Slicer3 plugins

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Slicer3 plugins
Common architecture for interactive and batch
processing
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Each module has
an entry in the module menu
a panel of user interface controls
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The grand vision
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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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Common architecture for interactive and batch
processing
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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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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 Ima
  ges
  

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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)

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Registration Command Line Modules

• Registration
• Affine registration
• Deformable BSpline registration
• (Utah) Deformable BSpline registration
• Linear registration
• RealignVolume

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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