3D Slicer Version 3'0 and Diffusion MRI

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3D Slicer Version 3.0 and Diffusion MRI

• Steve Pieper, PhD

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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. ODonnell, D. Gering and many more.

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Overview

• Where did 3D Slicer come from?
• What are the goals? What is it used for? What is
  it made of?
• What can we expect next?

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What is 3D 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

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Slicer2 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
  ODonnell 1999-2001
• Ongoing Development of Slicers 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

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Neurosurgery Mapping
Provided by Archip, Warfield
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
pre-operative MRI, fMRI, and DT-MRI with
intra-operative MRI for enhanced visualization
and navigation in image-guided neurosurgery.
Neuroimage. 2007 Apr 135(2)609-24
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Tracking of Devices
MicroBird Sensor Optical Tracking
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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 Oct16(5)355-68.
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1000 Slicer-Guided Craniotomies
http//www.brighamandwomens.org/ofcurrentinterest/
craniotomy.aspx
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Image Gallery
Many More Examples
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NA-MIC Roots NIH

• Roadmap Initiative
• http//grants1.nih.gov/grants/guide/rfa-files/RFA-
  RM-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

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NA-MIC Governance

• Software Sharing
• http//grants1.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

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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 3D Slicer

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NA-MIC A Network of Peers

• 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

• 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
• GaTech 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
• UofT Jim Kennedy

Provided by Pieper, Kikinis
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Slicer 3

• Next Generation of the 3D 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

Courtesy S. Pieper
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What is Slicer3?

• Total Rework of 3D 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, GaTech, UNC, U Utah, MGH,
  UCI, Harvard, WashU
• NAC, NCIGT, NA-MIC, mBIRN, fBIRN

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Slicer3 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
• fMRI Analysis
• Batch Oriented / Distributed Processing Options

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Stochastic Tractography Example in Slicer3

• Tri Ngo (MIT), Marek Kubicki (BWH), Carl-Fredrik
  Westin (BWH) Polina Golland (MIT)
• New multithreaded ITK Filter (itkStochasticTractog
  raphyFilter)
• 3D Slicer Command Line Module
• Allows the algorithm to be executed without 3D
  Slicer
• Or Use of Auto-Generated GUI to Explore
  Parameters in Real Time

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Slicer3 is Coming Soon

• Not yet ready for workshops like this
• See http//wiki.na-mic.org/index.php/Slicer3 for
  more information