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Morphometry BIRN

Morphometry BIRN. Karl Helmer helmer@nmr.mgh.harvard.edu. Overview. mBIRN’s charge is to provide tools and scalable infrastructure needed for longitudinal and multi-site structural MRI studies However, the problem is generalizable to: how to analyze, manage, store and share large data sets?

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Morphometry BIRN

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  1. Morphometry BIRN Karl Helmer helmer@nmr.mgh.harvard.edu

  2. Overview • mBIRN’s charge is to provide tools and scalable infrastructure needed for longitudinal and multi-site structural MRI studies • However, the problem is generalizable to: how to analyze, manage, store and share large data sets? • Most mBIRN tools are not neuroimaging specific • The focus of mBIRN is on interoperability

  3. Multiple Development Sites Harvard WUSTL BWH UC – San Diego UC – Irvine UC – Los Angles Johns Hopkins Duke

  4. Data Flow Framework Workflows Workbench Pipeline Data Processing Integrate Database Management Data Acquisition Local XNAT Remote XNAT Data Grid Share Analyze Visualize Discover

  5. Workflows • mBIRN Workbench: • Platform independent • Modular environment • Contains a database • Queries using Partner’s Health Care • clinical schema • Customize to run with own applications • LONI Pipeline: • Graphical environment • Includes a diverse set of applications • Will automatically parallelize available • processes

  6. Database eXtensible Neuroimaging Archive Toolkit (XNAT) Data management platform for capturing, visualizing, exploring, and sharing imaging and clinical data. • Web application built on an extensible relational / XML database; supports custom table • Interoperable with end-user tools • Interoperable with the BIRN Data Grid

  7. Interoperability of Tools and Database Query: Return all females aged 55 – 70 with cardiovascular disease and a history of smoking… FreeSurfer 3D Slicer Data resulting from queries within XNAT can be sent to applications for further analysis. QDEC

  8. Summary Data Processing (Workflows) Data Acquisition (Protocols) Data Storage (Database) mBIRN Data Discovery (Analysis and Visualization)

  9. Links to Further Information Morphometry BIRN PI – Bruce Rosen (bruce@nmr.mgh.harvard.edu) Project Manager = Karl Helmer (helmer@nmr.mgh.harvard.edu) 617.726.8636 FreeSurfer / QDEC : http://surfer.nmr.mgh.harvard.edu/ 3D Slicer: http://www.slicer.org/ XNAT: http://www.xnat.org/ LONI Pipeline: http://www.loni.ucla.edu/pipeline/index.aspx?software_id=2 LDDMM: http://cis.jhu.edu/software/ldmm/about.html Other tools and information on the BIRN website (www.nbirn.net)

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