National Alliance for Medical Image Computing Slicer3 plugins Common architecture for interactive and batch processing

National Alliance for Medical Image Computing Each module has … … an entry in the module menu … a panel of user interface controls

National Alliance for Medical Image Computing 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

National Alliance for Medical Image Computing 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 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

National Alliance for Medical Image Computing 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 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

National Alliance for Medical Image Computing 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

National Alliance for Medical Image Computing Registration Command Line Modules Registration –Affine registration –Deformable BSpline registration –(Utah) Deformable BSpline registration –Linear registration –RealignVolume

National Alliance for Medical Image Computing 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