Documentation/3.6

Main GUI

Main GUI

• Main Application GUI
• "Hot-keys" and Keyboard Shortcuts
• Loading Scenes and Individual Datasets through the Data Module
• Data Loading Details
• Saving Scenes and Data
• Creating and Restoring Scene Snapshots
• Extensions Management Wizard

Modules

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

Slicer3:Module_Documentation-3.5_TemplateNot yet 3.6

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

Please adhere to the naming scheme for the module documentation:

• [ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

Requirements for Modules

The module is feature complete, it does everything that it advertises it can do 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 keep in mind that our users are not computer scientists with a background in computer vision. 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 Acknowledegment tab of the module. Please see the Models module for an example. The people listed in the acknowledgement will be the primary people for support and maintenance relative of the module. See here for more information. Style Guide: All acknowledgment icons should be 100x100 pixels, preferably in png format. Accessing logos: Icons for BIRN, NAC, NA-MIC and IGT are included in Slicer3/Base/GUI//vtkSlicerBaseAcknowledgementLogoIcons.cxx/h and resources for them are in Slicer3/Base/GUI/Resources/vtkSlicerBaseAcknowledgementLogos_ImageData.h. The API for vtkSlicerModuleGUI provides access to these icons. Adding logos: Please add additional image resources and logo icons to these files as required in order to promote shared use (and to prevent duplication in the code.) Many modules are better suited to be downloadable extensions. The same module creation guidelines apply, but the actual implementation is done outside of the slicer source code repository. Follow "Ron's rules for tools"

Examples for the Help and Acknowledgment Panels

List of pre-existing Modules

• Atlas Creator (Sylvain Jaume) Not yet 3.6
• MRI Bias Field Correction (Sylvain Jaume) Not yet 3.6
• 4D Image (Viewer) (Junichi Tokuda) Not yet 3.6
• 4D Analysis (Time-intensity curve plotting and analysis) (Junichi Tokuda) Not yet 3.6
• Fast Marching segmentation (Andriy Fedorov) Not yet 3.6
• Gyri Contour Segmentation (Peter Karasev) Not yet 3.6
• Subvolume extraction with ROI widget (Andriy Fedorov) Not yet 3.6
• Registration Metrics (HD and DSC) (Haytham Elhawary) Not yet 3.6
• Measurements (rulers and angles) (Nicole Aucoin) Not yet 3.6
• Affine registration (Casey Goodlett) Not yet 3.6
• Collect Patient Fiducials (Andrew Wiles) Not yet 3.6

Core

• Camera Module (Sebastian Barre) Not yet 3.6
• Welcome Module (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis) Not yet 3.6
• Volumes Module (Alex Yarmarkovich, Steve Pieper) Not yet 3.6
  • Diffusion Editor (Kerstin Kessel) Not yet 3.6
• Models Module (Alex Yarmarkovich) Not yet 3.6
• Fiducials Module (Nicole Aucoin) Not yet 3.6
• Data Module (Alex Yarmarkovich) Not yet 3.6
• Slices Module (Jim Miller) Not yet 3.6
• Color Module (Nicole Aucoin) Not yet 3.6
• Interactive Editor (Steve Pieper) Not yet 3.6
• ROI Module (Alex Yarmarkovich) Not yet 3.6
• Volume Rendering Module (Yanling Liu, Alex Yarmarkovich) Not yet 3.6

Specialized Modules

Please adhere to the naming scheme for the module documentation:

• [[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

Wizards

• ChangeTracker (Andriy Fedorov) Not yet 3.6
• IA FE Meshing Module (Vince Magnotta) Not yet 3.6

Informatics Modules

• Fetch Medical Informatics Module (Wendy Plesniak) Not yet 3.6
• QDEC Module (Nicole Aucoin) Not yet 3.6
• Query Atlas Module (Wendy Plesniak) Not yet 3.6

