Imaging Processing Stream (FIPS, later this year)

Future goals: recommended protocol for multi-site fMRI acquisition + analyses

Function BIRN tools

Contact: Jessica Turner (turnerj@uci.edu)

Function BIRN tools

BIRN GCRC

collaborations

Taxonomy DB fMRI

experiment design

Cardiac MRI

Multi-site fMRI

fMRI acquisition, QA and stimulation protocols Human Imaging Database

• Extensible to new clinical assessments • Extensible to new imaging methods

Public multi-site fMRI dataset (available later this summer)

Analysis tools• 3DSlicer • SPM XML toolbox (already on the SPM Plug-in page)

• Functional Imaging Processing Stream (FIPS, later this year)

Future goals: calibration/correction development pipeline available for multi-site fMRI studies.

Scientific Goal:

Methods: Integrate multimodal, multiscale image data from

disparate data collections• MRI (T2, T1 , DTI, MR histology)• Cryosection• Histology and confocal light microscopy• Gene expression data • Electron microscopy

Sites• UCLA, Caltech, Duke, UCSD, UTHSC

Mouse BIRN

Mouse neuroanatomical data histology + genetic datacorrelates

Mouse models of human diseases: Parkinson’s, Alzheimer’s, Multiple Scleroris

Integrate and access multi-scale, multimodal, disparate data

LONI processing pipeline

3D Mouse AtlasGenetic Data

Microscope Images

GOAL: Integration

Genetic + Atlas data

Mouse BIRN Atlases

Data: different types, resolution, and distributed

Analysis and Visualization• LONI (processing pipeline, UCLA)• SHIVA (2D/3D visualization, UCLA)• BrainSuite2 (MRI processing, UCLA)• WebQTL (statistical genetics, UTHSC)

Mouse Atlases & Tools• Smart Atlas (atlas visualization & registration, UCSD)• Mouse Brain Atlas (2D genetic morphometry, UTHSC) • Mouse Development (3D atlas, Caltech)

Future goals• Improve tools interoperability

• Integrate data + other knowledge bases into common digital atlases

Mouse BIRN tools

Contact: Jyl Boline (jyl.boline@loni.ucla.edu)

BIRNBIRN Coordinating Center

GoalsDeliver and maintain a robust and scalable “End-to-End” Infrastructure“End-to-End” Infrastructure in the context of distributed biomedical research projects.

Methods• The BIRN Rack (BIRN site infrastructure)The BIRN Rack (BIRN site infrastructure)• The BIRN Virtual Data GridThe BIRN Virtual Data Grid• The BIRN Mediation InfrastructureThe BIRN Mediation Infrastructure• The BIRN PortalThe BIRN Portal

Site: UCSD

Providing an Intuitive Interface to the BIRN Cyberinfrastructure

Data Management

BIRN Portal:• Single Login from Internet• Seamless access to available applications

BIRN Portal:• Single Login from Internet• Seamless access to available applications

Data Visualization

Distributed Computation

Dissemination: What’s in for me?Dissemination: What’s in for me?

• Infrastructure Tools for BIRN Users- http://www.nbirn.net/Resources/Users/

• Dissemination mechanisms outside BIRN- Not fully structured yet- GCRC & other clinical collaborators

• Feedback from you- Practical specific tools of interest?- General IT infrastructure topics of interest?

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