View source for Modules:EMSegment-TemplateBuilder:EMSegment-TemplateBuilder-Steps

= EMSegment Template Builder Workflow Wizard Steps=

== (1/9)Define Parameters Set: Select parameter set or create new parameters ==
[[Image:EMSegment-Workflow-1-9.png|thumb|580px|Step 1/9]]
 * For now, use tutorial 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 ==
[[Image:EMSegment-Workflow-2-9.png|thumb|580px|Step 2/9]]
 * Right click to add or delete nodes
 * Label corresponds to eventual voxel values in segmentation result
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== (3/9)Assign Atlas: Assign atlases for anatomical structures ==
[[Image:EMSegment-Workflow-3-9.png|thumb|580px|Step 3/9]]
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== (4/9)Select Target Images: Choose the set of images that will be segmented ==
[[Image:EMSegment-Workflow-4-9.png|thumb|580px|Step 4/9]]
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== (5/9)Intensity Normalization: Normalize target images ==
[[Image:EMSegment-Workflow-5-9.png|thumb|580px|Step 5/9]]
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== (6/9)Specify Intensity Distributions: Define intensity distribution for each anatomical structure ==
[[Image:EMSegment-Workflow-6-9.png|thumb|580px|Step 6/9]]
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== (7/9)Edit Node-based Parameters: Specify node-based segmentation parameters ==
[[Image:EMSegment-Workflow-7-9.png|thumb|580px|Step 7/9]]
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== (8/9)Edit Registration Parameters: Specify atlas-to-target registration parameters ==
[[Image:EMSegment-Workflow-8-9.png|thumb|580px|Step 8/9]]
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== (9/9)Run Segmentation: Save work and apply EM Algorithm to segment target images ==
[[Image:EMSegment-Workflow-9-9.png|thumb|580px|Step 9/9]]
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= 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 labelmap==
== (Optional) Generate and display surfaces from the segmentation results==

   1. Select the "Model Generation" -> "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 


<gallery>
Image:EMSVisualizeTutorialResultsData.png|EMSegmenter Applied to MR T1 & T2 tutorial data
Image:EMSegment31Structures.png|Segmentation of brain structures using EMSegmenter
</gallery>