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NA-MIC National Alliance for Medical Image Computing http: //na-mic. org 3 D Slicer & NA-MIC National Alliance for Medical Image Computing http: //na-mic. org 3 D Slicer & NA-MIC: Overview and Applications Steve Pieper, Ph. D

Acknowledgments • 2 F. Jolesz, R. Kikinis, C. Tempany, P. Black, S. Wells, CF. Acknowledgments • 2 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…. National Alliance for Medical Image Computing http: //na-mic. org

Overall Goal for NA-MIC • Why Medical Research? – To Help Patients! 3 National Overall Goal for NA-MIC • Why Medical Research? – To Help Patients! 3 National Alliance for Medical Image Computing http: //na-mic. org

How to Make this Happen? • • 4 Enable World-Class Biomedical Research Develop a How to Make this Happen? • • 4 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 • Autism Development • Correlate Localized Brain Development with Observed Behavioral Characteristics of Autism • Structural and Diffusion Imaging at 2 yo and 4 yo • Cortical Thickness and Subcortical Volume Metrics Blue: Growth Red: Atrophy Green: No Change Images: Hazlett et al 5 National Alliance for Medical Image Computing http: //na-mic. org

Schizophrenia • Structural and Diffusion to Discover Disruptions Correlated with Symptoms • First Generation 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 6 National Alliance for Medical Image Computing http: //na-mic. org Images Ngo et al.

Prostate Disorders • Segmentation tool for Brachytherapy Planning and Biopsy • Navigation for Biopsy 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. 7 National Alliance for Medical Image Computing http: //na-mic. org

Lupus Lesions • Automatic Analysis of White Matter Abnormalities in Neuropsychiatric SLE (Lupus) • 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 T 1 8 Hyperintense T 2 National Alliance for Medical Image Computing http: //na-mic. org Hyperintense on FLAIR Images: Bockholt et al

Patient-Specific Finite Element Model Development • • Iowa: Kiran H. Shivanna, Vincent A. Magnotta, 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 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, De. Vries 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 – – R 21 (EB 001501) R 01 (EB 005973) National Alliance for Medical Image Computing http: //na-mic. org

Alcohol and Stress • Primate (Rhesus and Vervet) Models to Study the Effect of 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) Chlorocebus aethiops (vervet) * Rhesus template and atlas graciously provided by Martin Styner and collaborators 10 National Alliance for Medical Image Computing http: //na-mic. org Images: Wyatt et al

Image Guided Therapy (IGT) • Is the active visualization of medical images to aid Image Guided Therapy (IGT) • Is the active visualization of medical images to aid in decision making during a procedure. • Allows physician to – See Beyond the Surface – Define. Targets – 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 3 rd, 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 11 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 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, f. MRI, and DT-MRI with intra-operative MRI for enhanced visualization and navigation in imageguided neurosurgery. Neuroimage. 2007 Apr 1; 35(2): 609 -24 12 National Alliance for Medical Image Computing http: //na-mic. org

Liver Lesion Treatment • Needle Placement for CT-Guided Radio Frequency Ablation (RFA) – Unresectable Liver Lesion Treatment • Needle Placement for CT-Guided Radio Frequency Ablation (RFA) – Unresectable Hepatocellular Carcinoma (HCC) and Liver Metastases • Open Source Environment – Slicer 3 and IGSTK • Automated Liver Segmentation • Path Planning Tools for Multiple Overlapping Lesions • Validation on Swine Model 13 National Alliance for Medical Image Computing http: //na-mic. org Images: Cleary et al

NA-MIC Governance Software Sharing: http: //grants 1. nih. gov/grants/guide/rfa-files/RFA-RM-04 -003. html • …software should NA-MIC Governance Software Sharing: http: //grants 1. 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 … 14 National Alliance for Medical Image Computing http: //na-mic. org

BSD Style License • • Open Source No license fees No restriction on use 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 15 National Alliance for Medical Image Computing http: //na-mic. org

FOSS – A Public Highway… • Open-source is like a Public Road System – 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 16 National Alliance for Medical Image Computing http: //na-mic. org Provided by Pieper, Kikinis

NA-MIC: A Network of Peers • • • Leadership: – BWH: Ron Kikinis, (Overall 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 – Ga. Tech: 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 – Uof. T: Jim Kennedy DBP 2007 – UNC: H. Cody – BWH: M. Kubicki – Mind Institute: J. Bockolt – Queens University: G. Fichtinger 17 • • 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 • • National and International Events – MIT, MGH, UNC, EPFL, 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… 18 National Alliance for Medical Image Computing http: //na-mic. org

What is 3 D Slicer? • Reference NA-MIC Kit Implementation • A platform for What is 3 D 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 19 National Alliance for Medical Image Computing http: //na-mic. org

Slicer Features • I/O: – Image: DICOM, NIf. TI, Analyze, Meta, NRRD, MGZ. . Slicer Features • I/O: – Image: DICOM, NIf. TI, 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. 20 National Alliance for Medical Image Computing http: //na-mic. org

More Slicer Features • Segmentation: Manual Editor, Semi-Automated (Region Growing), Statistical Classifiers, Atlas Based 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, 21 National Alliance for Medical Image Computing http: //na-mic. org

Integrated Scene • XML-Based MRML File Stores Scene Description – Volumes (Images, Label Maps) 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) 22 National Alliance for Medical Image Computing http: //na-mic. org Provided by N. Archip et al