Documentation/Nightly/Extensions/BoneTextureExtension

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For the stable Slicer documentation, visit the 4.8 page.


Introduction and Acknowledgements

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,
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

Extension Description

Logo-BoneTextureExtension.png

This extensions contain several modules that can be used to compute feature maps of N-Dimensional images using two well-known texture analysis methods: the study of Grey Level Co-occurrence Matrix (GLCM) and the study of Grey Level Run Length Matrix (GLRLM). The main algorithms used in this extension are part of a remote module of insight toolkit (ITK) called itkTextureFeatures

Key Features:

  • Estimated texture features:
    • 8 co-occurrence textural features: energy, entropy, correlation, inverse difference moment, inertia, cluster shade, cluster prominence and Haralick correlation
    • 10 run length textural 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 and long run high grey level emphasis.
  • Input configurable parameters: locality of the texture, offset directions for co-occurrence and run length computation, the number of bins for the intensity histograms, and the intensity range or the range of run lengths.

Usage

Main modules interface

BoneTexture User Interface
BoneTextureSerializer User Interface

Input example

Input scan
Input mask

Texture features

Texture feature result table

Texture feature maps

Co-occurrence texture feature maps

Energy
Entropy
Correlation
Inverse difference moment
ColorBar.jpg
Inertia
Cluster shade
Cluster prominence
Haralick correlation
ColorBar.jpg

Run Length texture feature maps

Short run emphasis
Long run emphasis
Grey level non uniformity
Run length non uniformity
Low grey level run emphasis
ColorBar.jpg
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
ColorBar.jpg


Bone Morphometry feature maps

BVTV
TbTh
TbSp
TbN
BSBV
ColorBar.jpg

Modules

Additional Information

Similar Extensions

N/A

Information for Developers

The source code is available on github