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Manual Segmentation-3747
Manual Segmentation-3747
Manual Segmentation-3747
Manual Segmentation-3747
Manual Segmentation-3747
Manual Segmentation-3747
Manual Segmentation-3747
Manual Segmentation-3747
Manual Segmentation-3747
Manual Segmentation-3747
Manual Segmentation-3747
Manual Segmentation-3747
Manual Segmentation-3747
Manual Segmentation-3747
Manual Segmentation-3747
Manual Segmentation-3747
Manual Segmentation-3747
Manual Segmentation-3747
Manual Segmentation-3747
Manual Segmentation-3747
Manual Segmentation-3747
Manual Segmentation-3747
Manual Segmentation-3747
Manual Segmentation-3747
Manual Segmentation-3747
Manual Segmentation-3747
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Manual Segmentation-3747

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

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

Published in: Technology, Business
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  • Transcript

    • 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 .

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