Informatics tools & services for NA-MIC
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NA-MICNational Alliance for Medical Image Computing http://na-mic.org
Informatics tools & services for NA-MIC
Dan Marcus
Neuroinformatics Research Group
Washington University
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National Alliance for Medical Image Computing http://na-mic.org
Overview
1. Introduction to the Neuroinformatics Research Group (NRG)
2. Introduction to XNAT
3. New XNAT features
4. XNAT and NA-MIC Kit
5. XNAT Central and DBPs
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National Alliance for Medical Image Computing http://na-mic.org
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
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National Alliance for Medical Image Computing http://na-mic.org
Introduction to NRG
Mohana Ramaratnam, Dan Marcus, Tim Olsen, Kevin Archie, Misha Milchenko (not pictured)
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National Alliance for Medical Image Computing http://na-mic.org
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
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National Alliance for Medical Image Computing http://na-mic.org
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
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National Alliance for Medical Image Computing http://na-mic.org
Example XNAT deployments
www.brainscape.org central.xnat.org
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National Alliance for Medical Image Computing http://na-mic.org
Project orientation
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National Alliance for Medical Image Computing http://na-mic.org
Improved upload & download
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National Alliance for Medical Image Computing http://na-mic.org
Improved pipeline services
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National Alliance for Medical Image Computing http://na-mic.org
Improved user interface
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National Alliance for Medical Image Computing http://na-mic.org
User-defined study measures
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National Alliance for Medical Image Computing http://na-mic.org
XNAT and NA-MIC Kit
NA-MIC needs:
• Improved management of ‘local’ image data
• Integration with Slicer and Batchmake
• Data sharing with collaborators
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National Alliance for Medical Image Computing http://na-mic.org
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
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National Alliance for Medical Image Computing http://na-mic.org
XNAT and NA-MIC Kit
Osirix
• Local database
• Integration with viewer & processing
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National Alliance for Medical Image Computing http://na-mic.org
XNAT and NA-MIC Kit
Flickr
• Tags
• Sets
• API
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National Alliance for Medical Image Computing http://na-mic.org
XNAT Central & NA-MIC DBPs
• Reference data
• Data from studies in pub. database
• Collaboration data
• Personal data
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National Alliance for Medical Image Computing http://na-mic.org
XNAT/NA-MIC bliss
Please seek us out for discussion!
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National Alliance for Medical Image Computing http://na-mic.org
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National Alliance for Medical Image Computing http://na-mic.org
Recap of MGH contributions
• QDEC: GUI for group analysis of Freesurfer-processed subject data
• Combined volumetric and surface (CVS) registration
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National Alliance for Medical Image Computing http://na-mic.org
QDEC GUI for group analysis
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis
“Does the correlation between cortical thickness and age differ from zero?”
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National Alliance for Medical Image Computing http://na-mic.org
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!
Template
FLIRT
HAMMER
CVS
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National Alliance for Medical Image Computing http://na-mic.org
XNAT 1.x: Three tiers
Engine
Database
Clients
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National Alliance for Medical Image Computing http://na-mic.org
XNAT 1.x: Three tiers
Engine
Database
Clients
Web application
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National Alliance for Medical Image Computing http://na-mic.org
XNAT 1.x: Three tiers
Engine
Database
Clients
Web application
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National Alliance for Medical Image Computing http://na-mic.org
XNAT 2.0: Service orientation
XNAT Services
Meta-data
Pipeline File Tags Security
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National Alliance for Medical Image Computing http://na-mic.org
XNAT 2.0: Service orientation
XNAT Services
Meta-data
Pipeline File Tags Security
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National Alliance for Medical Image Computing http://na-mic.org
XNAT 2.0: Service orientation
XNAT Services
Meta-data
Pipeline File Tags Security
XNAT Applications
Web DesktopCmd.line
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National Alliance for Medical Image Computing http://na-mic.org
XNAT 2.0: Service orientation
XNAT Services
Meta-data
Pipeline File Tags Security
XNAT Applications
Web DesktopCmd.line
Non-XNATApps
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National Alliance for Medical Image Computing http://na-mic.org
Advantages of SOA
• Componentized
• Deployment flexibility
• Agility
• Better interoperability
• Federation