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Slicer for Neurosurgical Planning

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

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Slicer for Neurosurgical Planning

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  1. Slicer for Neurosurgical Planning IBMSPS 2009 6th 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. 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. 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. 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. 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. 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. Planning Example

  8. Clinical Applications • Change Tracker • MR Spectroscopy • Fiducial Tractography • Open IGT Link

  9. 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. 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. 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. 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. 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

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