Difference between revisions of "Modules:EMSegment-TemplateBuilder:EMSegment-TemplateBuilder-Steps"

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[[Modules:EMSegment-TemplateBuilder|Return to EMSegment Template Builder Documentation]]
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= EMSegment Template Builder Workflow Wizard Steps=
 
= EMSegment Template Builder Workflow Wizard Steps=
  
 
== (1/9) Define Parameters Set: Select parameter set or create new parameters ==
 
== (1/9) Define Parameters Set: Select parameter set or create new parameters ==
[[Image:EMSegment-Workflow-1-9.png|thumb|580px|Step 1/9]]
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[[Image:EMSegment-Workflow-1-9.png|thumb|300px|Step 1/9]]
 
  * For now, use tutorial set
 
  * For now, use tutorial set
 
  * Later use this interface to create a new parameter set
 
  * Later use this interface to create a new parameter set
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== (2/9) Define Hierarchy: Define a hierarchy of anatomical structures ==
 
== (2/9) Define Hierarchy: Define a hierarchy of anatomical structures ==
[[Image:EMSegment-Workflow-2-9.png|thumb|580px|Step 2/9]]
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[[Image:EMSegment-Workflow-2-9.png|thumb|300px|Step 2/9]]
 
  * Right click to add or delete nodes
 
  * Right click to add or delete nodes
 
  * Label corresponds to eventual voxel values in segmentation result
 
  * Label corresponds to eventual voxel values in segmentation result
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== (3/9) Assign Atlas: Assign atlases for anatomical structures ==
 
== (3/9) Assign Atlas: Assign atlases for anatomical structures ==
[[Image:EMSegment-Workflow-3-9.png|thumb|580px|Step 3/9]]
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[[Image:EMSegment-Workflow-3-9.png|thumb|300px|Step 3/9]]
 
* To change or add new atlas volumes: Load new volumes into Slicer3, then Select new volumes at this step
 
* To change or add new atlas volumes: Load new volumes into Slicer3, then Select new volumes at this step
 
<br style="clear:both;"/>
 
<br style="clear:both;"/>
  
 
== (4/9) Select Target Images: Choose the set of images that will be segmented ==
 
== (4/9) Select Target Images: Choose the set of images that will be segmented ==
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[[Image:EMSegment-Workflow-4-9.png|thumb|300px|Step 4/9]]
 
* To change or add new atlas volumes: Load new volumes into Slicer3, then Select new volumes at this step
 
* To change or add new atlas volumes: Load new volumes into Slicer3, then Select new volumes at this step
 
* You can reorder target images; order is important
 
* You can reorder target images; order is important
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* First target is fixed image  
 
* First target is fixed image  
 
* Rigid, mutual information registration
 
* Rigid, mutual information registration
[[Image:EMSegment-Workflow-4-9.png|thumb|580px|Step 4/9]]
 
 
<br style="clear:both;"/>
 
<br style="clear:both;"/>
  
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* Simple, default strategy
 
* Simple, default strategy
 
* Default parameter sets available from pulldown
 
* Default parameter sets available from pulldown
[[Image:EMSegment-Workflow-5-9.png|thumb|580px|Step 5/9]]
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[[Image:EMSegment-Workflow-5-9.png|thumb|300px|Step 5/9]]
 
<br style="clear:both;"/>
 
<br style="clear:both;"/>
  
 
== (6/9) Specify Intensity Distributions: Define intensity distribution for each anatomical structure ==
 
== (6/9) Specify Intensity Distributions: Define intensity distribution for each anatomical structure ==
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{|
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|[[Image:EMSegment-Workflow-6-9.png|thumb|300px|Step 6/9]]
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|[[Image:EMSegment-Workflow-6-9-sample.png|thumb|300px|Step 6/9 - Sample Voxels]]
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|[[Image:EMSegment-Workflow-6-9-sample-remove.png|thumb|300px|Step 6/9 - Remove Voxels]]
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|}
 
* Intensity distributions define appearance of each leaf structure
 
* Intensity distributions define appearance of each leaf structure
 
* Gaussian
 
* Gaussian
 
* Dimensionality equal to number of target images
 
* Dimensionality equal to number of target images
 
* Two methods
 
* Two methods
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** Specify mean and covariance manually
 
