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3D Slicer for Surgical Planning

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					NA-MIC
National Alliance for Medical Image Computing
http://na-mic.org



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.
     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….




                                                                       V E   R I   TAS




     National Alliance for Medical Image Computing
     http://na-mic.org                     Slide courtesy R. Kikinis
      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



      National Alliance for Medical Image Computing
      http://na-mic.org                               Images: www.slicer.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)




       National Alliance for Medical Image Computing
                                                       Slide courtesy N. Hata
       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                    Image provided by N. Hata



• Integrated scene concept

     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
                              Slide courtesy R. Kikinis   Provided by N. Archip et al

     RAS (Right-Anterior-Superior)
      National Alliance for Medical Image Computing
      http://na-mic.org
Planning Example




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



   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
       National Alliance for Medical Image Computing
       http://na-mic.org                     Slide courtesy R. Kikinis         Pohl and Federov
      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



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

     National Alliance for Medical Image Computing
     http://na-mic.org                     Slide courtesy R. Kikinis   JJ. Lemaire
      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)


      National Alliance for Medical Image Computing
      http://na-mic.org                     Slide courtesy R. Kikinis   Golby, Hata, Liu, Tokada, Ibanez,
                                                                                Papademetrios
      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
      National Alliance for Medical Image Computing
      http://na-mic.org

				
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