TubeTK/Documentation/InteractivePDFSegmenter: Difference between revisions

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#* File -> Add Volume
#* File -> Add Volume
# '''Open the Interactive PDF Segmenter module'''
# '''Open the Interactive PDF Segmenter module'''
#* [[File:InteractivePDFSegmenterTutorial_step2.png|800px]]
# '''Set the input and output volumes'''
# '''Set the input and output volumes'''
#* Input Volume 1: brainSliceDOUBLE
#* Input Volume 1: brainSliceDOUBLE
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#** Creates a new volume called "Volume": this will hold the final segmentation
#** Creates a new volume called "Volume": this will hold the final segmentation
# '''Set the view layout to "Red slice only"'''
# '''Set the view layout to "Red slice only"'''
#* [[File:InteractivePDFSegmenterTutorial_step4a.png|800px]]
#* [[File:InteractivePDFSegmenterTutorial_step4b.png|800px]]
# '''Create the label map roughly outlining the structures to be segmented and the background'''
# '''Create the label map roughly outlining the structures to be segmented and the background'''
#* Label Map: Create new volume
#* Label Map: Create new volume
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#** Click on the "Paint" button to begin editing
#** Click on the "Paint" button to begin editing
#** Use a different label color for each structure of interest: choose the label by clicking the colored push button
#** Use a different label color for each structure of interest: choose the label by clicking the colored push button
#* [[File:InteractivePDFSegmenterTutorial_step5a.png|800px]]
#** Create a label for the background as well
#** Create a label for the background as well
#* In the following example, green represents gray matter, yellow represents white matter, and brown represents the cerebrospinal fluid (CSF):
#* In the following example, green represents gray matter, yellow represents white matter, and brown represents the cerebrospinal fluid (CSF)
#* [[File:InteractivePDFSegmenterTutorial_step5b.png|800px]]
#* Void Id: 0
#* Void Id: 0
#** Value that specifies nothing in the label map
#** Value that specifies nothing in the label map
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#* Click the "Segment" button
#* Click the "Segment" button
#* Select "Volume" as the label map to view the results
#* Select "Volume" as the label map to view the results
#* [[File:InteractivePDFSegmenterTutorial_step7a.png|800px]]
#* [[File:InteractivePDFSegmenterTutorial_step7b.png|800px]]
#* To view the label outlines, select "Show label volume outlines"
#* To view the label outlines, select "Show label volume outlines"
#* [[File:InteractivePDFSegmenterTutorial_step7c.png|800px]]
#* [[File:InteractivePDFSegmenterTutorial_step7d.png|800px]]

Revision as of 03:47, 7 January 2011

Documentation

TODO: insert algorithm description here, including parameter descriptions

Tutorial

Tutorial Data

  • The 2D brain image used in this example is distributed as part of Slicer4, and is located in Slicer4/Testing/Data/Input/brainSliceDOUBLE.mha

Tutorial Steps

  1. Load brainSliceDOUBLE.mha:
    • File -> Add Volume
  2. Open the Interactive PDF Segmenter module
  3. Set the input and output volumes
    • Input Volume 1: brainSliceDOUBLE
    • Input Volume 2 (optional): None
    • Input Volume 3 (optional): None
    • Output Volume: Create new volume
      • Creates a new volume called "Volume": this will hold the final segmentation
  4. Set the view layout to "Red slice only"
  5. Create the label map roughly outlining the structures to be segmented and the background
    • Label Map: Create new volume
      • Creates a new volume called "Volume1": this will hold the input label map
    • A small version of Slicer's Editor module is embedded into the Interactive PDF Segmenter
    • Create a label map roughly outlining the structures of interest and the background by using the paint, erase and threshold functions
      • Click on the "Paint" button to begin editing
      • Use a different label color for each structure of interest: choose the label by clicking the colored push button
      • Create a label for the background as well
    • In the following example, green represents gray matter, yellow represents white matter, and brown represents the cerebrospinal fluid (CSF)
    • Void Id: 0
      • Value that specifies nothing in the label map
  6. Specify the segmentation parameters
    • The goal segmentation buttons provide example parameters depending on whether the shapes of the expected segmentations are jagged, smooth or intermediate
    • In this example, we will use custom parameters
    • Erosion Radius: 0
    • Hole Fill Iterations: 2
    • False Positive Ratio: 1.00
    • Probability Smoothing Standard Deviation: 1.00
    • Draft Mode: Off
    • Reclassify Object Mask: On
    • Reclassify Not Object Mask: On
  7. Run the segmentation
    • Click the "Segment" button
    • Select "Volume" as the label map to view the results
    • To view the label outlines, select "Show label volume outlines"
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