** Sample voxels from images
 
** Sample voxels from images
[[Image:EMSegment-Workflow-6-9-sample.png|thumb|580px|Step 6/9 - Sample Voxels]] [[Image:EMSegment-Workflow-6-9-sample-remove.png|thumb|580px|Step 6/9 - Remove Voxels]]
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*** Load first target image into Slicer3 slicer view
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# Load first target image into Slicer3 slicer view
*** Choose anatomical structure
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# Choose anatomical structure
*** Choose `manual sampling’
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# Choose `manual sampling’
*** Ctrl-left-click on image to add voxels
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# Ctrl-left-click on image to add voxels
*** To remove an unwanted sample right-click on it and choose “remove”
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# To remove an unwanted sample right-click on it and choose “remove”
*** Change back to “manual” mode to tweak distribution
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# Change back to “manual” mode to tweak distribution
** Specify mean and covariance manually
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* Tip: sample first, then fine tune manually
 
* Tip: sample first, then fine tune manually
 
[[Image:EMSegment-Workflow-6-9.png|thumb|580px|Step 6/9]]
 
 
<br style="clear:both;"/>
 
<br style="clear:both;"/>
  
 
== (7/9) Edit Node-based Parameters: Specify node-based segmentation parameters ==
 
== (7/9) Edit Node-based Parameters: Specify node-based segmentation parameters ==
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[[Image:EMSegment-Workflow-7-9.png|thumb|300px|Step 7/9]]
 
* Segmentation parameters for every tree node
 
* Segmentation parameters for every tree node
 
* Influence
 
* Influence
 
** Prior weight relative to other structures
 
** Prior weight relative to other structures
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** Alpha (parent nodes only)
 
** Atlas
 
** Atlas
 
** Input channels
 
** Input channels
 
** Smoothing (parent nodes only)
 
** Smoothing (parent nodes only)
 
* Stopping Conditions
 
* Stopping Conditions
[[Image:EMSegment-Workflow-7-9.png|thumb|580px|Step 7/9]]
 
 
<br style="clear:both;"/>
 
<br style="clear:both;"/>
  
 
== (8/9) Edit Registration Parameters: Specify atlas-to-target registration parameters ==
 
== (8/9) Edit Registration Parameters: Specify atlas-to-target registration parameters ==
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[[Image:EMSegment-Workflow-8-9.png|thumb|300px|Step 8/9]]
 
* Moving image registered to first target image (You can choose any image loaded into Slicer3)
 
* Moving image registered to first target image (You can choose any image loaded into Slicer3)
 
* Same transformation applied to all atlas images before segmentation begins
 
* Same transformation applied to all atlas images before segmentation begins
[[Image:EMSegment-Workflow-8-9.png|thumb|580px|Step 8/9]]
 
 
<br style="clear:both;"/>
 
<br style="clear:both;"/>
  
 
==(9/9) Run Segmentation: Save work and apply EM Algorithm to segment target images==
 
==(9/9) Run Segmentation: Save work and apply EM Algorithm to segment target images==
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[[Image:EMSegment-Workflow-9-9.png|thumb|300px|Step 9/9]]
 
* Select output and run registration
 
* Select output and run registration
 
* You can troubleshoot preprocessing by saving intermediate results
 
* You can troubleshoot preprocessing by saving intermediate results
 
* Choose an output labelmap
 
* Choose an output labelmap
 
* ROI governs segmentation processing (one-based, not zero-based)
 
* ROI governs segmentation processing (one-based, not zero-based)
 
[[Image:EMSegment-Workflow-9-9.png|thumb|580px|Step 9/9]]
 
 
<br style="clear:both;"/>
 
<br style="clear:both;"/>
  
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* Adjust opacity of the label map
 
* Adjust opacity of the label map
 
* (Optional) Generate and display surfaces from the segmentation results
 
* (Optional) Generate and display surfaces from the segmentation results
# Select the "Model Generation" -> "Model Maker" module
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# Select the "Surface Models" -> "Model Maker" module
 
