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http://hdl.handle.net/1926/522
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NA-MICNational Alliance for Medical Image Computing http://na-mic.org
Slicer TutorialModule: Segmentation
May 26, 2005
National Alliance for Medical Image Computing http://na-mic.org
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.
National Alliance for Medical Image Computing http://na-mic.org
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.
National Alliance for Medical Image Computing http://na-mic.org
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".
National Alliance for Medical Image Computing http://na-mic.org
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.
National Alliance for Medical Image Computing http://na-mic.org
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.
National Alliance for Medical Image Computing http://na-mic.org
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.
National Alliance for Medical Image Computing http://na-mic.org
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.
National Alliance for Medical Image Computing http://na-mic.org
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.
National Alliance for Medical Image Computing http://na-mic.org
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.
National Alliance for Medical Image Computing http://na-mic.org
Change Island Example
• Before After
National Alliance for Medical Image Computing http://na-mic.org
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.
National Alliance for Medical Image Computing http://na-mic.org
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.
National Alliance for Medical Image Computing http://na-mic.org
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.
National Alliance for Medical Image Computing http://na-mic.org
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.
National Alliance for Medical Image Computing http://na-mic.org
Erode Example
• Before After
National Alliance for Medical Image Computing http://na-mic.org
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.
National Alliance for Medical Image Computing http://na-mic.org
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.
National Alliance for Medical Image Computing http://na-mic.org
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.
National Alliance for Medical Image Computing http://na-mic.org
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.
National Alliance for Medical Image Computing http://na-mic.org
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.
National Alliance for Medical Image Computing http://na-mic.org
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.
National Alliance for Medical Image Computing http://na-mic.org
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.
National Alliance for Medical Image Computing http://na-mic.org
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.
National Alliance for Medical Image Computing http://na-mic.org
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.
National Alliance for Medical Image Computing http://na-mic.org
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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