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

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This module provide a simple to serialize the BoneTexture module once the good set of parameters has been chosen.<br>
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This module provides a simple way to serialize the BoneTexture module.<br>
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In order two make it work, all the input data should be in the same folder and named as following:
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In order to make it work, all the input data should be in the same folder and named as following:
 
* The input scan should be named ScanXXX.nrrd, where XXX is the ID of the case
 
* The input scan should be named ScanXXX.nrrd, where XXX is the ID of the case
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* If it exist, the input mask should be named SegmCXXX.nrrd, where XXX is the ID corresponding to the the input scan
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* If it exists, the input mask should be named SegmCXXX.nrrd, where XXX is the ID corresponding to the the input scan
  
 
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|[[Image:BoneTextureSerealizer-Input.png|thumb|500px|Image:BoneTextureSerializer Input]]
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|[[Image:BoneTextureSerealizer-Input.png|thumb|500px|BoneTextureSerializer Input]]
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| This section allow the user to specify the input folder, the folder specified should contain all the inputs (scans and segmentation) has described previously.
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| This section allows the user to specify the input folder, the folder specified should contain all the inputs (scans and segmentations) as described previously.
 
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{|
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|[[Image:BoneTexture-Parameter.png|thumb|500px|Image:BoneTextureSerializer parameters]]
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|[[Image:BoneTexture-Parameter.png|thumb|500px|BoneTextureSerializer parameters]]
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|This section allow the user to choose:
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|This section allows the user to choose:
 
* The Type of features wanted: Run length features or co-occurrence features
 
* The Type of features wanted: Run length features or co-occurrence features
 
* All the parameters necessary to run each algorithms
 
* All the parameters necessary to run each algorithms
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* The type of output wanted: texture features or texture maps
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* The type of outputs wanted: texture features or texture maps
 
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|[[Image:BoneTexture-GLCMParam.png|thumb|500px|GLCM Parameters]]
 
|[[Image:BoneTexture-GLCMParam.png|thumb|500px|GLCM Parameters]]
 
|[[Image:BoneTexture-GLRLMParam.png|thumb|500px| GLRLM Parameters]]
 
|[[Image:BoneTexture-GLRLMParam.png|thumb|500px| GLRLM Parameters]]
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|[[Image:BoneTexture-BMParam.png|thumb|500px| BM Parameters]]
 
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{|
 
{|
 
|[[Image:BoneTextureSerializer-Exportation.png|thumb|500px|Image:BoneTextureSerializer Image:BoneTextureSerializer]]
 
|[[Image:BoneTextureSerializer-Exportation.png|thumb|500px|Image:BoneTextureSerializer Image:BoneTextureSerializer]]
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|This section allow the folder where all the results will be saved:
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|This section allows the user to specify the folder where all the results will be saved:
 
* The texture features for the whole image will be saved in a csv file
 
* The texture features for the whole image will be saved in a csv file
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* The texture maps can ether be saved all in a same file (a diffusion weighted image containing all the feature maps of a defined case) or separated (each feature map will be saved as a single volume)
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* The texture maps can either be saved all in a same file (a diffusion weighted image containing all the feature maps of a case) or separated (each feature map will be saved as a single volume)
 
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Latest revision as of 21:58, 17 October 2017

Home < Documentation < Nightly < Modules < BoneTextureSerializer


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 provides a simple way to serialize the BoneTexture module.
In order to make it work, all the input data should be in the same folder and named as following:

  • The input scan should be named ScanXXX.nrrd, where XXX is the ID of the case
  • If it exists, the input mask should be named SegmCXXX.nrrd, where XXX is the ID corresponding to the the input scan

Interface

BoneTextureSerializer-Interface.png

Use Cases

Inputs

BoneTextureSerializer Input
 This section allows the user to specify the input folder, the folder specified should contain all the inputs (scans and segmentations) as described previously.

Parameters

BoneTextureSerializer parameters
 This section allows the user to choose:
  • The Type of features wanted: Run length features or co-occurrence features
  • All the parameters necessary to run each algorithms
  • The type of outputs wanted: texture features or texture maps
GLCM Parameters
GLRLM Parameters
BM Parameters

Exportation

Image:BoneTextureSerializer Image:BoneTextureSerializer
 This section allows the user to specify the folder where all the results will be saved:
  • The texture features for the whole image will be saved in a csv file
  • The texture maps can either be saved all in a same file (a diffusion weighted image containing all the feature maps of a case) or separated (each feature map will be saved as a single volume)

Additional Information

Similar Modules

N/A

Information for Developers

The source code is available on github

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