NA-MICNational Alliance for Medical Image Computing http://na-mic.org

Informatics tools & services for NA-MIC

Dan Marcus

Neuroinformatics Research Group

Washington University

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

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

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)

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

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

National Alliance for Medical Image Computing http://na-mic.org

Example XNAT deployments

www.brainscape.org central.xnat.org

National Alliance for Medical Image Computing http://na-mic.org

Project orientation

National Alliance for Medical Image Computing http://na-mic.org

Improved upload & download

National Alliance for Medical Image Computing http://na-mic.org

Improved pipeline services

National Alliance for Medical Image Computing http://na-mic.org

Improved user interface

National Alliance for Medical Image Computing http://na-mic.org

User-defined study measures

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

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

National Alliance for Medical Image Computing http://na-mic.org

XNAT and NA-MIC Kit

Osirix

• Local database

• Integration with viewer & processing

National Alliance for Medical Image Computing http://na-mic.org

XNAT and NA-MIC Kit

Flickr

• Tags

• Sets

• API

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

National Alliance for Medical Image Computing http://na-mic.org

XNAT/NA-MIC bliss

Please seek us out for discussion!

National Alliance for Medical Image Computing http://na-mic.org

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

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?”

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

National Alliance for Medical Image Computing http://na-mic.org

XNAT 1.x: Three tiers

Engine

Database

Clients

National Alliance for Medical Image Computing http://na-mic.org

XNAT 1.x: Three tiers

Engine

Database

Clients

Web application

National Alliance for Medical Image Computing http://na-mic.org

XNAT 1.x: Three tiers

Engine

Database

Clients

Web application

National Alliance for Medical Image Computing http://na-mic.org

XNAT 2.0: Service orientation

XNAT Services

Meta-data

Pipeline File Tags Security

National Alliance for Medical Image Computing http://na-mic.org

XNAT 2.0: Service orientation

XNAT Services

Meta-data

Pipeline File Tags Security

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

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

National Alliance for Medical Image Computing http://na-mic.org

Advantages of SOA

• Componentized

• Deployment flexibility

• Agility

• Better interoperability

• Federation