Registration

• Overview of all Registration Modules
  • Register Images (Upgraded Version) (Casey Goodlett, Stephen Aylward) Not yet 3.6
  • Register Images Multires (Casey Goodlett, Stephen Aylward) Not yet 3.6
  • Fiducial-Based Registration (Casey Goodlett) Not yet 3.6
  • Transforms Module (Alex Yarmarkovich) Not yet 3.6
  • Linear Registration (Daniel Blezek) Not yet 3.6
  • Affine Registration (Daniel Blezek) Not yet 3.6
  • Deformable B-Spline Registration (Bill Lorensen) Not yet 3.6
  • Demons Registration (Tom Vercauteren) Not yet 3.6
  • ACPC Transform (Nicole Aucoin) Not yet 3.6

Segmentation

• EM Segment (Sylvain Jaume, Nicolas Rannou) Not yet 3.6
• EM Segment Command-Line (Brad Davis, Will Schroeder) Not yet 3.6
• EM Segment Simple (Brad Davis, Will Schroeder) Not yet 3.6
• EM Segment Template Builder (Brad Davis, Will Schroeder) Not yet 3.6
• Simple Region Growing (Jim Miller) Not yet 3.6
• Otsu Threshold (Bill Lorensen) Not yet 3.6

Statistics

• Label Statistics (Steve Pieper) Not yet 3.6

Diffusion

DWI

• Estimation
  • Diffusion Tensor Estimation (Raul San Jose Estepar) Not yet 3.6
• Python Extract Baseline DWI Volume (Julien de Siebenthal) Not yet 3.6
• Filter
  • Joint Rician LMMSE Image Filter (Antonio Tristán Vega, Santiago Aja-Fernandez) Not yet 3.6
  • Rician LMMSE Image Filter (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer) Not yet 3.6
  • Unbiased Non Local Means filter for DWI (Antonio Tristán Vega, Santiago Aja-Fernandez) Not yet 3.6
• Python Shift DWI Values (Julien de Siebenthal) Not yet 3.6
• Python Recenter Scalar to DWI Volume (Julien de Siebenthal) Not yet 3.6

DTI

• Resample DTI Volume (Francois Budin) Not yet 3.6
• Diffusion Tensor Scalar Measurements (Raul San Jose Estepar) Not yet 3.6
• Analysis

Tractography

• Label Seeding (Raul San Jose Estepar) Not yet 3.6
• Fiducial Seeding (Alex Yarmakovich, Steve Pieper) Not yet 3.6
• FiberBundles (Alex Yarmakovich) Not yet 3.6
• Python Stochastic Tractography (Julien de Siebenthal) Not yet 3.6
• ROI Select (Lauren O'Donnell) Not yet 3.6

IGT

• OpenIGTLinkIF Module (Junichi Tokuda) Not yet 3.6
• NeuroNav Module (Haiying Liu) Not yet 3.6
• ProstateNav Module (Junichi Tokuda) Not yet 3.6

Filtering

• Checkerboard Filter (Bill Lorensen) Not yet 3.6
• Histogram Matching (Bill Lorensen) Not yet 3.6
• Image Label Combine (Alex Yarmarkovich) Not yet 3.6
• Resample Volume (Bill Lorensen) Not yet 3.6
• Resample Volume2 (Francois Budin) Not yet 3.6
• Threshold Image (Nicole Aucoin) Not yet 3.6
• Arithmetic
  • Add Images (Bill Lorensen) Not yet 3.6
  • Subtract Images (Bill Lorensen) Not yet 3.6
  • Cast Image (Nicole Aucoin) Not yet 3.6
  • Mask Image (Steve Pieper) Not yet 3.6
• Denoising
  • Gradient Anisotropic Filter (Bill Lorensen checked this in) Not yet 3.6
  • Curvature Anisotropic Diffusion (Bill Lorensen) Not yet 3.6
  • Gaussian Blur (Julien Jomier, Stephen Aylward) Not yet 3.6
  • Median Filter (Bill Lorensen) Not yet 3.6
• Morphology
  • Voting Binary Hole Filling (Bill Lorensen) Not yet 3.6
  • Grayscale Fill Hole (Bill Lorensen) Not yet 3.6
  • Grayscale Grind Peak (Bill Lorensen) Not yet 3.6

Surface Models

• Modelmaker (Nicole Aucoin) Not yet 3.6
• Grayscale Model Maker (Bill Lorensen) Not yet 3.6

