Documentation/4.3

For the latest Slicer documentation, visit the read-the-docs.

Nightly 4.10 4.8 4.6 4.5 4.4 4.3 4.2 4.1 4.0 3.6 3.5 3.4 3.2 ALL VERSIONS

Where to start ? Training pages Information on how to use Slicer 4.3 FAQ Set of common questions/answers Users mailing list / Sign-up / Browse archives How to Report a problem / Create a feature request  NEW Slicer Application Main Application GUI Settings  NEW Extensions Manager  NEW Mouse Buttons, "Hot-keys" and Keyboard Shortcuts Computer Configurations Loading or Saving data and listing of supported data formats. Slicer Lookup Tables Setting up and using stereoscopic viewing QtTesting - Easy way to record and play macros		Module Categories Core Modules Wizards Informatics Registration Segmentation Quantification Diffusion IGT Filtering Surface Models Converters Endoscopy Work in Progress Developer Tools Legacy Extension Categories   NEW What are these categories ? See here Category 1 Category 2 Category 3		Developers Corner Information for Software Developers  UPDATED Source code, contribute patch, develop modules Developers mailing list / Browse archives Intended for discussion of programming related questions Miscellaneous Documentation guidelines Slicer user documentation principle and guidelines Visual blog Set of screenshots showing Slicer in action. Release Notes Platform specific issues and considerations Announcements & Acknowledgments [1] Real-life example cases of using the Slicer registration tools, incl. datasets and step-by-step instructions to follow and try yourself.

Modules by Category

Core Modules

Add Data Dialog
Browse the image gallery

• Annotations (Nicole Aucoin)
• Colors (Nicole Aucoin)
• Data (Julien Finet)
• DICOM (Steve Pieper)
• Editor (Steve Pieper)
  • WatershedFromMarkers (Bradley Lowekamp)
• Markups (Nicole Aucoin)
• Models (Nicole Aucoin)
• SceneViews (Nicole Aucoin)
• Transforms (Alex Yarmarkovich)
• View Controllers (Jim Miller)
• Volumes (Steve Pieper)
• Volume Rendering (Julien Finet)
• Welcome to Slicer (Wendy Plesniak)

Informatics

• Sample Data (Steve Pieper)

Registration

• Introduction to Registration (Dominik Meier)
• General Brainsfit Registration (Hans Johnson)
• Resample Image (BRAINS) (Hans Johnson)
• Specialized
  • ACPC Transform (Nicole Aucoin)
  • Demon Registration (BRAINS) (Hans Johnson)
  • Fiducial Registration (Stephen Aylward)
  • Vector Demon Registration (Hans Johnson)
  • Reformat (Michael Jeulin-Lagarrigue)
  • Segmentation Aided Registration (Yi Gao)

Segmentation

• EMSegment Easy (no atlas) (Kilian Pohl)
• EMSegment (with atlas) (Kilian Pohl)
• Simple Region Growing Segmentation (Jim Miller, Harini Veeraraghavan)
• KSlice Interactive Segmenter (Ivan Kolesov, Peter Karasev, Patricio Vela, Allen Tannenbaum, Karl Fritscher, Steve Pieper )
• Editor (Steve Pieper)
• Specialized
  • EMSegment Command-line (Kilian Pohl)
  • Foreground Masking (BRAINS) (Hans Johnson)
  • Robust Statistics Segmenter (Yi Gao)
  • Left Atrial Scar Segmenter (Liangjia Zhu)
  • Left Atrium Segmenter (Liangjia Zhu)
  • Fast GrowCut Effect (Liangjia Zhu)

Quantification

• Data Probe (Steve Pieper)
• Label Statistics (Steve Pieper)
• PET Standard Uptake Value Computation (Nicole Aucoin)
• Change quantification
  • Intensity Difference Metric (Andrey Fedorov)

