3D Slicer. NA-MIC National Alliance for Medical Image Computing 4 February 2011
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1 NA-MIC 3D Slicer 4 February 2011 Andrey Fedorov, PhD Steve Pieper, PhD Ron Kikinis, MD Surgical Planning Lab Brigham and Women's Hospital
2 Acknowledgments Picture courtesy Kapur, Jakab, Kikinis
3 The 3D Slicer 3D Slicer is a platform for delivering image computing technology for personalized medicine research Basic and clinical visualization Longitudinal imaging Registration Segmentation Picture courtesy Marianna Jakab
4 Our Approach Open community process Modular and extensible architecture Free open source software (BSD) Works on your computer
5 Open Community Process Community support mailing lists web-based bug reporting wiki for documentation svn for code management Open to all: academia, industry, government, international Twice a year working weeks called project weeks Focused workshops (DTI, IGT) Picture courtesy Sonia Pujol
6 Modular Software Architecture NA-MIC Kit: 3D Slicer, VTK, ITK, CMake, CTest, CDash, KWWidgets, XNAT, Teem Other open source: Qt, Python, Tcl/Tk, SVN Slicer extensions Picture courtesy Will Schroeder
7 Impact Package Slicer KWW VTK ITK CMake / CTest / CPack CDash XNat Total Lines of code Person years 1,270, ,208 1,853, , ,454 78, ,985 4,782,601 Price tag at 100k per person year 361 $36,122, $ 5,406, $53,808, $23,719, $8,590, $1,897, $5,149, $134,694,344
8 Free Open Source Software NA-MIC kit has BSD license No protected IP No lawyers needed Lowers barriers to collaboration Software can move with scientists Co-existence of proprietary and open Fenway Park Community Garden Picture courtesy Steve Pieper
9 Works on Your Computer Easy download and installation Runs natively on your computer on Windows, Mac and Linux behind your institutional firewall Training concept: Self guided tutorials Training events Registration and segmentation support Picture courtesy Dominik Meier
10 Basic Visualization Window/Level Corner Annotations Pseudocolor Mosaic Multi-modality
11 3D Visualization Rendering techniques MIP (Maxiumum Intensity Projection) SSD (Shaded Surface Display) Pseudocolor + Gradient Lighting Ray casting using transfer functions Color and Opacity Transfer Functions Composite display Reference Labels for Standard Views Left/Right, Anterior/Posterior, Inferior/Superior Volume rendered CT of a brain aneurysm with composited crosssection Picture courtesy Yuhana Froesen
12 Longitudinal Imaging (4D) Volumes Acquired Over Multiple Visits Time-series (DCE) visualization and processing Comparison View Linked Cursors Subtraction Imaging and Quantification Guttmann, Meier, Fedorov BWH Miller - GE
13 Multi-Modality Imaging Integrated Visualization of What is Known About the Subject Anatomical Space as Common Coordinate System Segmented Anatomy and Volume Rendering for Context Statistics Volumes Interactive Visualization (View, Visibility, Cropping, Slicing ) Image Guided Therapies Plesniak, Aucoin et al - BWH Jakab and Berenyi - University of Debrecen
14 Registration Preprocedure MR Intraprocedure CT Intra-subject Pre-Intra-Post Procedure Longitudinal Tracking of Disease Progression Inter-subject Support Group Comparison (fmri) Map Anatomical Atlas to Individual Degrees of Freedom (DOFs) Rigid (Rotation + Translation) Similarity (Rigid + Uniform Scale) Affine (Rigid + Nonuniform Scale and Shear) Polyaffine (Locally Affine Interpolation) B-Spline (Cubic Displacement) Vector Field Oguro - BWH
15 Segmentation Definition: Assignment of Anatomical Labels to Image Regions Not an Exact Science Anatomists Disagree Definition Depends on Scale and Modality Manual editing capabilities Automated techniques Intensity Driven: Function of Image Measurements Thresholding is Most Common (Typically Bad for MRI) Level sets, Grow Cut Atlas Driven: Registration of Manually Labeled Data Also difficult for clinical scans Hybrid Approaches Typically Required E.g. Expectation Maximization (EM) Pohl IBM Kikinis, Shenton - BWH
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17 Slicer building blocks Data What can I load/create in Slicer? Presentation How can I explore my data? Analysis How can I process my data?
18 Data Volumes Labels Transforms Models...
19 Presentation Slice viewers Overlays Color maps Window/level Annotations Reformat Lightbox 3D viewer Layouts
20 Presentation Slice viewers Lightbox 3D viewer Layouts
21 Presentation Slice viewers Lightbox 3D viewer Layouts
22 Presentation Slice viewers Lightbox 3D viewer Layouts
23 Putting it all together
24 Slicer Scene = data + presentation Slicer Scene is saved as a.mrml file MRML = Medical Reality Markup Language
25 Scene snapshots Recorded scene configurations customized for a specific task Contouring for visit 1 Visit 3 Visit 2 Contour review
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