1. NA-MIC National Alliance for Medical Image Computing http://na-mic.org 3D Slicer Version 3.0 and Diffusion MRI Steve Pieper, PhD

2. National Alliance for Medical Image Computing http://na-mic.org 2 Acknowledgments F. Jolesz, R. Kikinis, S. Wells, CF. Westin, M. Halle, T. Kapur, W.Schroeder, J. Miller, N. Aucoin, K. Hayes, S. Barre, W. Plesniak, R. Estepar, L. O’Donnell, D. Gering and many more….

3. National Alliance for Medical Image Computing http://na-mic.org 3 Overview Where did 3D Slicer come from? What are the goals? What is it used for? What is it made of? What can we expect next?

4. National Alliance for Medical Image Computing http://na-mic.org 4 What is 3D Slicer? A platform for exploring novel image analysis and visualization techniques Current Release 2.6 A freely-downloadable program –Source code and executables available for Windows, Linux, and Mac OS X Slicer is a research platform: –NOT an FDA approved medical device –NOT finished – some parts will work better than others

5. National Alliance for Medical Image Computing http://na-mic.org 5 Slicer2 Background SPL / MIT Image Guided Surgery and Visualization (Kikinis, Westin, Hata, Halle, others) Slicer Application Pulled Together by Dave Gering 1997-1999 with VTK and Tcl Further Development and Architecture by Lauren O’Donnell 1999-2001 Ongoing Development of Slicer’s Base Primarily by Steve Pieper and Nicole Aucoin Many Modules and Contributions by Various Authors –BWH, MIT, MGH, Georgia Tech, UCSD, JHU… Sponsorted by NIH Grants including NAC, and BIRN

6. National Alliance for Medical Image Computing http://na-mic.org 6 Alignment of all pre-operative datasets to the intra-operative images achieved during the neurosurgery. Provided by Archip, Warfield Neurosurgery Mapping Archip N, Clatz O, Whalen S, Kacher D, Fedorov A, Kot A, Chrisochoides N, Jolesz F, Golby A, Black PM, Warfield SK. Non-rigid alignment of pre- operative MRI, fMRI, and DT-MRI with intra-operative MRI for enhanced visualization and navigation in image- guided neurosurgery. Neuroimage. 2007 Apr 1;35(2):609-24

7. National Alliance for Medical Image Computing http://na-mic.org 7 Tracking of Devices MicroBird Sensor Optical Tracking

8. National Alliance for Medical Image Computing http://na-mic.org 8 Prostate Segmentation tool for Brachytherapy Planning and Biopsy Navigation for Biopsy Future FUS and Robot Applications Haker SJ, Mulkern RV, Roebuck JR, Barnes AS, Dimaio S, Hata N, Tempany CM.: Magnetic resonance-guided prostate interventions. Top Magn Reson Imaging. 2005 Oct;16(5):355-68.

9. National Alliance for Medical Image Computing http://na-mic.org 9 1000 Slicer-Guided Craniotomies http://www.brighamandwomens.org/ofcurrentinterest/craniotomy.aspx

10. National Alliance for Medical Image Computing http://na-mic.org 10 Image Gallery

11. National Alliance for Medical Image Computing http://na-mic.org 11 NA-MIC Roots: NIH Roadmap Initiative http://grants1.nih.gov/grants/guide/rfa-files/RFA- RM-04-003.html –…will create a networked national effort to build the computational infrastructure for biomedical computing in the nation… –The establishment of the NIH NCBC was called for in the Biomedical Information Science and Technology Initiative report in 1999

12. National Alliance for Medical Image Computing http://na-mic.org 12 NA-MIC Governance Software Sharing: http://grants1.nih.gov/grants/guide/rfa-files/RFA-RM-04-003.html …software should be freely available … …permit the commercialization of enhanced or customized versions … …include the ability of researchers outside the center and its collaborating projects to modify the source code and to share modifications …

