NA-MIC National Alliance for Medical Image Computing 3D Slicer Version 3.0 and Diffusion MRI Steve...

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

3D Slicer Version 3.0 and Diffusion MRISteve Pieper, PhD

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

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….

V E 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?


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


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 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


Alignment of all pre-operative datasets to the intra-operative images achieved during the neurosurgery.

Provided by Archip, Warfield

Neurosurgery Mapping

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 1;35(2):609-24


Tracking of Devices

MicroBird Sensor Optical Tracking


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.


1000 Slicer-Guided Craniotomies

http://www.brighamandwomens.org/ofcurrentinterest/craniotomy.aspx


Image GalleryMany More ExamplesMany More Examples


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


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 …

http://grants1.nih.gov/grants/guide/rfa-files/RFA-RM-04-003.html


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


NA-MIC: A Network of Peers• 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

• 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• 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


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


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


Stochastic Tractography Example in Slicer3

• 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


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

http://wiki.na-mic.org/index.php/Slicer3

NA-MIC National Alliance for Medical Image Computing 3D Slicer Version 3.0 and Diffusion MRI Steve...

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