NA-MIC
National Alliance for Medical Image Computing
http://na-mic.org
Core 1b – Engineering
Data Management
Daniel Marcus
Washington University
Data Management
• Key component of clinical research
– e.g. Huntington’s Disease DBP
• Protects integrity of data
• Enables collaboration and data sharing
– e.g. Insight repository
• Enables integration with clinical workflows
– e.g. DICOM
National Alliance for Medical Image Computing
http://na-mic.org
Data Management Platform
National Alliance for Medical Image Computing
http://na-mic.org
• DICOM in Slicer 4
– Query, Send,
Database
• Adding support for
scenes
• Built on dcm-tk
National Alliance for Medical Image Computing
http://na-mic.org
Midas
• Provides online file storage and management.
• Release 3.2
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Easier installation (click and configure)
Support for PgSQL, MySQL and other common databases
Improved user interface & search system
Based on Zend PHP Framework
New plugins mechanism for modularization
• Tightly integrated with NA-MIC software processes
• Hosting testing data for ITK, VTK, and select Slicer Modules
• CMake has built-in commands for fetching its data
• Hosting downloads and extensions
• Receives binaries, packages, and data from client dashboard
machines
National Alliance for Medical Image Computing
http://na-mic.org
Midas: Roadmap for 2012
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Federation of data between instances
Better DICOM protocol support
Improved client libraries
Support for unstructured metadata with MongoDB
Improved visualization with WebGL
– Save a scene in Slicer and view it on the web!
National Alliance for Medical Image Computing
http://na-mic.org
• Manages imaging-centric research workflows
• Secure database backend
• Rich web-based user
interface
• Comprehensive RESTful API
• What’s next:
– Slicer4 integration
National Alliance for Medical Image Computing
http://na-mic.org
DBP: Huntington’s Disease
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Longitudinal, multi-site study
Imaging, clinical, behavioral,
genetic, etc.
XNAT services
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Image upload
Quality control
Data integration
Data distribution
Anonymization
Pipelines (pyxnat, nipype)
Current status
– 30+ sites
– ~4,000 imaging sessions
– 5.3 TB of data
National Alliance for Medical Image Computing
http://na-mic.org
DICOM Integration with XNAT
Gateway
Non-secure (no encryption)
Secure (encrypted)
National Alliance for Medical Image Computing
http://na-mic.org
Direct Integration with Slicer
• Goal: Data exchange of between Slicer and
XNAT
– Bi-directional
– File-format agnostic (DICOM, NIFTI, NRRD, MRML)
– Glorious user experience
• Approach: Leverage existing capabilities.
– Qt’s browser widget
– XNAT’s RESTful API
• Current status:
– Slicer 4 & XNAT API are rockin’
– UI is in development
National Alliance for Medical Image Computing
http://na-mic.org
XNAT REST API
• Full programmatic access to XNAT data and services.
– Hierarchical access
– Search
– Pipelines
• Docs @ http://docs.xnat.org/XNAT+REST+API
• Some examples:
https://central.xnat.org/data/projects/IGT_GLIOMA
https://central.xnat.org/data/projects/IGT_GLIOMA/experiments/00001
https://central.xnat.org/data/projects/IGT_GLIOMA/experiments/00001/scans/1
National Alliance for Medical Image Computing
http://na-mic.org
View Only Scene Files