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NA-MICNational Alliance for Medical Image Computing http://na-mic.org
3D Slicer & NA-MIC:Overview and Applications
Steve Pieper, PhD
National Alliance for Medical Image Computing http://na-mic.org
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Acknowledgments• 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….
V E R I TAS
National Alliance for Medical Image Computing http://na-mic.org
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Overall Goal for NA-MIC
• Why Medical Research?– To Help Patients!
National Alliance for Medical Image Computing http://na-mic.org
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How to Make this Happen?
• 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
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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: GrowthRed: Atrophy
Green: No Change
Images: Hazlett et al
National Alliance for Medical Image Computing http://na-mic.org
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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
Images Ngo et al.
National Alliance for Medical Image Computing http://na-mic.org
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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.
National Alliance for Medical Image Computing http://na-mic.org
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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 Hyperintense T2 Hyperintense on FLAIR
Images: Bockholt et al
National Alliance for Medical Image Computing http://na-mic.org
Patient-Specific Finite Element Model Development
• 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• Published / Accepted
– Devries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning. Skeletal Radiol. 2008 Jan;37(1):35-42. 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– 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 Self-Administration 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)
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Chlorocebus aethiops (vervet)
* Rhesus template and atlas graciously provided by Martin Styner and collaborators
Images: Wyatt et al
National Alliance for Medical Image Computing http://na-mic.org
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• Is the 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
Image Guided Therapy (IGT)
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-Oct;25(5):67-73
National Alliance for Medical Image Computing http://na-mic.org
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Alignment of all pre-operative datasets to the intra-operative images achieved during the neurosurgery.
Provided by Archip, Warfield
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
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
13 Images: Cleary et al
National Alliance for Medical Image Computing http://na-mic.org
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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 …
National Alliance for Medical Image Computing http://na-mic.org
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BSD Style License
• 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
National Alliance for Medical Image Computing http://na-mic.org
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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
Provided by Pieper, Kikinis
National Alliance for Medical Image Computing http://na-mic.org
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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– 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
National Alliance for Medical Image Computing http://na-mic.org
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Dissemination and Training
• 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…
National Alliance for Medical Image Computing http://na-mic.org
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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
National Alliance for Medical Image Computing http://na-mic.org
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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.
National Alliance for Medical Image Computing http://na-mic.org
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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,
National Alliance for Medical Image Computing http://na-mic.org
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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) Provided by N. Archip et al