Transcript 3D Slicer Version 3.0 and Diffusion MRI Steve Pieper, PhD

NA-MIC
National Alliance for Medical Image Computing
http://na-mic.org
3D Slicer Version
3.0 and Diffusion
MRI
Steve Pieper, PhD
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. O’Donnell, D. Gering and many more….
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R I
TAS
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
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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 O’Donnell 1999-2001
Ongoing Development of Slicer’s 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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Provided by Archip, Warfield
Neurosurgery Mapping
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 preoperative MRI, fMRI, and DT-MRI with
intra-operative MRI for enhanced
visualization and navigation in imageguided neurosurgery. Neuroimage.
2007 Apr 1;35(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 Oct;16(5):355-68.
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1000 Slicer-Guided Craniotomies
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http://www.brighamandwomens.org/ofcurrentinterest/craniotomy.aspx
Many More Examples
Image Gallery
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NA-MIC Roots: NIH
• Roadmap Initiative
• http://grants1.nih.gov/grants/guide/rfa-files/RFARM-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
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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
DBP 2007
– UNC: H. Cody
– BWH: M. Kubicki
– Mind Institute: J. Bockolt
– Queens University: G. Fichtinger
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National Alliance for Medical Image Computing
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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
Provided by Pieper, Kikinis
Slicer 3
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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
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Courtesy S. Pieper
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
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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
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Tri Ngo (MIT), Marek Kubicki
(BWH), Carl-Fredrik Westin
(BWH) & Polina Golland (MIT)
New multithreaded ITK Filter
(itkStochasticTractographyFilter)
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
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