Difference between revisions of "Documentation/Nightly/Modules/ComputeGLRLMFeatureMaps"

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This module can be used in order to compute run length texture feature maps of an input image. The computation of the run length features is based on the grey level run length matrix (GLRLM) computed with [https://itk.org/Doxygen/html/classitk_1_1Statistics_1_1ScalarImageToRunLengthFeaturesFilter.html itk::itkScalarImageToRunLengthFeaturesImageFilter] for each pixel’s neighborhood.<br>
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This module can be used in order to compute run length texture feature maps of an input image. The computation of the run length features is based on the grey level run length matrix (GLRLM) computed with [https://itk.org/Doxygen/html/classitk_1_1Statistics_1_1ScalarImageToRunLengthFeaturesFilter.html itk::itkRunLengthTextureFeaturesImageFilter] for each pixel’s neighborhood.<br>
 
The GLRLM matrix describes each neighborhood local texture, it is then used to compute the following run length texture features:  
 
The GLRLM matrix describes each neighborhood local texture, it is then used to compute the following run length texture features:  
 
* short run emphasis
 
* short run emphasis
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** <span style="color:green">'''Input mask'''</span> [<span style="color:orange">-s --inputMask</span>] (<span style="color:purple">None</span>) : A mask defining the region over which texture features will be calculated
 
** <span style="color:green">'''Input mask'''</span> [<span style="color:orange">-s --inputMask</span>] (<span style="color:purple">None</span>) : A mask defining the region over which texture features will be calculated
 
** <span style="color:green">'''Inside Mask Value'''</span> [<span style="color:orange">-i --inputMask</span>] (<span style="color:purple">1</span>) : The pixel value that defines the ”inside” of the mask
 
** <span style="color:green">'''Inside Mask Value'''</span> [<span style="color:orange">-i --inputMask</span>] (<span style="color:purple">1</span>) : The pixel value that defines the ”inside” of the mask
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** <span style="color:green">'''Neighborhood radius'''</span> [<span style="color:orange">-n --neighborhoodRadius</span>] (<span style="color:purple">4</span>) : The size of the neighborhood radius
 
** <span style="color:green">'''Number of Intensity bins'''</span> [<span style="color:orange">-b --binNumber</span>] (<span style="color:purple">10</span>) : The number of intensity bins
 
** <span style="color:green">'''Number of Intensity bins'''</span> [<span style="color:orange">-b --binNumber</span>] (<span style="color:purple">10</span>) : The number of intensity bins
 
** <span style="color:green">'''Pixel Intensity Min'''</span> [<span style="color:orange">-p --pixelIntensityMin</span>] (<span style="color:purple">0</span>) : Minnimum of the pixel intensity range over which the features will be calculated
 
** <span style="color:green">'''Pixel Intensity Min'''</span> [<span style="color:orange">-p --pixelIntensityMin</span>] (<span style="color:purple">0</span>) : Minnimum of the pixel intensity range over which the features will be calculated
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** <span style="color:green">'''Distance Max'''</span> [<span style="color:orange">-D --distanceMax</span>] (<span style="color:purple">1.0</span>) : Maximum of the distance range over which the features will be calculated
 
** <span style="color:green">'''Distance Max'''</span> [<span style="color:orange">-D --distanceMax</span>] (<span style="color:purple">1.0</span>) : Maximum of the distance range over which the features will be calculated
 
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{{documentation/{{documentation/version}}/module-section|Additional Information}}
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* [http://www.insight-journal.org/browse/publication/985 InsightJournal article]
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* [https://github.com/InsightSoftwareC BoneTextureExtension Tutorial]
  
 
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{{documentation/{{documentation/version}}/module-section|Information for Developers}}
 
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The source code is available on [https://github.com/Kitware/BoneTextureExtension/tree/master/ComputeGLRLMFeatures github]
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The source code is available on [https://github.com/Kitware/BoneTextureExtension/tree/master/ComputeGLRLMFeatureMaps github]
  
 
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Latest revision as of 14:36, 13 July 2017

Home < Documentation < Nightly < Modules < ComputeGLRLMFeatureMaps


For the latest Slicer documentation, visit the read-the-docs.


Introduction and Acknowledgements

Extensions: BoneTextureExtesion
Author: Jean-Baptise Vimort, Kitware Inc.
Contributors: Beatriz Paniagua (Kitware Inc), Lucia Cevidanes (University of Michigan - School of Dentistry), Erika Benavides (University of Michigan - School of Dentistry), Antônio Carlos de Oliveira Ruellas (University of Michigan - School of Dentistry)
Contact: Jean-Baptiste Vimort, <email>jb.vimort@kitware.com</email>
Acknowledgments: This work was supported by the National Institute of Health (NIH) National Institute for Dental and Craniofacial Research (NIDCR) grant R21DE025306 (Textural Biomarkers of Arthritis for the Subchondral Bone in the Temporomandibular Joint), NIDCR grant R01DE024450 (Quantification of 3D bony Changes in Temporomandibular Joint Osteoarthritis) and National Institute of Biomedical Imaging and Bioengineering NIBIB) grant R01EB021391 (Shape Analysis Toolbox for Medical Image Computing Projects).
License: Apache License, Version 2.0

  • Kitware Inc.

  • University of Michigan


Module Description

This module can be used in order to compute run length texture feature maps of an input image. The computation of the run length features is based on the grey level run length matrix (GLRLM) computed with itk::itkRunLengthTextureFeaturesImageFilter for each pixel’s neighborhood.
The GLRLM matrix describes each neighborhood local texture, it is then used to compute the following run length texture features:

  • short run emphasis
  • long run emphasis
  • grey level non uniformity
  • run length non uniformity
  • low grey level run emphasis
  • high grey level run emphasis
  • short run low grey level emphasis
  • short run high grey level emphasis
  • long run low grey level emphasis
  • long run high grey level emphasis


Use Cases

ComputeGLRLMFeatureMaps-Interface.png
  • Inputs:
    • Input volume [index: 0] : Input Volume
    • Output volume [index: 1] : Output diffusion-weighted volume where the 10 feature maps will be stored
    • Input mask [-s --inputMask] (None) : A mask defining the region over which texture features will be calculated
    • Inside Mask Value [-i --inputMask] (1) : The pixel value that defines the ”inside” of the mask
    • Neighborhood radius [-n --neighborhoodRadius] (4) : The size of the neighborhood radius
    • Number of Intensity bins [-b --binNumber] (10) : The number of intensity bins
    • Pixel Intensity Min [-p --pixelIntensityMin] (0) : Minnimum of the pixel intensity range over which the features will be calculated
    • Pixel Intensity Max [-P --pixelIntensityMax] (4000) : Maximum of the pixel intensity range over which the features will be calculated
    • Distance Min [-d --distanceMin] (0.0) : Minnimum of the distance range over which the features will be calculated
    • Distance Max [-D --distanceMax] (1.0) : Maximum of the distance range over which the features will be calculated

Additional Information

Similar Modules

N/A

Information for Developers

The source code is available on github

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