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NA-MIC National Alliance for Medical Image Computing http: //na-mic. org 3 D Slicer Version NA-MIC National Alliance for Medical Image Computing http: //na-mic. org 3 D Slicer Version 3. 0 and Diffusion MRI Steve Pieper, Ph. D

Acknowledgments • F. Jolesz, R. Kikinis, S. Wells, CF. Westin, M. Halle, T. Kapur, 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…. 2 National Alliance for Medical Image Computing http: //na-mic. org

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

What is 3 D Slicer? • A platform for exploring novel image analysis and What is 3 D 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 4 National Alliance for Medical Image Computing http: //na-mic. org

Slicer 2 Background • • • SPL / MIT Image Guided Surgery and Visualization Slicer 2 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 5 National Alliance for Medical Image Computing http: //na-mic. org

Provided by Archip, Warfield Neurosurgery Mapping Alignment of all pre-operative datasets to the intra-operative Provided by Archip, Warfield Neurosurgery Mapping 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 preoperative MRI, f. MRI, and DT-MRI with intra-operative MRI for enhanced visualization and navigation in imageguided neurosurgery. Neuroimage. 2007 Apr 1; 35(2): 609 -24 6 National Alliance for Medical Image Computing http: //na-mic. org

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

Prostate • Segmentation tool for Brachytherapy Planning and Biopsy • Navigation for Biopsy • 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. 8 National Alliance for Medical Image Computing http: //na-mic. org

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

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

NA-MIC Roots: NIH • Roadmap Initiative • http: //grants 1. nih. gov/grants/guide/rfa-files/RFARM-04 -003. html NA-MIC Roots: NIH • Roadmap Initiative • http: //grants 1. nih. gov/grants/guide/rfa-files/RFARM-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 11 National Alliance for Medical Image Computing http: //na-mic. org

NA-MIC Governance Software Sharing: http: //grants 1. nih. gov/grants/guide/rfa-files/RFA-RM-04 -003. html • …software should NA-MIC Governance Software Sharing: http: //grants 1. 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 … 12 National Alliance for Medical Image Computing http: //na-mic. org

2004: NA-MIC Begins… • New NIH Program: National Centers for Biomedical Computation • National 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 3 D Slicer 13 National Alliance for Medical Image Computing http: //na-mic. org

NA-MIC: A Network of Peers • • • Leadership: – BWH: Ron Kikinis, (Overall 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 – Ga. Tech: 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 – Uof. T: Jim Kennedy DBP 2007 – UNC: H. Cody – BWH: M. Kubicki – Mind Institute: J. Bockolt – Queens University: G. Fichtinger 14 • • National Alliance for Medical Image Computing http: //na-mic. org 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

Slicer 3 • • Next Generation of the 3 D Slicer software Beta Release Slicer 3 • • Next Generation of the 3 D 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 15 National Alliance for Medical Image Computing http: //na-mic. org Courtesy S. Pieper

What is Slicer 3? • Total Rework of 3 D Slicer – At least What is Slicer 3? • Total Rework of 3 D 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, Ga. Tech, UNC, U Utah, MGH, UCI, Harvard, Wash. U… • NAC, NCIGT, NA-MIC, m. BIRN, f. BIRN 16 National Alliance for Medical Image Computing http: //na-mic. org

Slicer 3 and Diffusion • • • Diffusion Data Structures Built in From the Slicer 3 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 – f. MRI Analysis Batch Oriented / Distributed Processing Options 17 National Alliance for Medical Image Computing http: //na-mic. org

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

Slicer 3 is Coming Soon… • Not yet ready for workshops like this • Slicer 3 is Coming Soon… • Not yet ready for workshops like this • See http: //wiki. na-mic. org/index. php/Slicer 3 for more information 19 National Alliance for Medical Image Computing http: //na-mic. org