1. NA-MIC National Alliance for Medical Image Computing http://na-mic.org Slicer for Neurosurgical Planning IBMSPS 2009 6 th Annual World Congress for Brain Mapping and Image Guided Therapy Harvard Medical School, Boston MA USA Neuroimage Analysis Workshop: Slicer3 Open-Source Software for 3D Visualization and Image-Guided Therapy Tuesday August 25, 2009 Surgical Planning Laboratory, 1249 Boylston St. Boston MA USA Presenter: Lauren O’Donnell, Ph.D.

2. National Alliance for Medical Image Computing http://na-mic.org Acknowledgements F. Jolesz, C. Tempany, A. Golby, P. Black, S. Wells, CF. Westin, M. Halle, N. Hata, T. Kapur, A.Tannenbaum, M. Shenton, E. Grimson, P.Golland, W.Schroeder, J. Miller, N. Aucoin, A. Yarmarkovich, W. Lorensen, X. Tao, K. Hayes, S. Barre, W. Plesniak, R. Gollub, S. Pujol and many more…. Slide courtesy R. Kikinis

3. National Alliance for Medical Image Computing http://na-mic.org 3D Slicer History Open-source software application –For computer scientists –For clinical researchers Initiated in 1998 –Surgical Planning Laboratory at the Brigham and Women's Hospital –MIT Artificial Intelligence Laboratory Slicer3 –New, completely rearchitected –May of 2009: version 3.4 Images: www.slicer.org

4. National Alliance for Medical Image Computing http://na-mic.org Slicer in IGT To facilitate application of state-of-art medical image processing in IGT Software design to support common functions across applications –Brain (biopsy, craniotomy, NdYAG laser ablation) –Prostate (brachytherapy, biopsy) –Liver and kidney (Microwave, Cryo, laser ablation) –Endoscopy (broncho-, neuro-, feto-scopy) Slide courtesy N. Hata

5. National Alliance for Medical Image Computing http://na-mic.org Slicer3 Features for Planning Image registration –Align multiple modalities by mutual information Image segmentation –Tumor visualization in 3D Image overlay –fMRI and anatomical images Diffusion tensor –Anisotropy and orientation –Tractography of white matter Integrated scene concept Image provided by N. Hata

6. National Alliance for Medical Image Computing http://na-mic.org Slicer3 Integrated Scene XML-Based MRML File Stores Scene Description –Volumes (Images, Label Maps) –Models –Hierarchical Affine Transforms –Scene Data (Cameras, Colors, Fiducials, etc). Patient-Centric –Manipulated in World Coordinates based on Patient RAS (Right-Anterior-Superior) Provided by N. Archip et al Slide courtesy R. Kikinis

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

8. National Alliance for Medical Image Computing http://na-mic.org Clinical Applications Change Tracker MR Spectroscopy Fiducial Tractography Open IGT Link

9. National Alliance for Medical Image Computing http://na-mic.org Change Tracker “Watchful Waiting” of Brain Tumors –Longitudinal Volumes –Change Analysis Algorithms Leverages Slicer Infrastructure –Registration –CompareView –Volume Rendering –MRML Scene Files –Workflow Wizard With the Brain Science Foundation Pohl and Federov Slide courtesy R. Kikinis

10. National Alliance for Medical Image Computing http://na-mic.org MRSI MRSI Volume Analysis and Display Multi-Spectral, Multi-Modal MRSI Choline Map Turnover of Cell Membranes MRSI NAA Map Integrity of CNS Tissue Structural MRI Integrated Slicer Module for MRSI Calculations B. Menze Slide courtesy R. Kikinis

11. National Alliance for Medical Image Computing http://na-mic.org Fiducial Tractography Fiducial: –Movable seed point Interactive Probing of Fiber Bundles –Peritumoral Fibers fMRI Display in Context with Structural and Diffusion Volumes JJ. Lemaire Slide courtesy R. Kikinis

12. National Alliance for Medical Image Computing http://na-mic.org Open IGT Link December 2007: Concept January 2008: Prototype and Name July 2008: BrainLab VVLink with Yale (Papademetrios) December 2008: Real Time MR Control February 11, 2009: Initial Clinical Application with Dr. Alex Golby Multi-Site Collaboration coordinated by NCIGT (Jolesz, Hata et al) Golby, Hata, Liu, Tokada, Ibanez, Papademetrios Slide courtesy R. Kikinis

13. National Alliance for Medical Image Computing http://na-mic.org More Information 3D Slicer is –multi-platform –free open source software (FOSS) –for visualization and image computing 3D Slicer consists of –more than 550 thousand lines of code, mostly C++. Enabled by –Participation of several large scale NIH funded efforts Including NA-MIC, NAC, BIRN, CIMIT and NCIGT communities. –Several federal funding sources Including NCRR, NIBIB, NIH Roadmap, NCI, NSF and the DOD as well as others www.slicer.org