Manual Segmentation-3747

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http://hdl.handle.net/1926/522

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  • 1. Slicer Tutorial Module: Segmentation May 26, 2005
  • 2. Segmentation
    • Segmentation: separating and labeling anatomical structure images.
    • Result is a label map.
    • Semi-automatic process using editing tools.
      • Include thresholding, morphological operations, island-removal, and free-hand drawing.
      • Segment data in 3D or slice-by-slice.
    • Merge volumes to construct complex images.
    • Example: segment skin from an MR scan.
  • 3. Segmenting Data
    • On the Main menu, click Editor .
      • The Editor panel appears.
    • Click the Volumes tab.
      • The Volumes tab appears.
      • Click Setup .
        • The name of data appears in Original Grayscale field.
      • Select NEW for the Working Labelmap .
      • Enter name for this segmentation.
        • Example: "ventricles".
      • Click Start Editing .
        • The Effects tab appears.
  • 4. Threshold Tool
    • Threshold : automatically outlines structures based on voxel value.
    • Lo slider: excludes low-intensity voxels.
    • Hi slider: excludes high-intensity voxels.
    • Click Output and select a color, or enter an Output color number.
    • Click Apply .
      • The outlined areas are called "islands".
  • 5. Results of Thresholding
    • This example is segmenting CT skull bone.
    • Thresholding has changed the label to blue.
    • Notice that the skull is well-defined and separated from the rest of the image.
  • 6. Exercise: Thresholding (1/2)
    • Load volume as in previous exercise.
    • Click Editor button.
    • Click Volumes tab.
    • Click Setup button.
    • On Original Grayscale drop-down list, select volume.
    • Select NEW for the Working Labelmap .
    • Enter “Descriptive Name".
    • Click Start Editing .
  • 7. Exercise: Thresholding (2/2)
    • Click Threshold or Th .
    • Click Output , select a color for selected voxels.
    • Use Lo slider to exclude low-intensity voxels.
    • Use Hi slider to exclude high-intensity voxels.
      • Example: if 140 is a common value on 2D Viewer , let Lo =130 and Hi =150.
    • Choose Scope : 1 Slice or 3D .
    • Choose to filter 1 Slice , 3 Slices , or 3D .
    • Click Apply .
    • Result: label map.
  • 8. Change Label Tool
    • Changes the value of the label of pixels to another value.
    • Useful when merging two data sets together, and you want to keep the data sets distinct from each other.
    • Click Change Label .
    • Enter Value to change .
    • Click Output and select a color, or enter a color number.
    • Click Apply .
    • The new output color will replace the value.
  • 9. Exercise: Change Label
    • Use on label map or original volume.
    • On Editor , Effects tab, click CL or Change Label .
    • Enter Value to change .
    • Click Output and select a color.
    • Choose Scope : 1 Slice or 3D .
    • Click Apply .
    • The new output color replaces the value.
  • 10. Change Island Tool
    • Changes color of an island*.
      • *Island: a group of connected pixels with the same label.
    • Useful after thresholding, to separate anatomy further.
    • Click Change Island .
    • Click New Label and select a color, or enter a color number.
    • Click any part of the island.
    • Pixels that are part of that island will receive the New Label value.
  • 11. Change Island Example
    • Before After
  • 12. Exercise: Change Island
    • Use on island in label map or original volume.
    • On Editor , Effects tab, click CI or Change Island .
    • Click New Label and select a new color.
    • Click any part of the island.
    • Changes island to New Label value.
  • 13. Measure Island Tool
    • Calculates the volume of an island of pixels.
    • Click Measure Island .
    • Click Island Label and select a color, or enter a color number.
    • Click any part of the island.
    • Slicer will display the Size , in pixels.
    • Also displays the size of the Largest island within the selected Scope .
  • 14. Exercise: Measure Island
    • Use on island in label map or original volume.
    • On Effects panel, click Measure Island .
    • Click Island Label and select pixel color.
    • Select 1 Slice or 3D for Scope .
