Open Source Concepts in Image Guided Therapy

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Open Source Concepts in Image Guided Therapy

• Ron Kikinis, M.D.,
• Professor of Radiology, Harvard Medical School,
  Director, Surgical Planning Laboratory, Brigham
  and Womens Hospital

Founding Director, Surgical Planning Laboratory,
Brigham and Womens Hospital Principal
Investigator, the National Alliance for Medical
Image Computing, and the Neuroimage Analysis
Center Research Director, National Center for
Image Guided Therapy
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Acknowledgments

• F. Jolesz, C. Tempany, P. Black, S. Wells, CF.
  Westin, M. Halle, S. Pieper, N. Hata, T. Kapur,
  A.Tannenbaum, M. Shenton, E. Grimson, P.Golland,
  W.Schroeder, and many more.

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Overview

• Introduction
• Slicer
• Robots
• NA-MIC
• Open IGT

Science over 500 peer-reviewed papers since 1990
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Image Guided Therapy (IGT)

• Active visualization of medical images to aid in
  decision making during a procedure.
• Allows physician to
• See Beyond the Surface
• DefineTargets
• Control the Interventions
• Enables new procedures, decreases invasiveness,
  optimizes resection

Dimaio SP, Archip N, Hata N, Talos IF, Warfield
SK, Majumdar A, Mcdannold N, Hynynen K, Morrison
PR, Wells WM 3rd, Kacher DF, Ellis RE, Golby AJ,
Black PM, Jolesz FA, Kikinis R. Image-guided
neurosurgery at Brigham and Women's Hospital.IEEE
Eng Med Biol Mag. 2006 Sep-Oct25(5)67-73
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MIC The Problem

• More image data, more complexity
• Medical Image Computing aims to extract relevant
  information from images

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MIC The Science

• Algorithm research
• Software tool development
• Biomedical research (applications)

Courtesy R. Jose et al.
Courtesy P. Black et al.
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MIC The Approach

• Research and development conducted by
  interdisciplinary teams

Pohl et al.
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Overview

• Introduction
• Slicer
• Robots
• NA-MIC
• Open IGT

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Slicer 3 Software

• Next Generation of Slicer
• At least 80 of code rewritten
• gt 500K lines of code
• 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

• Google slicer 101

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Courtesy S. Pieper
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Slicer Features

• Multi-Platform
• Visualization
• Filtering
• Registration
• Segmentation
• DTI
• Quantification
• IGT Capabilities device interfaces
• Plug-in architecture
• Interfaces into informatics frameworks

• Specialties Involved
• Medical Imaging
• Applied Math
• Software Engineering
• Visualization
• Statistics
• Computer Vision
• Neuroscience
• Robotics
• User Interface
• Information Design

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Segmentation
B. Davis, S. Barre, Y. Yuan, W. Schroeder, P.
Golland, K. Pohl
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Rigid Registration
Overlay Before
After
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Non-rigid Deformation
CWM
BWH
Toward real-time image guided neurosurgery using
distributed and grid computing (with Andriy
Fedorov, Andriy Kot, Neculai Archip, Peter Black,
Olivier Clatz, Alexandra Golby, Ron Kikinis, and
Simon K. Warfield. In Proceedings of the 2006
ACM/IEEE Conference on Supercomputing, Tampa,
Florida, November 11- 17, 2006.
() Non-rigid alignment of preoperative MRI,
fMRI, DT-MRI, with intra-operative MRI for
enhanced visualization and navigation In
image-guided neurosurgery (with N. Archip, O.
Clatz, A. Fedorov, A. Kot, S. Whalen, D. Kacher,
F. Jolesz, A. Golby, P.Black, S. Warfield) in
NeuroImage, 35(2)609-624, 2007.
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Fusion of Pre-OP Data
Provided by A. Golby
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Augmented Endoscopy
Micro Sensor for Tracking
Sierra R, Dimaio SP, Wada J, Hata N, Szekely G,
Kikinis R, Jolesz F, Links Patient specific
simulation and navigation of ventriculoscopic
interventions. Stud Health Technol Inform.
2007125433-5
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Overview

• Introduction
• Slicer
• Robots
• NA-MIC
• Open IGT

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Robotic Devices Hardware
Feasibility Next Step Open 0.5T Closed
3T
Robot-Assisted Needle Placement in Open-MRI
System Architecture, Integration and Validation,
S. P. DiMaio, S. Pieper, K. Chinzei, N. Hata, E.
Balogh, G. Fichtinger, C. M. Tempany, R. Kikinis.
Studies in Health Technologies and Informatics
(Medicine Meets Virtual Reality),
2005119126-31.
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IGT Robotics
A system for MRI-guided Prostate Interventions,
S. P. DiMaio, G. S. Fischer, S. J. Haker, N.
Hata, I. Iordachita, C. M. Tempany, R. Kikinis,
G. Fichtinger. Proceedings of IEEE / RAS-EMBS
International Conference of Biomedical Robotics
and Biomechatronics, February 2006.
Provided by DiMaio et al.
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Open robots?

