1. NA-MIC National Alliance for Medical Image Computing http://na-mic.org National Alliance for Medical Image Computing: NAMIC Ron Kikinis, M.D. http://na-mic.org

2. National Alliance for Medical Image Computing http://na-mic.org Overview Introduction Core 1 Core 2 Core 3 Support Cores Slicer Demo

3. National Alliance for Medical Image Computing http://na-mic.org Introduction What is our problem? What is our science?

4. National Alliance for Medical Image Computing http://na-mic.org What is our problem? Imaging: Data Acquisition –Increasing production –Increasing complexity Image Computing: –Information extraction –Example: Diffusion Tensor Imaging

5. National Alliance for Medical Image Computing http://na-mic.org Provided by Meier, Mamata, et al. Line scan diffusion tensor imaging Diffusion weighting through sensitivity for slow motion 6 volume acquisitions provide the components of the diffusion tensor 20 min to 1 hour depending on scanner and resolution Imaging

6. National Alliance for Medical Image Computing http://na-mic.org Diffusion Tensor MRI Stejskal-Tanner formula: Provided by Westin, et al.

7. National Alliance for Medical Image Computing http://na-mic.org Image Computing Too much data Need to identify relevant information

8. National Alliance for Medical Image Computing http://na-mic.org All Tensors Provided by Odonnell, et al.

9. National Alliance for Medical Image Computing http://na-mic.org Visualization and Interaction Provided by Westin, et al.

10. National Alliance for Medical Image Computing http://na-mic.org From Tensors to Tracts Provided by Westin, et al.

11. National Alliance for Medical Image Computing http://na-mic.org DTI Visualization Provided by O’Donnell, Westin et al. Thickness and color describe the quality of fit

12. National Alliance for Medical Image Computing http://na-mic.org DT-MRI Tractography Provided by Westin et al.

13. National Alliance for Medical Image Computing http://na-mic.org Fusion of DTI and fMRI F. Talos, Westin, Wells et al.

14. National Alliance for Medical Image Computing http://na-mic.org What is our science? Computational tools for image analysis Software engineering methods and applications for image analysis

15. National Alliance for Medical Image Computing http://na-mic.org Provided by S. Timoner Capturing Variability

16. National Alliance for Medical Image Computing http://na-mic.org Shape Description Map of shape variability of the Thalamus Blue: high variability 4 years of graduate student work Provided by S. Timoner

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

18. National Alliance for Medical Image Computing http://na-mic.org Overview Introduction Core 1 Core 2 Core 3 Support Cores Slicer Demo

19. National Alliance for Medical Image Computing http://na-mic.org Core 1: Overview Harvard Georgia TechUNC UtahMIT Segmentation Registration Foundational Methods Structural Features and Statistics Connective Features and Statistics 1. Shape and Atlas Based Segmentation 2. Statistical Shape Analysis 3, DTI Connectivity Analysis 1. Diffusion-based Registration 2.Group Effect Maps 3. Automatic Segmentation 1. DTI Processing 2. Surface Processing 3. PDE Implementations 1. Combined Statistical/PDE Methods 1. Quantitative DTI Analysis 2. Cross-Sectional Shape Analysis 2. Stochastic Flow Models

20. National Alliance for Medical Image Computing http://na-mic.org Core 1: Objectives Computational tools for image analysis –Extract anatomical structures at many scales –Measure properties of extracted structures –Determine connectivity between extracted structures –Relate disease factors to measurements

21. National Alliance for Medical Image Computing http://na-mic.org UNC – Gerig: DTI Fiber statistics Structural analysis of DTI tracts –Extraction and analysis –Measurements along tracts –NAMIC-ready in ITK Uncinate fasciculus Major fiber tracts

22. National Alliance for Medical Image Computing http://na-mic.org Overview Introduction Core 1 Core 2 Core 3 Support Cores Slicer Demo

23. National Alliance for Medical Image Computing http://na-mic.org Core 2: Overview GE IsomicsUCSD UCLAKitware Software Integration Software Engineering Software Quality Software Engineering Tools Data Access Tools 1. Cross-platform Build 2. Cross-platform Distribution 3. Cross-language API’s1. Software Architecture2. Software Process3. Software Quality1. Graphical programming interfaces 2. Coordinate pre-compiled tools 3. Data format interpreters1. DBP Applications 1. Grid Middleware 2. Data Grid 2. Application Methodology Distributed Computing Applications 3. Data Mediation3. Application Quality Assurance

24. National Alliance for Medical Image Computing http://na-mic.org Core 2: Objectives Create a software development environment and culture that encourages and supports scientific algorithm innovation while at the same time produces high quality software that meets the needs of the driving biological projects

25. National Alliance for Medical Image Computing http://na-mic.org The Open Source Model Open source software is an important enabling technology for translational research in medical image computing

26. National Alliance for Medical Image Computing http://na-mic.org NA-MIC Kit Application –3D Slicer Toolkits –ITK, VTK, LONI pipeline Software Engineering Tools –Cmake, Ctest, Dart2, Doxygen, CableSwig, others

27. National Alliance for Medical Image Computing http://na-mic.org Isomics - Pieper End User Application Engineering –Based on 3D Slicer (www.slicer.org)www.slicer.org –Cross-platform GUI for Segmentation, Registration, fMRI, DTI… –New Algorithms Integrated through ITK Wrapping –Grid-Compatible Distributed Computation P41, MBIRN, fBIRN

28. National Alliance for Medical Image Computing http://na-mic.org 3D Slicer Draw on Orthogonal Planes Connectivity Tools Math Morphology Image Masking and Logical Operations Level Sets Provided by S. Pieper

29. National Alliance for Medical Image Computing http://na-mic.org Overview Introduction Core 1 Core 2 Core 3 Support Cores Slicer Demo

30. National Alliance for Medical Image Computing http://na-mic.org Core 3.1: Harvard, Dartmouth –Fronto-temporal connections –Cognitive and behavioral data Core 3.2: UCI, Toronto –Brain regions involving DLPFC –Clinical, cognitive, genetic data Core 3: Overview

31. National Alliance for Medical Image Computing http://na-mic.org Example R. Al-Hakim, J. Fallon Segmentation of Area 46 (not 51)

32. National Alliance for Medical Image Computing http://na-mic.org Overview Introduction Core 1 Core 2 Core 3 Support Cores Slicer Demo

33. National Alliance for Medical Image Computing http://na-mic.org Support Cores (# 4-7) Service, Training Dissemination Crucial Support for the Scientific and Engineering Enterprise Support Core PIs also have Strong Scientific Credentials Collaboration History through BIRN and ITK

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

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

36. National Alliance for Medical Image Computing http://na-mic.org Core 7: Management Operational Support –Process Definition –Communication and Coordination –Reporting –Project Management Proactive Management –Project Tracking and Oversight –Process Change Management –New DBP Planning

37. National Alliance for Medical Image Computing http://na-mic.org NA-MIC-Organization Structure

38. National Alliance for Medical Image Computing http://na-mic.org For More Information www.na-mic.org Information about Collaborations (NIH PA)

39. National Alliance for Medical Image Computing http://na-mic.org Overview Introduction Core 1 Core 2 Core 3 Support Cores Slicer Demo

40. National Alliance for Medical Image Computing http://na-mic.org For More Information www.na-mic.org Information about Collaborations (NIH PA)