    • Click any part of the island.
    • Observe Size of island in pixels.
    • Observe size of Largest island within Scope .
  • 15. Erode & Dilate Tool
    • Removes pixels at border of all islands.
    • Separates two partially connected structures; removes many small islands.
    • Dilate : adds pixels around all islands.
    • Click Erode .
    • Click Value to Erode and select color, or enter color number. Erode acts only on pixels with selected color.
    • Fill value: 0.
    • Iterations : number of times to apply.
    • Neighborhood Size : 4 for less erosion, 8 for more.
    • Click Erode , Dilate , Erode & Dilate , or Dilate & Erode .
  • 16. Erode Example
    • Before After
  • 17. Exercise: Erode & Dilate
    • Use Threshold to change values: use vivid color.
    • Click V for green 2D image.
    • Editor  Volumes tab  Start Editing
    • Effects tab: Green Active Slice , Erode .
    • Value to Erode : use Threshold value.
    • Scope : 3D
    • Click Dilate : threshold value spreads.
    • Click Erode : threshold value area shrinks.
  • 18. Draw Tool (1 of 2)
    • Draw : specifies pixels for segmenting by drawing directly on them.
    • Useful when automatic methods cannot segment data correctly.
    • Click Draw .
    • Click Output and select a color, or enter color number.
      • Pixels you draw on get this color.
    • Point Radius : fineness of line.
      • 1 or 2 selects individual points.
    • Mode : behavior of left mouse button.
      • Draw : for drawing on points.
      • Select : for selecting points.
      • Move : for moving selected points.
  • 19. Draw Tool (2 of 2)
    • Select All : selects all points.
    • Deselect All : deselects all points.
    • Delete Selected : deletes selected points.
    • Delete All : deletes all points.
    • Shape : shape of left mouse in the draw window.
    • Draw on the region of interest (ROI) with left mouse button.
    • Click Apply .
      • Slicer will fill the ROI with the Output color.
    • Mistake? Use Draw with Black output to erase.
    • Delete last selected point of polygon with Delete Selected .
  • 20. Exercise: Draw
    • Load volume.
    • Editor  Volumes tab  Start Editing
    • Effects tab: Green Active Slice , Draw .
    • Click Output : select color.
    • On 2D Viewer , choose area to draw around.
    • Click mouse on edge of area.
    • Move mouse around area, clicking as you move.
    • When area outlined, click Apply .
    • Area is covered by selected color.
  • 21. Remove Islands Tool
    • Remove Islands : Automatically removes areas based on size.
    • Useful for removing small areas that should not have been thresholded.
    • Example: use an area of 10 to remove all islands less than 10 voxels in size.
  • 22. Exercise: Remove Islands
    • Use Threshold on volume.
    • Click Remove Islands or RI .
    • Min. Island Area : 10
    • Label of the sea : 0
    • Scope : 3D
    • Click on 2D Viewer in sea (outside island).
    • Eliminates the smaller islands.
  • 23. Save Island Tool
    • Save Island retains the selected island, and removes disconnected pixels with the same label.
    • Useful for separating a single connected structure from other structures.
  • 24. Exercise: Save Island
    • Color some voxels using Threshold or Draw .
    • Click Save Island or SI .
    • Scope : 3D
    • Click an island in 2D Viewer .
      • Warning: all other same-colored islands disappear.
  • 25. Saving Segmented Data
    • Segmented data: a label map
    • On the Main menu, click Editor .
      • The Editor panel appears.
    • Click the Volumes tab.
    • The Volumes tab appears.
    • Select Save .
    • Select the name of your label map for Volume to Save .
    • Select a file name.
      • Simplest to use same name as the Volume to Save .
    • Save file to the appropriate directory.
  • 26. Exercise: Saving Label Map
    • Use any of the previous methods to create a simple label map.
      • Example: Threshold .
    • Click Editor  Volumes tab  Save
    • Select the Volume to Save .
    • Add file name to end of Filename Path .
    • Click Save .