• Open design specifications
• Commodity materials

Provided by D. Pace et al.
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Overview

• Introduction
• Slicer
• Robots
• NA-MIC
• Open IGT

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NAMIC Multi-Site

• National Alliance for Medical Image Computing
• From local to wide-area
• One of seven National Centers for Biomedical
  Computing funded by NIH

Al Hakim et al.
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NA-MIC An Alliance of Peers

• Leadership
• BWH Ron Kikinis, (Overall PI)?
• Core 1 Algorithms
• Utah Ross Whitaker (Core 1 PI), Guido Gerig?
• MIT Polina Golland, Eric Grimson
• UNC Martin Styner
• MGH Bruce Fischl, Dave Kennedy
• GaTech Allen Tannenbaum
• Core 2 Engineering
• Kitware Will Schroeder (Core 2 PI)?
• GE Jim Miller
• Isomics Steve Pieper
• UCSD Mark Ellisman, Jeff Grethe
• UCLA Art Toga
• Core 3 DBP 2004-2007
• BWH Martha Shenton
• Dartmouth Andy Saykin
• UCI Steve Potkin
• UofT Jim Kennedy

• 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, R. Manandhar

Provided by Pieper, Kikinis
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NA-MIC is Big Science

• Plus
• Big Science can be a force multiplier
• Development and adoption of best practices
• Faster and higher-quality dissemination of new
  techniques and of new science
• Minus
• Change in culture needed
• Replace
• My research
• with
• Our research

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FOSS in NA-MIC

• Free
• Open Source
• No restrictions on use
• No requirement to give back derived code (you
  decide how much you want to share)
• Software

I. Courouge et al.
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The FOSS Value Proposition

• Cost effective Reduced duplication
• High quality Openness enables validation,
  debugging and local control
• Lowers barriers for scientific exchange

Fletcher et al.
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The NA-MIC Kit

• Designed for Research (but compatible with
  commercial activities)
• FOSS 3D Slicer, ITK, VTK, KWW
• Software engineering methodology
• Portable multi-platform cmake
• Multi-site development nightly builds dart
• Quality assurance automated testing ctest

Fischl et al.
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FOSS and Commercial Use

• Value-added commercialization is the proper
  mechanism for clinical use of open research
  results
• BSD style licenses are fully compatible with
  commercial use
• Automated testing and multi-platform support
  lower the threshold for the translational work

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Overview

• Introduction
• Slicer
• Robots
• NA-MIC
• Open IGT

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NCIGT

• NIH funded National Center for Image Guided
  Therapy
• Leverages NA-MIC software platform
• Open Concepts in IGT where appropriate

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The Two Worlds of IGT

• Clinical devices
• Government regulated (for protection of patients)
• Freeze the procedure and devices
• Characterize/test behavior
• Document
• Research devices
• Regulated through local research protocols
• Frequent modifications
• Characterization/testing is an afterthought
• Documentation is always behind

Siemens
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Types of IGT Research

• Testing of devices provided by commercial vendors
• Performed in a clinical environment
• Developing new devices
• Requires dedicated research time and dedicated
  personnel

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Proprietary Approaches

• Hardware is inherently proprietary
• Funding agencies often require commercialization
  which results in proprietary approaches

Mako Surgical Corp.
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Consequences

• Proprietary software and hardware
• Scientific exchange is more difficult
• Leveraging the work of others becomes more
  difficult
• Locks researchers to the vendor
• Consequence Graduate students are forced to
  duplicate work by others

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Lessons learned

• Open science concepts for devices
• Open interfaces
• Open designs
• Increased reliance on commodity technology

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Open Interfaces

• USB keys are an excellent example for a
  successful hardware/software standard
• Devices available from different vendors
• Same device works on different computers with a
  variety of operating systems
• Opentracker and IGSTK are emerging BSD licensed
  packages that provide open interfaces to
  proprietary tracking systems

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Open IGT for Research

• Free Open Source Software
• NA-MIC methodology allows multi-party development
  and quality assurance
• Potential to bridge the gap between research and
  clinical devices
• Open Standards for Hardware interfaces
• Computer industry offers good templates
  Standardization through ACM and IEEE
• Open Designs for Research Hardware(remember the
  Lego robot?)

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Thank You!

• For more information
• http//www.spl.harvard.edu
• http//www.ncigt.org
• http//www.na-mic.org