# For "Input Volume", select the $My_Segmentation_Result  
 
# For "Input Volume", select the $My_Segmentation_Result  
 
# For "Output Directory", create and select $PLAYPEN_DIR/Models
 
# For "Output Directory", create and select $PLAYPEN_DIR/Models
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Image:EMSegment31Structures.png|Segmentation of brain structures using EMSegmenter
 
Image:EMSegment31Structures.png|Segmentation of brain structures using EMSegmenter
 
</gallery>
 
</gallery>
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[[Modules:EMSegment-TemplateBuilder|Return to EMSegment Template Builder Documentation]]

Latest revision as of 20:39, 17 July 2009

Home < Modules:EMSegment-TemplateBuilder:EMSegment-TemplateBuilder-Steps

Return to EMSegment Template Builder Documentation

EMSegment Template Builder Workflow Wizard Steps

(1/9) Define Parameters Set: Select parameter set or create new parameters

Step 1/9
* For now, use tutorial set
* Later use this interface to create a new parameter set


(2/9) Define Hierarchy: Define a hierarchy of anatomical structures

Step 2/9
* Right click to add or delete nodes
* Label corresponds to eventual voxel values in segmentation result


(3/9) Assign Atlas: Assign atlases for anatomical structures

Step 3/9
  • To change or add new atlas volumes: Load new volumes into Slicer3, then Select new volumes at this step


(4/9) Select Target Images: Choose the set of images that will be segmented

Step 4/9
  • To change or add new atlas volumes: Load new volumes into Slicer3, then Select new volumes at this step
  • You can reorder target images; order is important
  • You can choose to align target images
  • First target is fixed image
  • Rigid, mutual information registration


(5/9) Intensity Normalization: Normalize target images

  • You can choose to normalize target images
  • Simple, default strategy
  • Default parameter sets available from pulldown
Step 5/9


(6/9) Specify Intensity Distributions: Define intensity distribution for each anatomical structure

Step 6/9
Step 6/9 - Sample Voxels
Step 6/9 - Remove Voxels
  • Intensity distributions define appearance of each leaf structure
  • Gaussian
  • Dimensionality equal to number of target images
  • Two methods
    • Specify mean and covariance manually
    • Sample voxels from images
  1. Load first target image into Slicer3 slicer view
  2. Choose anatomical structure
  3. Choose `manual sampling’
  4. Ctrl-left-click on image to add voxels
  5. To remove an unwanted sample right-click on it and choose “remove”
  6. Change back to “manual” mode to tweak distribution
  • Tip: sample first, then fine tune manually


(7/9) Edit Node-based Parameters: Specify node-based segmentation parameters

Step 7/9
  • Segmentation parameters for every tree node
  • Influence
    • Prior weight relative to other structures
    • Alpha (parent nodes only)
    • Atlas
    • Input channels
    • Smoothing (parent nodes only)
  • Stopping Conditions


(8/9) Edit Registration Parameters: Specify atlas-to-target registration parameters

Step 8/9
  • Moving image registered to first target image (You can choose any image loaded into Slicer3)
  • Same transformation applied to all atlas images before segmentation begins


(9/9) Run Segmentation: Save work and apply EM Algorithm to segment target images

Step 9/9
  • Select output and run registration
  • You can troubleshoot preprocessing by saving intermediate results
  • Choose an output labelmap
  • ROI governs segmentation processing (one-based, not zero-based)


Generate EM Segmentation Result Gallery

  • Select the first target volume for display
  • Select the segmentation results volume in the Labelmap chooser
  • Adjust opacity of the label map
  • (Optional) Generate and display surfaces from the segmentation results
  1. Select the "Surface Models" -> "Model Maker" module
  2. For "Input Volume", select the $My_Segmentation_Result
  3. For "Output Directory", create and select $PLAYPEN_DIR/Models
  4. For "Model Scene File", select $PLAYPEN_DIR/Models.mrml
  5. Enable "Generate All Models"
  6. Set "End Label" to the highest label that you produced (e.g., 8 fro the tutorial)
  7. Enable "Joint Smoothing"
  8. Click on Apply (this will generate the models and will take approximately 5 minutes)
  9. Load the models into Slicer (File->Import Scene; select $PLAYPEN_DIR/Models.mrml)
  10. Use The Models module to manipulate display attributes


Return to EMSegment Template Builder Documentation