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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