Diffusion

• DWI to Full Brain Tractography (Demian Wasserman)
• Denoising
  • DWI Joint Rician LMMSE Image Filter (Demian Wasserman)
  • DWI Rician LMMSE Filter (Demian Wasserman)
• Tractography
  • Tractography Display (Demian Wasserman)
  • Tractography Interactive Seeding (Alex Yarmarkovich)
  • Tractography Label Map Seeding (Demian Wasserman)
  • UKF Tractography
• Utilities
  • DWI To DTI Estimation (Demian Wasserman)
  • Diffusion Tensor Scalar Measurements (Demian Wasserman)
  • Diffusion Weighted Volume Masking (Demian Wasserman)
  • FiberBundleLabelSelect (Alex Yarmarkovich)
  • Resample DTI Volume (Demian Wasserman)
• Data Conversion
  • DTIImport (Sonia Pujol)
  • DTIExport (Sonia Pujol)
  • Fiber Bundle to Label Map (Steve Pieper)

IGT

• OpenIGTLink IF (Junichi Tokuda)

Filtering

• N4ITK Bias Field Correction (Andrey Fedorov)
• CheckerBoard Filter (Jim Miller)
• Extract Skeleton (Jim Miller)
• Histogram Matching (Jim Miller)
• Image Label Combine (Alex Yarmarkovich)
• Resample Scalar/Vector/DWI Volume (Francois Budin)
• Threshold Scalar Volume (Nicole Aucoin)
• Voting Binary Hole Filling Image Filter (Jim Miller)
• Simple Filters (Bradley Lowekamp)
• Arithmetic
  • Add Scalar Volumes (Jim Miller)
  • Cast Scalar Volume (Nicole Aucoin)
  • Mask Scalar Volume (Nicole Aucoin)
  • Multiply Scalar Volumes (Jim Miller)
  • Subtract Scalar Volumes (Jim Miller)
• Denoising
  • Gradient Anisotropic Diffusion (Jim Miller)
  • Curvature Anisotropic Diffusion (Jim Miller)
  • Gaussian Blur Image Filter (Stephen Aylward)
  • Median Image Filter (Jim Miller)
• Morphology
  • Grayscale Fill Hole Image Filter (Jim Miller)
  • Grayscale Grind Peak Image Filter (Jim Miller)

Surface Models

• Grayscale Model Maker (Jim Miller)
• Label Map Smoothing
• Merge Models (Nicole Aucoin)
• Model Maker (Nicole Aucoin)
• Model To LabelMap (Nicole Aucoin)
• Probe Volume With Model (Lauren O'Donnell)
• SurfaceToolbox (Luca Antiga)

Converters

• Create DICOM Series (Jim Miller)
• Crop Volume (Andrey Fedorov)
• Dicom to Nrrd Converter (Jim Miller)
• Orient Scalar Volume (Jim Miller)
• Vector to Scalar Volume (Steve Pieper)

Endoscopy

• Endoscopy (Steve Pieper)

Work in Progress

• MultiVolume Support
  • MultiVolume Importer (Andrey Fedorov)
  • MultiVolume Explorer (Andrey Fedorov)
• Data Store (Charles Marion)

Developer Tools

• Cameras (Julien Finet)
• Event Broker (Julien Finet)
• Execution Model Tour (JC Fillion-Robin)
• Module Template (JC Fillion-Robin)
• Performance Tests
• Tractography

Legacy

• Converters
  • BSpline To Deformation Field
• Diffusion
  • Denoising
    • DWI Unbiased Non Local Means Filter
• Filtering
  • MRI Bias Field Correction (Sylvain Jaume)
  • Otsu Threshold Image Filter (Bill Lorensen)
  • Resample Scalar Volume (Jim Miller)
• Registration
  • Rigid Registration (Jim Miller)
  • Affine Registration (Daniel Blezek)
  • BSpline Deformable Registration
  • Expert Automated Registration
  • Linear Registration
  • MultiResolution Affine Registration (Casey Goodlett)
• Segmentation
  • Otsu Threshold Segmentation (Bill Lorensen)

