Modules

SlicerSALT is a collection of 3D Slicer modules focused on various shape analysis tasks. Documentation for each module is below.

• Covariate Significance Testing User Tutorial
  • Covariate Significance Testing Description
  • Covariate Significance Testing Installation on SlicerSALT
  • MFSDA Installation on 3D Slicer
  • Covariate Significance Testing Module
    • Setting up Input Files
    • Input Surface Meshes Visualization
    • Setting up Input Files
    • Setting up Output Directory
    • Running Covariate Significance Testing Module
    • Output Shape Template Visualization
  • Acknowledgements - Resources - Questions
• SlicerDentalModelSeg User tutorial
  • Algorithm
    • Read 3D scan, apply random rotation and extract point features.
    • Teeth segmentation
  • Extension Overview
  • SlicerJawSegmentation Installation on SlicerSALT
  • JawSegmentation Installation on 3D Slicer
  • CrownSegmentation Module
    • Inputs
    • Advanced
    • Outputs
  • Acknowledgements - Resources - Questions
• Statistics on Object Differences User Tutorial
  • Installation on SlicerSALT
  • Difference Statistics Module
    • Inputs
    • Running the module and Outputs
  • Acknowledgements - Resources - Questions
• GROUPS User Tutorial
  • GROUPS Tool Description
  • Description of GROUPS
  • Step 1 : Landmark-based Rigid Alignment
  • Step 2: Group-wise Shape Registration
  • Installation of GROUPS Tool
    • GROUPS Installation on SlicerSALT
    • GROUPS Installation on 3D Slicer
  • Rigid Alignment Use
    • Rigid Alignment Command-Line Tool
    • Rigid Alignment Module
    • Group-wise Registration Use
  • Acknowledgements - Resources - Questions
• Registration Based Correspondence User Tutorial
  • Registration Based Correspondence Tool Description
    • Input Parameters
    • Advanced I/O Parameters
    • Quality control via Shape Population Viewer
  • Acknowledgements - Resources - Questions
• Shape Regression User Tutorial
  • Outline
  • Description of Shape Regression
    • Acceleration Controlled Shape Regression
    • Impact of Parameters
  • Installing the Software
    • Installation of ShapeRegression Module through SlicerSALT
    • Installation of ShapeRegression Module through 3D Slicer
  • Shape Regression Workflow
    • Shape Regression Model Estimation
    • Shape Regression Debugging and Quality Control
  • Acknowledgements - Resources - Questions
• SPHARM-PDM User Tutorial
  • SPHARM-PDM Tool Description
    • Step 1: Post Process Segmentation
    • Step 2: Generate Mesh Parameters
    • Step 3: Parameters to SPHARM Mesh
    • Installation of SPHARM-PDM Tool
    • SPHARM-PDM Module
    • Features and Parameters
    • Running SPHARM-PDM
    • Quality control using ShapePopulationViewer
    • Quality control using Models module
  • Acknowledgements - Resources - Questions
• Shape analysis via Skeletal Models User Tutorial
  • Introduction to skeletal representations
  • The Slabular S-rep
  • The SlicerSkeletalRepresentations extension
  • S-rep MRML Nodes
  • S-rep modules workflow
    • S-rep Extension in SlicerSALT
    • S-rep Extension Installation on 3D Slicer
  • SRep Module
    • SRep: Visualization
    • SRep: Interpolation
  • SRep Creation
    • Evolutionary S-rep Fitting Module
    • SRepCreator Module
    • SRepRefinement Module
  • Acknowledgements - Resources - Questions
• Surface Mapping & Deep Learning Tutorial
  • Authors
  • Overview
    • Installation
  • 1. SurfacePlaneMapper
    • Description
    • Module Parameters
    • Input Directory Structure
      • Option 1: .txt Feature Files
      • Option 2: .vtk Feature Files
    • Sphere Template
    • Output Directory Structure
  • 2. SlicerSurfaceLearner
    • Description
    • Key Features
    • How To Use
    • Tips for Selecting Training Parameters
      • Data Preparation
    • Output Directory Structure
    • Checkpoints
    • TensorBoard Logging
      • Steps to use TensorBoard:
  • Acknowledgements - Resources - Questions
• Shape Variation Analyzer User Tutorial
  • ShapeVariationAnalyzer Tool Description
  • Description of ShapeVariationAnalyzer
    • Step 1: Create the groups
    • Step 2: Preview and Update
    • Step 3: Generate and Explore Models
    • Step 4: Evaluate the models
  • Installation of SVA Tool
    • SVA Installation on SlicerSALT
    • SVA Installation on 3D Slicer
  • How to use ShapeVariationAnalyzer
    • Setting up the input directories
    • Create the Groups
  • Acknowledgements - Resources - Questions