Documentation/4.2

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Where to start ? Training pages Information on how to use Slicer 4.2 FAQ   UPDATED Set of common questions/answers Users mailing list / Sign-up / Browse archives How to Report a problem 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 Slicer Registration Case Library 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

• Annotations (Nicole Aucoin)
• Colors (Nicole Aucoin)
• Data (Julien Finet)
• DICOM (Steve Pieper)
• Editor (Steve Pieper)
• 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)

Wizards

• ChangeTracker (Andrey Fedorov)

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

• EMSegment Easy (no atlas) (Kilian Pohl)
• EMSegment (with atlas) (Kilian Pohl)
• Simple Region Growing Segmentation (Jim Miller, Harini Veeraraghavan)
• Specialized
  • EMSegment Command-line (Kilian Pohl)
  • Foreground Masking (BRAINS) (Hans Johnson)
  • Robust Statistics Segmenter (Yi Gao)

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)
  • UKFTractography
• Utilities
  • DWI To DTI Estimation (Demian Wasserman)
  • Diffusion Tensor Scalar Measurements (Demian Wasserman)
  • Diffusion Weighted Volume Masking (Demian Wasserman)
  • Resample DTI Volume (Demian Wasserman)
• Data Conversion
  • DTIImport (Sonia Pujol)
  • DTIExport (Sonia Pujol)

IGT

• OpenIGTLink IF (Junichi Tokuda)
• Volume Reslice Driver (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)
• 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)

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)

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)
• CARMA (Alan Morris)
• PkModeling (Emma Zhu, Jim Miller)
• FacetedVisualizer (Harini Veeraraghavan, Jim Miller)
• Reporting (Andrey Fedorov, Nicole Aucoin, Steve Pieper) (work in progress)
  • LabelToDICOMSEGConverter
  • DICOM SEG Import
• SlicerRT (Csaba Pinter, Andras Lasso, Kevin Wang, Steve Pieper)
  • DICOM-RT import
  • Contours
  • Dose volume histogram
  • Dose accumulation
  • Dose comparison
  • Isodose line and surface display
  • Contour comparison
  • Contour morphology
  • Deformation field visualizer
  • Modules from Plastimatch (Greg Sharp)
    • Plastimatch Automatic deformable image registration
    • Plastimatch DICOM-RT import
    • Plastimatch DICOM-RT export
    • Plastimatch LANDWARP Landmark
    • Plastimatch XFORMWARP
• VolumeResliceDriver (Junichi Tokuda, Laurent Chauvin)
• IGyne (Guillaume Pernelle, Xiaojun Chen, Yi Gao, Jan Egger)
• LongitudinalPETCT (Paul Mercea, Andrey Fedorov)
• TubeTK (Stephen Aylaward, Jean-Christophe Fillion-Robin, Christopher Mullins, Michael Jeulin-L, Matthew McCormick)
• UKFTractography (Ryan Eckbo, Yogesh Rathi)
• XNATSlicer (Sunil Kumar, Dan Marcus, Steve Pieper)
• Port Placement (Andinet Enquobahrie, Luis G. Torres)

Cat 3

• LesionSegmentation (Mark Scully)
  • LesionSegmentation->TrainModel (Mark Scully)
  • LesionSegmentation->PredictLesions (Mark Scully)