Difference between revisions of "Modules:SpineSegmentation-Documentation-3.6"
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** Data Set 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:''' | * '''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: | + | |
+ | {| | ||
+ | | | ||
+ | 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-3.6Return to Slicer 3.6 Documentation
Module Name
SpineSegmentation module for Slicer 3.6
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
|
Step 2/9. Select the SpineSegmentation module
|
Step 3/9. Select the input image
|
Step 4/9. Create a Slicer node for the output image
|
Step 5/9. Create a Slicer node for the output model
|
Step 6/9. Apply the segmentation algorithm
|
Step 7/9. Review segmentation result
|
Step 8/9. Save result image and model
|
Step 9/9. Find contact information for help and paper reference
|
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
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.