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

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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

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