Documentation/3.4

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Revision as of 22:28, 7 February 2009 by Kikinis (talk | contribs) (→‎Filtering)
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Home < Documentation < 3.4

Note: This page is currently under construction

Introduction

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
Examples for the Help and

Acknowledgment Panels

SlicerHelpExample.png
SlicerAcknowledgementExample.png

Main GUI

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


Other Modules

Please adhere to the naming scheme for the module documentation:

    • [ [Modules:MyModuleNameNoSpaces-Documentation-3.4|My Module Name With Spaces] ] (First Last Name)

Wizards

IGT

Batch processing

Converters

Demonstration

Filtering

Surface Models

    • Modelmaker (Nicole Aucoin)
    • Grayscale Model Maker (Nicole Aucoin)


    • Valley Contour Segmentation (Peter Karasev)
    • Freesurfer Surface Section Extraction (Katharina Quintus)
    • Python Surface Connectivity (Luca Antiga, Daniel Blezek)
    • Python Surface ICP Registration (Luca Antiga, Daniel Blezek)
    • Python Surface Toolbox (Luca Antiga, Daniel Blezek)
    • Clip Model (Alex Yarmarkovich)
    • Distance Transform Model (Steve Pieper)
    • Model into Label Volume (Nicole Aucoin, Bill Lorensen)
    • Probe Volume with Model (Paint) (Lauren O'Donnell)

Python Modules

    • Python Explode Volume Transform (Luca Antiga, Daniel Blezek)
    • Python Numpy Script (Luca Antiga, Daniel Blezek)
    • Python Resample Volume (Luca Antiga, Daniel Blezek)
    • Python Reslice as Volume (Luca Antiga, Daniel Blezek)
    • Python Script (Luca Antiga, Daniel Blezek)

Registration

    • Affine Registration (Daniel Blezek)
    • Deformable B-Spline Registration (Bill Lorensen)
    • Diffeomorphic Demons Algorithm (Tom Vercauteren, Enger Konukoglu, Killian Pohl)
    • Linear Registration (Daniel Blezek)
    • Realign Volume (Nicole Aucoin)
    • Rigid Registration (Daniel Blezek)
    • Test Grid Transform Registration (Yinglin Lee)
    • (Utah) Deformable B-Spline Registration (Experimental) (Sam Gerber, Jim Miller, Steve Pieper, Ross Whitaker)

Segmentation

    • EM Segment Command-Line (Brad Davis, Will Schroeder)
    • EM Segment Simple (Brad Davis, Will Schroeder)
    • EMSegmentTemplateBuilder (Brad Davis, Will Schroeder)
    • Simple Region Growing (Jim Miller)
    • Otsu Threshold (Bill Lorensen)

Statistics

    • Calculate Volume Statistics (Tri Ngo)
    • Label Statistics (Steve Pieper)

DWI and Tractography

DWI

    • Estimation
      • Diffusion Tensor Estimation (Raul San Jose Estepar)
      • Python Diffusion Tensor Estimation (Julien von Siebenthal)
    • Python Extract Baseline DWI Volume (Julien von Siebenthal)
    • Filter
      • Joint Rician LMMSE Image Filter (Antonio Tritan Vega, Santiago Aja Fernandez)
      • Rician LMMSE Image Filter (Antonio Tritan Vega, Santiago Aja Fernandez)
      • Unbiased Non Local Means filter for DWI (Antonio Tritan Vega, Santiago Aja Fernandez)
    • Python Shift DWI Values (Julien von Siebenthal)
    • Python Recenter Scalar to DWI Volume (Julien von Siebenthal)

DTI

    • Resample DTI Volume (Francois Budin)
    • Display (Alex Yarmakovich)
    • Diffusion Tensor Scalar Measurements (Raul San Jose Estepar)
    • Analysis
      • Fiducial Seeding (Steve Pieper, Alex Yarmakovich)
      • ROI Select (Lauren O'Donnell)
      • ROI Seeding (Raul San Jose Estepar)
      • Python Stochastic Tractography (Julien von Siebenthal)

Documented Modules

(please do not touch this section for now. Ron)

Main GUI

Modules

Core and Loadable Modules

CLI Modules

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