Modules:EMSegment-TemplateBuilder:EMSegment-TemplateBuilder-Steps

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

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

Step 4/9

(5/9)Intensity Normalization: Normalize target images

Step 5/9

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

Step 6/9

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

Step 7/9

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

Step 8/9

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

Step 9/9

Generate EM Segmentation Result Gallery

(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 

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  EMSegmenter Applied to MR T1 & T2 tutorial data

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  Segmentation of brain structures using EMSegmenter