Extensions by Category

Cat 2

• SkullStripper (Xiaodong Tao)
• SwissSkullStripper (Bill Lorensen)
• Cardiac MRI Toolkit (Alan Morris, Salma Bengali)
• PkModeling (Emma Zhu, Jim Miller)
• FacetedVisualizer (Harini Veeraraghavan, Jim Miller)
• Reporting (Andrey Fedorov, Nicole Aucoin, Steve Pieper) (work in progress)
• SlicerRT (Csaba Pinter, Andras Lasso, Kevin Wang, Greg Sharp, Steve Pieper)
  • DICOM-RT import
  • DICOM-RT export
  • Contours
  • Dose volume histogram
  • Dose accumulation
  • Dose comparison
  • Isodose line and surface display
  • Contour comparison
  • Contour morphology
  • Subject hierarchy
  • Modules from Plastimatch (Greg Sharp)
    • Plastimatch Automatic deformable image registration
    • Plastimatch LANDWARP Landmark
    • Plastimatch XFORMWARP
• SlicerIGT (Tamas Ungi, Junichi Tokuda)
• Matlab Bridge (Andras Lasso, Jean-Christophe Fillion-Robin, Kevin Wang)
• iGyne (Xiaojun Chen and iGyne Team)
• LongitudinalPETCT (Paul Mercea, Andrey Fedorov)
• DTIProcess (Francois Budin)
• DTIAtlasFiberAnalyzer (Francois Budin)
• FiberViewerLight (Francois Budin)
• DTIPrep (Francois Budin)
• DTIAtlasBuilder (Adrien Kaiser)
• ShapePopulationViewer (Alexis Girault)
• ModelToModelDistance (Francois Budin, Juliette Pera, Beatriz Paniagua)
• TubeTK (Stephen Aylward, Jean-Christophe Fillion-Robin, Christopher Mullins, Michael Jeulin-L, Matthew McCormick)
• UKFTractography (Ryan Eckbo, Yogesh Rathi)
• TrackerStabilizer (Laurent Chauvin, Jayender Jagadeesan)
• ChangeTracker (Andrey Fedorov)
• SobolevSegmenter (Arie Nakhmani)
• QuickTools (Julien Finet)
  • Image Maker
• XNATSlicer
• ErodeDilateLabel (Junichi)
• ThingiverseBrowser (Nigel Goh)
• Virtual Fracture Reconstruction (Karl Fritscher, Peter Karasev)
• AirwaySegmentation (Pietro Nardelli)
• ModelClip (Xiaojun Chen,Jun Lin,Qiqin Zhan)
• SurfaceMirror (Xiaojun Chen,Jiaxi Luo, Ruqing Ye)
• Scoliosis (Franklin King, Tamas Ungi)
  • Spinal Curvature Measurement (Franklin King, Tamas Ungi)
• Port Placement (Andinet Enquobahrie, Luis G. Torres)
• Plus Remote (Franklin King, Tamas Ungi)
• Transform Visualizer (Franklin King, Andras Lasso, Csaba Pinter)
• WindowLevelEffect (Andrey Fedorov, Steve Pieper)
• PerkTutor (Tamas Ungi, Matthew Holden)
  • PerkEvaluator
  • TransformRecorder
  • WorkflowSegmentation
• SlicerToKiwiExporter (Jean-Christophe Fillion-Robin)
• GelDosimetry (Csaba Pinter)
• MRI SNR Measurement (Babak Matinfar)
• CurveMaker (Junichi Tokuda)
• OpenCAD (Vivek Narayan, Jayender Jagadeesan)
• CornerAnnotation (Atsushi Yamada)

Cat 3

• LesionSegmentation (Mark Scully)
  • LesionSegmentation->TrainModel (Mark Scully)
  • LesionSegmentation->PredictLesions (Mark Scully)
• IASEM (Bradley Lowekamp)