Jorge Jovicich, Ph.D. Massachusetts General Hospital - Harvard Medical School Biomedical Informatics Research Network Overview Testbeds Morphometry BIRN.

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Presentation transcript:

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 Mediator 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 Gbps (goal 100 Gbps)

Clinical Measures Genotype Data Local Storage Standardized Acquisition MRI Protocol Data Protection INSTITUTION A BIRN Rack SRB MCAT HID INSTITUTION B BIRN Rack SRB MCAT HID Portal Mediator 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 resources Mediator: 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 data correlates Diseases: Unipolar Depression, Alzheimer’s, Mild Cognitive Impairment

Multi-site MRI Calibration Integrate Analysis & Visualization Tools Data Management Processing Workflows Morphometry BIRN Application Cases fBIRN Mouse BIRN BIRN CC Left Hippocampus Volume (mm 3 ) CVLT Discriminability Score

Morphometry BIRN Tools Contact: Jorge Jovicich  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 data correlates Disease: Schizophrenia

Statistical Map superimposed 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

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

Integrate and access multi-scale, multimodal, disparate data LONI processing pipeline 3D Mouse Atlas Genetic 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

BIRN BIRN Coordinating Center  Goals “End-to-End” Infrastructure Deliver and maintain a robust and scalable “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? Infrastructure Tools for BIRN 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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