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Informatics tools & services for NA-MIC

Informatics tools & services for NA-MIC. Dan Marcus Neuroinformatics Research Group Washington University. Overview. Introduction to the Neuroinformatics Research Group (NRG) Introduction to XNAT New XNAT features XNAT and NA-MIC Kit XNAT Central and DBPs. Introduction to NRG.

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Informatics tools & services for NA-MIC

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  1. Informatics tools & services for NA-MIC Dan Marcus Neuroinformatics Research Group Washington University

  2. Overview • Introduction to the Neuroinformatics Research Group (NRG) • Introduction to XNAT • New XNAT features • XNAT and NA-MIC Kit • XNAT Central and DBPs

  3. Introduction to NRG • NRG  Neuroimaging Laboratories  Mallinckrodt Institute of Radiology  Washington University School of Medicine • Neuroinformatics software (XNAT is our flagship product) • Data & analysis centers (ADRC, BIRN, Brainscape, XNAT Central, etc.) • http://nrg.wustl.edu

  4. Introduction to NRG Mohana Ramaratnam, Dan Marcus, Tim Olsen, Kevin Archie, Misha Milchenko (not pictured)

  5. Introduction to XNAT • Informatics platform for managing biomedical imaging & related data • File repository for image data • Relational database for metadata and non-image measures • User interface tools • Auxiliary services (e.g. DICOM, FTP) • http://www.xnat.org

  6. Introduction to XNAT • XNAT 1.3 available at www.xnat.org • XNAT 1.4 beta available from CVS repository at http://nrg.wustl.edu/viewvc (install instructions posted to google group http://groups.google.com/group/xnat_discussion). • XNAT 1.4 production scheduled for March release • XNAT 2.0 in conceptual stage

  7. Example XNAT deployments www.brainscape.org central.xnat.org

  8. Project orientation

  9. Improved upload & download

  10. Improved pipeline services

  11. Improved user interface

  12. User-defined study measures

  13. XNAT and NA-MIC Kit NA-MIC needs: • Improved management of ‘local’ image data • Integration with Slicer and Batchmake • Data sharing with collaborators

  14. XNAT and NA-MIC Kit XNAT solution: • Desktop XNAT that delivers basic XNAT functionality • Push and pull data from ‘central’ XNAT repositories via web services • Integration with Slicer and Batchmake via XCEDE XML • Data sharing via lightweight web services

  15. XNAT and NA-MIC Kit Osirix • Local database • Integration with viewer & processing

  16. XNAT and NA-MIC Kit Flickr • Tags • Sets • API

  17. XNAT Central & NA-MIC DBPs • Reference data • Data from studies in pub. database • Collaboration data • Personal data

  18. XNAT/NA-MIC bliss Please seek us out for discussion!

  19. Recap of MGH contributions • QDEC: GUI for group analysis of Freesurfer-processed subject data • Combined volumetric and surface (CVS) registration

  20. QDEC GUI for group analysis “Does the correlation between cortical thickness and age differ from zero?” http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis

  21. Template HAMMER CVS FLIRT CVS registration • Surface-based (2D) registration aligns cortical folds, but doesn’t apply to non-cortical structures. • Volumetric (3D) registration applies to the entire brain but doesn’t align cortical folds. • Solution: integrate them!

  22. XNAT 1.x: Three tiers Clients Engine Database

  23. Clients Engine Web application Database XNAT 1.x: Three tiers

  24. Web application XNAT 1.x: Three tiers Clients Engine Database

  25. XNAT Services Meta- data Pipeline File Tags Security XNAT 2.0: Service orientation

  26. XNAT Services Meta- data Pipeline File Tags Security XNAT 2.0: Service orientation

  27. XNAT Applications Web Desktop Cmd. line XNAT Services Meta- data Pipeline File Tags Security XNAT 2.0: Service orientation

  28. XNAT Applications Web Desktop Cmd. line XNAT Services Meta- data Pipeline File Tags Security XNAT 2.0: Service orientation Non-XNAT Apps

  29. Advantages of SOA • Componentized • Deployment flexibility • Agility • Better interoperability • Federation

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