13. National Alliance for Medical Image Computing http://na-mic.org 13 2004: NA-MIC Begins… New NIH Program: National Centers for Biomedical Computation National Alliance for Medical Image Computing (our center, one of seven national centers) –Focus on Image Analysis Software –Build Fully Open Source Infrastructure Create the “NA-MIC Kit” Leverage VTK, ITK, CMake, DART… –Create New Version of 3D Slicer

14. National Alliance for Medical Image Computing http://na-mic.org 14 NA-MIC: A Network of Peers Leadership: –BWH: Ron Kikinis, (Overall PI) Core 1 Algorithms –Utah: Ross Whitaker (Core 1 PI) –MIT: Eric Grimson –UNC: Guido Gerig –MGH: Bruce Fischl, Dave Kennedy –GaTech: Allen Tannenbaum Core 2 Engineering –Kitware: Will Schroeder (Core 2 PI) –GE: Jim Miller –Isomics: Steve Pieper, A. Yarmarkovich –UCSD: Mark Ellisman –UCLA: Art Toga Core 3 DBP 2004-2007 –BWH: Martha Shenton –Dartmouth: Andy Saykin –UCI: Steve Potkin –UofT: Jim Kennedy DBP 2007 –UNC: H. Cody –BWH: M. Kubicki –Mind Institute: J. Bockolt –Queens University: G. Fichtinger Core 4 Service –Kitware: Will Schroeder Core 5 Training –MGH: Randy Gollub Core 6 Dissemination –Isomics: Steve Pieper, Tina Kapur Core 7 Management –BWH: S. Manandhar Provided by Pieper, Kikinis

15. National Alliance for Medical Image Computing http://na-mic.org 15 Slicer 3 Next Generation of the 3D Slicer software Beta Release in Jan 2007 Slicer 3.0 Base Release scheduled for June 2007 Advanced Modules Being Added Continually http://www.slicer.org Courtesy S. Pieper

16. National Alliance for Medical Image Computing http://na-mic.org 16 What is Slicer3? Total Rework of 3D Slicer –At least 80% of code rewritten –New versions of VTK (5.0), ITK (3.2) –Improved Look and Feel (KWWidgets) –Improved Modularity Analysis routines can be used as plugins or command line executables for batch processing –Draws on Multi-Institution Community Kitware, Inc., GE Research, Isomics, Inc., BWH, UCLA, UCSD, UIowa, MIT, GaTech, UNC, U Utah, MGH, UCI, Harvard, WashU… NAC, NCIGT, NA-MIC, mBIRN, fBIRN

17. National Alliance for Medical Image Computing http://na-mic.org 17 Slicer3 and Diffusion Diffusion Data Structures Built in From the Start –Fiber Bundles as Primitive –Volumes: Scalar, Vector (color), Diffusion Weighed, Diffusion Tensor –Integrated with Hierarchical Model Viewing Diffusion Visualization and Tractography Modes being Ported from Slicer 2 Platform for Advanced Diffusion Algorithms from NA-MIC –Stochastic Tractography –Population Atlases –Connectivity Metrics –Tract Based Population Comparisons Wide Range of Additional Algorithms in Development –Nonlinear Registration –Atlas Based Segmentation –fMRI Analysis Batch Oriented / Distributed Processing Options

18. National Alliance for Medical Image Computing http://na-mic.org 18 Stochastic Tractography Example in Slicer3 Tri Ngo (MIT), Marek Kubicki (BWH), Carl-Fredrik Westin (BWH) & Polina Golland (MIT) New multithreaded ITK Filter (itkStochasticTractographyFilter) 3D Slicer Command Line Module –Allows the algorithm to be executed without 3D Slicer –Or Use of Auto-Generated GUI to Explore Parameters in Real Time

19. National Alliance for Medical Image Computing http://na-mic.org 19 Slicer3 is Coming Soon… Not yet ready for workshops like this See http://wiki.na-mic.org/index.php/Slicer3 for more informationhttp://wiki.na-mic.org/index.php/Slicer3