Difference between revisions of "Modules:SpineSegmentation-Documentation-3.6"

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Below are the step-by-step instructions to load, process and save some sample data (see link above).
 
Below are the step-by-step instructions to load, process and save some sample data (see link above).
  
 +
Step 1.
 
{|
 
{|
 
|
 
|
Step 1. Load the sample data
+
Load the sample data
* '''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)
 
 
|[[Image:SpineSegmentation_Slicer3.6_documentation01.png|thumb|400px|1. load the sample data]]
 
|[[Image:SpineSegmentation_Slicer3.6_documentation01.png|thumb|400px|1. load the sample data]]
 
|}
 
|}
  
 +
Step 2/9.
 
{|
 
{|
 
|
 
|
Step 2/9. Select the SpineSegmentation module
+
Select the SpineSegmentation module.
* '''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)
 
 
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|400px|2. select SpineSegmentation module]]
 
|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|400px|2. select SpineSegmentation module]]
 
|}
 
|}
  
 +
Step 3/9.
 
{|
 
{|
 
|
 
|
Step 3/9. Select the input image
+
Select the input image.
* '''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)
 
 
|[[Image:SpineSegmentation_Slicer3.6_documentation03.png|thumb|400px|3. select input image]]
 
|[[Image:SpineSegmentation_Slicer3.6_documentation03.png|thumb|400px|3. select input image]]
 
|}
 
|}
  
 +
Step 4/9.
 
{|
 
{|
 
|
 
|
Step 4/9. Create a Slicer node for the output image
+
Create a Slicer node for the output image.
* '''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)
 
 
|[[Image:SpineSegmentation_Slicer3.6_documentation04.png|thumb|400px|4. create image node]]
 
|[[Image:SpineSegmentation_Slicer3.6_documentation04.png|thumb|400px|4. create image node]]
 
|}
 
|}
  
 +
Step 5/9.
 
{|
 
{|
 
|
 
|
Step 5/9. Create a Slicer node for the output model
+
Create a Slicer node for the output model
* '''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)
 
 
|[[Image:SpineSegmentation_Slicer3.6_documentation05.png|thumb|400px|5. create model node]]
 
|[[Image:SpineSegmentation_Slicer3.6_documentation05.png|thumb|400px|5. create model node]]
 
|}
 
|}
  
 +
* Step 6/9.
 
{|
 
{|
 
|
 
|
Step 6/9. Apply the segmentation algorithm
+
Apply the segmentation algorithm
* '''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)
 
 
|[[Image:SpineSegmentation_Slicer3.6_documentation06.png|thumb|400px|6. apply algorithm]]
 
|[[Image:SpineSegmentation_Slicer3.6_documentation06.png|thumb|400px|6. apply algorithm]]
 
|}
 
|}
  
 +
* Step 7/9.
 
{|
 
{|
 
|
 
|
Step 7/9. Review segmentation result
+
Review segmentation result.
* '''Input panel:'''
+
The sliders on the top of each 2D view allows for reviewing the segmentation result overlaid on the input image.
** '''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)
 
 
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|400px|7. review result]]
 
|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|400px|7. review result]]
 
|}
 
|}
  
 +
* Step 8/9.
 
{|
 
{|
 
|
 
|
Step 8/9. Save result image and model
+
Save result image and model.
* '''Input panel:'''
+
The output image and the 3D model can be saved using the Slicer user interface.
** '''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)
 
 
|[[Image:SpineSegmentation_Slicer3.6_documentation08.png|thumb|400px|8. save results]]
 
|[[Image:SpineSegmentation_Slicer3.6_documentation08.png|thumb|400px|8. save results]]
 
|}
 
|}
  
 +
* Step 9/9.
 
{|
 
{|
 
|
 
|
Step 9/9. Find contact information for help and paper reference
+
Find contact information for help and paper reference
 +
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|400px|9. help information]]
 +
|}
 +
 
 +
 
 +
===Quick Tour of Features and Use===
 
* '''Input panel:'''
 
* '''Input panel:'''
 
** '''Image input''' select the input image
 
** '''Image input''' select the input image
Line 170: Line 122:
 
** '''Cancel''' cancel the execution of the algorithm
 
** '''Cancel''' cancel the execution of the algorithm
 
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)
 
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)
|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|400px|9. help information]]
 
|}
 
  
 
== Development ==
 
== Development ==

Revision as of 03:49, 14 May 2010

Home < Modules:SpineSegmentation-Documentation-3.6

Return to Slicer 3.6 Documentation

Gallery of New Features


Module Name

SpineSegmentation module for Slicer 3.6

Load volume into Slicer3.6 and select the SpineSegmentation module
Select input and output nodes and click Apply
Processing takes approx. 3 minutes. The segmentation results are shown as a label map (blue) and a 3D model (3D view)

General Information

Module Type & Category

Type: Interactive or CLI

Category: Segmentation

Authors, Collaborators & Contact

  • Sylvain Jaume: MIT & logo, if desired
  • Contact: Sylvain Jaume, 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:

Known bugs

Links to known bugs in the Slicer3 bug tracker


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:

Doxygen documentation:

More Information

Acknowledgment

Include funding and other support here.

References

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