Documentation/3.4

Note: This page is currently under construction

Introduction

Integrating with Slicer3

This page is a portal for documentation about Slicer 3.4. For information for software developers, please go to the Developers page (see link in navigation box to the left).

How-To Tutorials

Slicer3 tutorial page

Feature Request and Problem Reports

We have an issues tracker for Slicer 3. You need to create an account for filing reports. We keep track of both feature requests and bug reports. Make sure to use the pull-down in the upper right to select Slicer 3.

List of Modules in need of documentation

• Requirements for modules to be added to the release:
  • The module is feature complete for the tasks advertised on 2-4-2009
  • The module has a test. See here for more information.
  • Module has documentation on the Slicer wiki. Please use the template provided here to structure your page.
  • Please add a pointer to the documentation on the Slicer wiki to the the Help tab of the module. See the Editor module in Slicer for an example.
  • The contributor (and their manager/advisor), the lab (with labs/institution logo) and the funding source (with grant number, logo optional) are listed in the Acknowledgement tab of the module. Please see the Models module for and example. The people listed in the acknowledgement will be the primary people for support and maintenance relative of the module.
• If your module has documentation in Slicer 3.2, please copy/paste/update into the 3.4 version

Main GUI

• Main Application GUI (Wendy Plesniak)
• List of Hotkeys and Keyboard Shortcuts (Wendy Plesniak)
• How to load data (Steve Pieper)
• Save Scene and Data Module (Wendy Plesniak)

Modules

• Please copy the template linked below, paste it into your page and customize it with your module's information.

Slicer3:Module_Documentation-3.4_Template

• See above for info to be put into the Help and Acknowledgement Tabs
• To put your lab's logo into a module, see here

Core and Loadable Modules

• ChangeTracker (Andriy Fedorov)
• Color Module (Nicole Aucoin)
• Data Module (Alex Yarmakovic)
• Interactive Editor (Steve Pieper)
• Fiducials Module (Nicole Aucoin)
• Gradient Anisotropic Filter (Nicole Aucoin)
• Meshing Module (Vince Magnotta)
• Models Module (Alex Yarmakovic)
• NeuroNav Module (Noby Hata)
• QDEC Module (Nicole Aucoin)
• Query Atlas Module (Wendy Plesniak)
• ROI Module (Alex Yarmakovic)
• Slices Module (Jim Miller)
• Transforms Module (Nicole Aucoin)
• Volume Rendering Module (Alex Yarmakovic)
• Volumes Module (Steve Pieper)
  • Diffusion Editor (Kerstin Kessel)

CLI Modules

• Batch processing
  • EM Segementer batch (Stephen Aylward)
  • Gaussian blur batch (Stephen Aylward)
  • Registration batch (Stephen Aylward)
• Converters
  • Create a Dicom Series
  • DICOM DWI loader
  • Dicom to NRRD
  • Orient Images
• Demonstration
  • Execution Model Tour
  • Scripted Module Example
• Diffusion Tensor
  • Resample DTI Volume
  • Estimation
    • Diffusion Tensor Estimation
  • Scalars
    • Diffusion Tensor Scalar Measurements
• Filtering
  • Calculate Volume Statistics
  • Change Tracker Command-line
  • Checkerboard Filter
  • Extract Skeleton
  • Histogram Matching
  • Image Label Combine
  • Otsu Threshold
  • Resample Volume
  • Resample Volume2
  • Threshold Image
  • Voting Binary Hole Filling
  • Zero Crossing Based Edge Detection Filter
  • Arithmetic
    • Add Images
    • Subtract Images
  • DWI
    • Joint Rician LMMSE Image Filter
    • Rician LMMSE Image Filter
    • Unbiased Non Local Means filter for DWI
  • Denoising
    • Curvature Anisotropic Diffusion
    • Gaussian Blur
    • Gradient Anisotropic Diffusion
    • Median Filter
  • Morphology
    • Greyscale Fill Hole
    • Greyscale Grind Peak
• Model Generation
  • Clip Model
  • Distance Transform Model
  • Grayscale Model Maker
  • Modelmaker
  • Model into Label Volume
  • Probe Volume with Model (Paint)
• Python Modules
  • Python Diffusion Tensor Estimation
  • Python Explode Volume Transform
  • Python Extract Baseline DWI Volume
  • Python Gaussian Smoothing
  • Python Gradient Anisotropic Diffusion
  • Python Numpy Script
  • Python Recenter Scalar to DWI Volume
  • Python Resample Volume
  • Python Reslice as Volume
  • Python Script
  • Python Shift DWI Values
  • Python Stochastic Tractography
  • Python Surface Connectivity
  • Python Surface ICP Registration
  • Python Surface Toolbox

• Registration
• Segmentation
  • EM Segementer
• Statistics
• Tractography

• Registration: the top two have been somewhat tested by Ron on T1 weighted MR images and work pretty fast
• Affine Registration
• Deformable BSpline Registration
• The following are somewhat undocumented and or experimental
  • Otsu Thresholding
  • Gyri Contour Segmentation
  • Resample Volume 2
  • Stochastic Tractography
  • Linear Registration (aka rigid registration)
  • Voting Binary Hole Filling
  • (UTAH)Deformable BSpline Registration
  • Level-Set Segmentation Framework
    • Region Selector
    • Target Preprocessing
    • Bubble Maker
    • Level-Set Label Map Evolver
  • Binary Morphological Operations
    • BinaryThresholding
    • LabelBinaryImages
    • BinaryErodeOperations
    • BinaryDilateOperations
  • Fuzzy Surface Creation

Modules on NITRC

Slicer on NITRC

We are using NITRC as a repository for contributed modules. As a general rule, we do not test them ourselves, it is the downloaders job to ensure that they do what they want them to do.

Click here to see a listing of Slicer 3 modules on NITRC.

This is how to get modules from NITRC into Slicer 3.4