3D Slicer Version 3.0 and Diffusion MRI

1. 3D Slicer Version 3.0 and Diffusion MRI Steve Pieper, PhD

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. 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. 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. 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. Neurosurgery Mapping Provided by Archip, Warfield Alignment of all pre-operative datasets to the intra-operative images achieved during the neurosurgery. 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. Tracking of Devices MicroBird Sensor Optical Tracking

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. 1000 Slicer-Guided Craniotomies http://www.brighamandwomens.org/ofcurrentinterest/craniotomy.aspx

10. Many More Examples Image Gallery

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. 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. 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. 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 NA-MIC: A Network of Peers Provided by Pieper, Kikinis

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. 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. 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. 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. Slicer3 is Coming Soon… • Not yet ready for workshops like this • See http://wiki.na-mic.org/index.php/Slicer3 for more information