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Published byJocelyn Parker Modified over 10 years ago
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National Alliance for Medical Image Computing http://na-mic.org Slicer3 plugins Common architecture for interactive and batch processing
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National Alliance for Medical Image Computing http://na-mic.org Each module has … … an entry in the module menu … a panel of user interface controls
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National Alliance for Medical Image Computing http://na-mic.org The grand vision… User Desktop AlgorithmsITKVTK Slicer Modules VTK Apps Using ITK Scripts of Slicer Mods Batch Programs Non-NAMIC Cmd tools BatchMake BIRN Grid Wizard Slicer 3.0
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National Alliance for Medical Image Computing http://na-mic.org 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
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National Alliance for Medical Image Computing http://na-mic.org Common architecture for interactive and batch processing User Desktop AlgorithmsITKVTK Slicer Modules VTK Apps Using ITK Scripts of Slicer Mods Batch Programs Non-NAMIC Cmd tools BatchMake BIRN Grid Wizard Slicer 3.0
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National Alliance for Medical Image Computing http://na-mic.org 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
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National Alliance for Medical Image Computing http://na-mic.org 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
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National Alliance for Medical Image Computing http://na-mic.org 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
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National Alliance for Medical Image Computing http://na-mic.org Registration Command Line Modules Registration –Affine registration –Deformable BSpline registration –(Utah) Deformable BSpline registration –Linear registration –RealignVolume
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National Alliance for Medical Image Computing http://na-mic.org 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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