• Freesurfer Surface Section Extraction (Katharina Quintus)
• Python Surface Connectivity (Luca Antiga, Daniel Blezek) Not yet 3.6
• Python Surface ICP Registration (Luca Antiga, Daniel Blezek) Not yet 3.6
• Python Surface Toolbox (Luca Antiga, Daniel Blezek) Not yet 3.6
• Clip Model (Alex Yarmarkovich) Not yet 3.6
• Model into Label Volume (Nicole Aucoin) Not yet 3.6

Batch processing

• EM Segmenter batch (Julien Jomier, Brad Davis) Not yet 3.6
• Gaussian Blur batch (Julien Jomier, Stephen Aylward) Not yet 3.6
• Register Images batch (Julien Finet, Stephen Aylward) Not yet 3.6
• Resample Volume batch (Julien Finet) Not yet 3.6

Converters

• Create a Dicom Series (Bill Lorensen) Not yet 3.6
• Dicom to NRRD (Xiaodong Tao) Not yet 3.6
• Orient Images (Bill Lorensen) Not yet 3.6
• Python Explode Volume Transform (Luca Antiga, Daniel Blezek) Not yet 3.6
• Extract Subvolume (Steve Pieper) Not yet 3.6

Slicer Extensions

Extensions for Downloading

Introduction

Slicer on NITRC

• Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.
• Some of the extensions do not use the Slicer license. Please review carefully.
• For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions. In case of problems with those modules, please talk directly to the developers of the extensions.
• The version that is available through the extension manager is chosen by the developer of that extension

We are using NITRC as the primary repository for contributed extensions. As a general rule, we do not test the extensions ourselves. Use them at your own risk. Click here to see a listing of Slicer 3 extensions on NITRC.

Extension manager dialog box

To add extension modules to an installed binary of slicer:

• Use the View->Extension Manager menu option
• The dialog will be initialized with the URL to the extensions that have been compiled to match your binary of slicer.
  • Note installing extensions from a different repository URL is likely to be unstable due to platform and software version differences.
  • You can select a local install directory for your downloaded extensions (be sure to choose a directory with enough free space).
• Select the extensions you wish to install and click to download them. Installed extensions will be available when you restart slicer.
• To turn modules on or off, you can use the Module Settings page of the View->Application Settings dialog.

• Extensions are compiled as part of the nightly build. In order to have your extension compiled nightly and made available to end users, please contact the Slicer team. For explanations for developers see here

Installation

• Click on the icon to start the extensions wizard

Listing of available plug-ins

• VMTK (Daniel Haehn)
  • You need to install the VmtkSlicerModule to run any of the other three.
  • VMTKEasyLevelSetSegmentation - providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface
  • VMTKLevelSetSegmentation - providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms
  • VMTKVesselEnhancement - providing vessel enhancement filters to highlight vasculature or tubular structures

• EM DTI Clustering (Mahnaz Maddah)

• Label Diameter Estimation (Andriy Fedorov)

• ABC (Marcel Prastawa)
• Modules:HAMMER (GuorongWu, XiaodongTao, JimMiller, DinggangShen)

Extensions Contact List

This is a first pass list of extension authors; more to come!

ABC	Marcel Prastawa	prastawa@sci.utah.edu
EMFiberClusteringModule	Mahnaz Maddah	maddah @nospam@ ge.com
BRAINSROIAuto	Greg Harris	gregory-harris @nospam@ uiowa.edu
Bubble Maker	Carlos Mendoza	carlos.sanchez.medoza @nospam@ gmail.com
Hammer Registration	Dinggang Shen	dgshen @nospam@ med.unc.edu
Lupus Lesion	Mark Scully	mscully @nospam@ mrn.org
VmtkSlicerModule	Daniel Haehn	haehn @nospam@ bwh.harvard.edu
Vmtkin3DSlicer	Daniel Haehn	haehn @nospam@ bwh.harvard.edu
BRAINSFit	Eun Young Kim	eunyoung-kim @nospam@ uiowa.edu
ARCTIC	Cedric Mathieu	ced.mathieu @nospam@ gmail.com