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

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(→‎Tutorial and Usage: parameter description, step-by-step instructions, user interface screenshots)
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** Data Set 1
 
** Data Set 1
  
===Quick Tour of Features and Use===
+
===Tutorial and Usage===
  
A list panels in the interface, their features, what they mean, and how to use them. For instance:
+
Below are the step-by-step instructions to load, process and save some sample data.
 +
To download the sample data, you need to go to http://nitrc.org and create a username.  
 +
The data are located at
 +
http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/TestingData/?root=sylvainproject
  
 
{|
 
{|
 
|
 
|
 +
Step 1. Load the sample data
 
* '''Input panel:'''
 
* '''Input panel:'''
** '''First input'''
+
** '''Image input''' select the input image
** '''Second input'''
+
** '''Image output''' create Slicer node for output image
* '''Parameters panel:'''
+
** '''Model output''' create Slicer node for output model
** '''First parameter'''
+
* '''Command panel:'''
** '''Second parameter'''
+
** '''Default''' reset input and output nodes to blank values
* '''Output panel:'''
+
** '''Cancel''' cancel the execution of the algorithm
** '''First output'''
+
** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)
** '''Second output'''
+
|[[Image:SpineSegmentation_Slicer3.6_documentation01.png|thumb|400px|1. load the sample data]]
* '''Viewing panel:'''
+
|}
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
+
 
 +
{|
 +
|
 +
Step 2/9. 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]]
 +
|}
 +
 
 +
{|
 +
|
 +
Step 3/9. 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]]
 +
|}
 +
 
 +
{|
 +
|
 +
Step 4/9. 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]]
 +
|}
 +
 
 +
{|
 +
|
 +
Step 5/9. 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]]
 +
|}
 +
 
 +
{|
 +
|
 +
Step 6/9. 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]]
 +
|}
 +
 
 +
{|
 +
|
 +
Step 7/9. Review segmentation result
 +
* '''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_documentation07.png|thumb|400px|7. review result]]
 +
|}
 +
 
 +
{|
 +
|
 +
Step 8/9. Save result image and 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_documentation08.png|thumb|400px|8. save results]]
 +
|}
 +
 
 +
{|
 +
|
 +
Step 9/9. Find contact information for help and paper reference
 +
* '''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_documentation09.png|thumb|400px|9. help information]]
 
|}
 
|}
  

Revision as of 02:59, 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

User Interface
Output
Caption

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 these use cases:

  • Use Case 1:
  • Use Case 2:

Examples of the module in use:

  • Example 1
  • Example 2

Tutorials

Links to tutorials explaining how to use this module:

  • Tutorial 1
    • Data Set 1

Tutorial and Usage

Below are the step-by-step instructions to load, process and save some sample data. To download the sample data, you need to go to http://nitrc.org and create a username. The data are located at

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

Step 1. 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)
1. load the sample data

Step 2/9. 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)
2. select SpineSegmentation module

Step 3/9. 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)
3. select input image

Step 4/9. 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)
4. create image node

Step 5/9. 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)
5. create model node

Step 6/9. 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)
6. apply algorithm

Step 7/9. Review segmentation result

  • 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)
7. review result

Step 8/9. Save result image and 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)
8. save results

Step 9/9. Find contact information for help and paper reference

  • 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)
9. help information

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.