Slicer3 plugins

National Alliance for Medical Image Computing http://na-mic.org

Slicer3 plugins

Common architecture for interactive and batch processing

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

National Alliance for Medical Image Computing http://na-mic.org

The grand vision…

UserDesktopAlgorithms ITK VTK Slicer

Modules

VTK AppsUsing ITK

Scripts ofSlicer Mods

BatchPrograms

Non-NAMICCmd tools BatchMake

BIRN GridWizard

Slicer 3.0

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

National Alliance for Medical Image Computing http://na-mic.org

Common architecture for interactive and batch processing

UserDesktopAlgorithms ITK VTK Slicer

Modules

VTK AppsUsing ITK

Scripts ofSlicer Mods

BatchPrograms

Non-NAMICCmd tools BatchMake

BIRN GridWizard

Slicer 3.0

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

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– Voting Binary Hole Filling– Zero Crossing Based Edge Detection Filter– Filtering.Arithmetic:

– Add Images– Subtract Images– – – – / Resample Volume 2– – – – – –

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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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