Transcript Document

NA-MIC
National Alliance for Medical Image Computing
http://na-mic.org
3D Slicer & NA-MIC:
Overview and
Applications
Steve Pieper, PhD
Acknowledgments
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F. Jolesz, R. Kikinis, C. Tempany, 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, K. Hayes, S. Barre, W.
Plesniak, R. Gollub, S. Pujol and many more….
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National Alliance for Medical Image Computing
http://na-mic.org
R I
TAS
Overall Goal for NA-MIC
• Why Medical Research?
– To Help Patients!
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National Alliance for Medical Image Computing
http://na-mic.org
How to Make this
Happen?
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Enable World-Class Biomedical Research
Develop a Comprehensive Platform
Create a Community of Developers and Users
Ensure Maximum Reusability of Software
National Alliance for Medical Image Computing
http://na-mic.org
Autism Development
• Correlate Localized Brain
Development with
Observed Behavioral
Characteristics of Autism
• Structural and Diffusion
Imaging at 2yo and 4yo
• Cortical Thickness and
Subcortical Volume Metrics
Blue: Growth
Red: Atrophy
Green: No Change
Images: Hazlett et al
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National Alliance for Medical Image Computing
http://na-mic.org
Schizophrenia
• Structural and Diffusion to Discover
Disruptions Correlated with
Symptoms
• First Generation DBP
– Regional Analysis of FA Based
on Manual Tract Identification
• Second Generation DBP
– Stochastic Tractography,
Improved Metrics, Registration
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National Alliance for Medical Image Computing
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Images Ngo et al.
Prostate Disorders
• 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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National Alliance for Medical Image Computing
http://na-mic.org
Lupus Lesions
• Automatic Analysis of White Matter Abnormalities in
Neuropsychiatric SLE (Lupus)
• About 1.5 Million Americans with Lupus, Underlying
Pathologic Processes Unknown – Possibly Vascular
Hypointense on T1
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Hyperintense T2
National Alliance for Medical Image Computing
http://na-mic.org
Hyperintense on FLAIR
Images: Bockholt et al
Patient-Specific Finite Element
Model Development
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Iowa: Kiran H. Shivanna, Vincent A. Magnotta, Nicole M. Grosland,
NA-MIC: Steve Pieper, Curt Lisle
• Automate the generation of high quality
hexahedral meshes
• Inclusion of soft tissues such as cartilage
• Automated Segmentation
• Validation
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Published / Accepted
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Devries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. Validation of phalanx bone threedimensional surface segmentation from computed tomography images using laser scanning. Skeletal Radiol. 2008 Jan;37(1):3542. Epub 2007 Oct 25.
Gassman EE, Powell SM, Kallemeyn NA, DeVries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM,
Automated Bony Region Identification Using Artificial Neural Networks: Reliability and Validation Measurements. Skeletal
Radiology (accepted / online).
Grant funding NIH
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R21 (EB001501)
R01 (EB005973)
National Alliance for Medical Image Computing
http://na-mic.org
Alcohol and Stress
• Primate (Rhesus and Vervet)
Models to Study the Effect of
Chronic Alcohol SelfAdministration on Brain
Structure and Function
• Compare Mother-Reared vs.
Nursery-Reared
• Apply Automated
Segmentation Tools to Assess
Cortical and Subcortical
Regions (EMSegmenter, Pohl
et al)
Chlorocebus aethiops (vervet)
* Rhesus template and atlas graciously provided by
Martin Styner and collaborators
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National Alliance for Medical Image Computing
http://na-mic.org
Images: Wyatt et al
Image Guided Therapy (IGT)
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Is the active visualization of
medical images to aid in decision
making during a procedure.
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Allows physician to
– See Beyond the Surface
– DefineTargets
– Control the Interventions
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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 SepOct;25(5):67-73
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National Alliance for Medical Image Computing
http://na-mic.org
Provided by Archip, Warfield
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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National Alliance for Medical Image Computing
http://na-mic.org
Liver Lesion Treatment
• Needle Placement for CT-Guided
Radio Frequency Ablation (RFA)
– Unresectable Hepatocellular
Carcinoma (HCC) and Liver
Metastases
• Open Source Environment
– Slicer3 and IGSTK
• Automated Liver Segmentation
• Path Planning Tools for Multiple
Overlapping Lesions
• Validation on Swine Model
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National Alliance for Medical Image Computing
http://na-mic.org
Images: Cleary et al
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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National Alliance for Medical Image Computing
http://na-mic.org
BSD Style License
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Open Source
No license fees
No restriction on use
– Clinical and commercial uses do not require our permission
No guarantees
– User is responsible for making sure that the software works, we promise
nothing. Same for compliance with all regulations.
– E.g. if you want to use our software for clinical trials, you have to apply
for the proper authorizations at your institution
NO requirement to give your code back to open source (NOT viral).
– You can contribute code back to us, if you want to do that and it is our
decision if we will accept it.
Acknowledge our contribution
See http://www.slicer.org for more information
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National Alliance for Medical Image Computing
http://na-mic.org
FOSS – A Public Highway…
• Open-source is like a Public
Road System
– Provides Infrastructure
for a Variety of Uses
– Driveways can Lead to
Anything:
• a Public Park
• a Private Facility
FOSS= Free Open Source Software
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National Alliance for Medical Image Computing
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Provided by Pieper, Kikinis
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
– 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
http://na-mic.org
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
Dissemination and Training
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National and International
Events
– MIT, MGH, UNC,
EPFL, NIH, UNM,
UCSD…
All Materials on Wiki
Project Weeks
– Full Week Each
Summer
– ½ Week at Winter
AHM
Workshops
– MICCAI 2005, 2006,
2007, 2008..
– OHBM, RSNA,
Munich, NCI…
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National Alliance for Medical Image Computing
http://na-mic.org
What is 3D Slicer?
• Reference NA-MIC Kit Implementation
• A platform for image analysis and
visualization
• Current Releases 2.7 and 3.0
– 2.7 most features and
documentation
– 3.0 focus of current activity
• 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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National Alliance for Medical Image Computing
http://na-mic.org
Slicer Features
• I/O:
– Image: DICOM, NIfTI, Analyze, Meta, NRRD, MGZ...
– Surface: vtk, vtp, stl, freesurfer, fiber bundle
• Coordinate Systems: Patient-Referenced Data
• Visualization: Volume Rendering, Surfaces, Slices
Planes, Clipping, Volume Overlays...
• Filtering: Denoising, Nonlinear/Aniostropic Smoothing,
Format Conversion
• Registration: Multimodal (e.g. CT/MR), Rigid, Affine,
BSpline. Apply Transforms to other volumes.
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National Alliance for Medical Image Computing
http://na-mic.org
More Slicer Features
• Segmentation: Manual Editor, Semi-Automated (Region
Growing), Statistical Classifiers, Atlas Based
• Diffusion Imaging: DICOM Import, Tensor Tools,
Tractography
• Quantification: Volume Measurements, Points, Lines
• Real-time: Networked Trackers and Volume I/O
• And more...
– Meshing, Fiducials, Batch Processing, Remote Data
I/O,
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National Alliance for Medical Image Computing
http://na-mic.org
Integrated Scene
• XML-Based MRML File Stores
Scene Description
– Volumes (Images,
Label Maps)
– Models
– Hierarchical Affine
Transforms
– Scene Data (Cameras,
Colors, Fiducials, etc).
• Manipulated in World
Coordinates based on Patient
RAS (Right-Anterior-Superior)
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National Alliance for Medical Image Computing
http://na-mic.org
Provided by N. Archip et al