Modules:SpineSegmentation-Documentation-3.6

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Gallery of New Features

Module Name

SpineSegmentation module for Slicer 3.6

The SpineSegmentation module is available through the Slicer extension module manager.

In 3 minutes of processing, a label map (blue) and a 3D model (3D view) are displayed.

The documentation link and reference can be found in the Help and Acknowledgement tabs.

General Information

Module Type & Category

Type: Interactive or CLI

Category: Segmentation

Authors, Collaborators & Contact

• Sylvain Jaume: MIT CSAIL
• Contact: sylvain at csail.mit.edu

Module Description

Image segmentation of the spinal cord and the cerebro-spinal fluid in T2-weighted MRI images. The SpineSegmentation module implements a model-based pattern recognition algorithm for fully automated segmentation.

Usage

Use Cases, Examples

This module is especially appropriate for this use case:

• Automated segmentation of MRI of the spine is critical during minimally invasive intervention when frequent acquisitions of intra-operative images prevents the manual segmentation of the image by an expert. The SpineSegmentation module provides a solution to reduce the burden on the radiologist.

Examples of the module in use:

• Image-guided surgery for the treatment of disk herniation

Tutorial

• Sample Data Set

The sample data sets MRI_Spine.mhd and MRI_Spine.zraw are available at the link below. You will need to create a username on http://nitrc.org. Then log onto nitrc.org and click on the link below. Right-click on MRI_Spine.mhd and MRI_Spine.zraw to copy those files to your local directory.

http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/TestingData/?root=sylvainproject

Below are the step-by-step instructions to load, process and save some sample data (see link above).

Step 1.

Load the sample data

1. load the sample data

Step 2/9.

Select the SpineSegmentation module.

2. select SpineSegmentation module

Step 3/9.

Select the input image.

3. select input image

Step 4/9.

Create a Slicer node for the output image.

4. create image node

Step 5/9.

Create a Slicer node for the output model

5. create model node

• Step 6/9.

Apply the segmentation algorithm

6. apply algorithm

• Step 7/9.

Review segmentation result. The sliders on the top of each 2D view allows for reviewing the segmentation result overlaid on the input image.

7. review result

• Step 8/9.

Save result image and model. The output image and the 3D model can be saved using the Slicer user interface.

8. save results

• Step 9/9.

Find contact information for help and paper reference

9. help information

Quick Tour of Features and Use

• Input panel:
  • Image input select the input image
  • Image output create Slicer node for output image
  • Model output create Slicer node for output model
• Command panel:
  • Default reset input and output nodes to blank values
  • Cancel cancel the execution of the algorithm
  • Apply apply the segmentation algorithm (takes approx. 3 min)

Development

Notes from the Developer(s)

Algorithms used, library classes depended upon, use cases, etc.

Dependencies

Other modules or packages that are required for this module's use.

Tests

On the Dashboard, these tests verify that the module is working on various platforms:

• MyModuleTest1 MyModuleTest1.cxx
• MyModuleTest2 MyModuleTest2.cxx

Known bugs

Links to known bugs in the Slicer3 bug tracker

• Bug 000: description

Usability issues

Follow this link to the Slicer3 bug tracker. Please select the usability issue category when browsing or contributing.

Source code & documentation

Links to the module's source code:

Source code:

• file.cxx
• file.h

Doxygen documentation:

• class1

More Information

Acknowledgment

Include funding and other support here.

References

Publications related to this module go here. Links to pdfs would be useful.