Slicer Tutorial Module: Segmentation May 26, 2005
Segmentation  <ul><li>Segmentation: separating and labeling anatomical structure images. </li></ul><ul><li>Result is a lab...
Segmenting Data <ul><li>On the  Main   menu, click  Editor . </li></ul><ul><ul><li>The  Editor   panel appears. </li></ul>...
Threshold Tool <ul><li>Threshold : automatically outlines structures based on voxel value. </li></ul><ul><li>Lo   slider: ...
Results of Thresholding <ul><li>This example is segmenting CT skull bone. </li></ul><ul><li>Thresholding has changed the l...
Exercise: Thresholding (1/2) <ul><li>Load volume as in previous exercise. </li></ul><ul><li>Click  Editor  button. </li></...
Exercise: Thresholding (2/2) <ul><li>Click  Threshold  or  Th . </li></ul><ul><li>Click  Output , select a color for selec...
Change Label Tool <ul><li>Changes the value of the label of pixels to another value.  </li></ul><ul><li>Useful when mergin...
Exercise: Change Label <ul><li>Use on label map or original volume. </li></ul><ul><li>On  Editor ,  Effects  tab, click  C...
Change Island Tool <ul><li>Changes color of an island*.  </li></ul><ul><ul><li>*Island: a group of connected pixels with t...
Change Island Example <ul><li>Before  After </li></ul>
Exercise: Change Island <ul><li>Use on island in label map or original volume. </li></ul><ul><li>On  Editor ,  Effects  ta...
Measure Island Tool <ul><li>Calculates the volume of an island of pixels.  </li></ul><ul><li>Click  Measure Island .  </li...
Exercise: Measure Island <ul><li>Use on island in label map or original volume. </li></ul><ul><li>On  Effects  panel, clic...
Erode & Dilate Tool <ul><li>Removes pixels at border of all islands. </li></ul><ul><li>Separates two partially connected s...
Erode Example <ul><li>Before  After </li></ul>
Exercise: Erode & Dilate <ul><li>Use  Threshold  to change values: use vivid color. </li></ul><ul><li>Click  V  for green ...
Draw Tool (1 of 2) <ul><li>Draw : specifies pixels for segmenting by drawing directly on them.  </li></ul><ul><li>Useful w...
Draw Tool (2 of 2) <ul><li>Select All : selects all points.  </li></ul><ul><li>Deselect All : deselects all points.  </li>...
Exercise: Draw <ul><li>Load volume. </li></ul><ul><li>Editor    Volumes  tab    Start Editing </li></ul><ul><li>Effects ...
Remove Islands Tool <ul><li>Remove Islands : Automatically removes areas based on size. </li></ul><ul><li>Useful for remov...
Exercise: Remove Islands <ul><li>Use  Threshold  on volume. </li></ul><ul><li>Click  Remove Islands  or  RI . </li></ul><u...
Save Island Tool <ul><li>Save Island  retains the selected island, and removes disconnected pixels with the same label.  <...
Exercise: Save Island <ul><li>Color some voxels using  Threshold  or  Draw . </li></ul><ul><li>Click  Save Island  or  SI ...
Saving Segmented Data <ul><li>Segmented data: a label map </li></ul><ul><li>On the  Main   menu, click  Editor . </li></ul...
Exercise: Saving Label Map <ul><li>Use any of the previous methods to create a simple label map. </li></ul><ul><ul><li>Exa...
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Manual Segmentation-3747

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  • Manual Segmentation-3747

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