1 / 30

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.

Download Presentation

Informatics tools & services for NA-MIC

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript


  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

More Related