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Slicer3 plugins

Slicer3 plugins. Common architecture for interactive and batch processing. Each module has …. … an entry in the module menu. … a panel of user interface controls. User Desktop. Slicer 3.0. Algorithms. ITK. VTK. Slicer Modules. Scripts of Slicer Mods. VTK Apps Using ITK. Batch

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Slicer3 plugins

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  1. Slicer3 plugins Common architecture for interactive and batch processing

  2. Each module has … … an entry in the module menu … a panel of user interface controls

  3. User Desktop Slicer3.0 Algorithms ITK VTK Slicer Modules Scripts of Slicer Mods VTK Apps Using ITK Batch Programs Non-NAMIC Cmd tools BatchMake BIRN Grid Wizard The grand vision…

  4. Slicer Development Effort Numbers Subversion Commits: 3,407 Lines of Code*: 371,428 Bugs & Features: 154 Submitted 63 Closed Active Developers†: 33 *: find . -iname \*.h -o -iname \*.cxx -o -iname \*.tcl -o -iname \*.java -o -name \*.py | grep -v svn | xargs wc †: svn log | grep "^r" | cut -d " " -f 3 | sort | uniq | wc

  5. User Desktop Slicer3.0 Algorithms ITK VTK Slicer Modules Scripts of Slicer Mods VTK Apps Using ITK Batch Programs Non-NAMIC Cmd tools BatchMake BIRN Grid Wizard Common architecture for interactive and batch processing

  6. Slicer Modules Built In Modules Interact Closely with GUI Volume Rendering, Models, Editor… Command Line Modules “Batch Mode” Registration, Filtering, DTI Tractography… Today we will look only at Command Line Modules

  7. Existing Command Line Modules Demonstration Execution Model Tour Your new hello world module Converters Create a DICOM Series Dicom DWI loader Dicom to Nrrd GE Dicom to NRRD Converter Orient Images Filtering Calculate Volume Statistics CheckerBoard Filter Extract Skeleton Histogram Matching Otsu Threshold Resample Volume / Resample Volume 2 Voting Binary Hole Filling Zero Crossing Based Edge Detection Filter Filtering.Arithmetic: Add Images Subtract Images

  8. Existing Command Line Modules Filtering.Denoising Curvature Anisotropic Diffusion Gaussian Blur Gradient Anisotropic Diffusion Median Filter Segmentation EMSegment Simple FreesurferSurfaceSectionExtraction Otsu Threshold Segmentation Simple region growing Filtering.Morphology Grayscale Fill Hole Grayscale Grind Peak Model Generation Grayscale Model Maker Label Map Smoothing Model Maker Multiple models example Probe Volume With Model (Paint) Meshing.VoxelMesh Voxel Meshing

  9. Registration Command Line Modules Registration Affine registration Deformable BSpline registration (Utah) Deformable BSpline registration Linear registration RealignVolume

  10. Diffusion Command Line Modules Diffusion Tensor Resample DTI Volume Diffusion Tensor Estimation Diffusion Tensor Scalar Measurements Simple DWI IO Test Rician LMMSE Image Filter Tractography.Editor: ROISelect Tractography.Seeding Stochastic Tractography Generate Connectivity Map Stochastic ROI Tract Filter Stochastic Stochastic Tractography Filter

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