Slicer for Neurosurgical Planning

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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 ODonnell, Ph.D.

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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
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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
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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
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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
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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
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Planning Example
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Clinical Applications

• Change Tracker
• MR Spectroscopy
• Fiducial Tractography
• Open IGT Link

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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
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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
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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
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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
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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