https://www.slicer.org/w/api.php?action=feedcontributions&user=Jb.vimort&feedformat=atomSlicer Wiki - User contributions [en]2024-03-29T04:39:50ZUser contributionsMediaWiki 1.33.0https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/SlicerVirtualReality&diff=58513Documentation/Nightly/Extensions/SlicerVirtualReality2018-02-07T21:57:21Z<p>Jb.vimort: </p>
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Extension: [[Documentation/{{documentation/version}}/Extensions/SlicerVirtualReality|SlicerVirtualReality]]<br><br />
Acknowledgments:<br />
This work was supported by .<br><br />
Author1: Jean-Baptiste Vimort ({{collaborator|name|kitware}})<br><br />
Author2: Jean-Christophe Fillion-Robin ({{collaborator|name|kitware}})<br><br />
Contributor1: Csaba Pinter (PerkLab, Queen's University)<br><br />
Contact: Jean-Christophe Fillion-Robin Aucoin, <email>jchris.fillionr@kitware.com</email><br><br />
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{{documentation/{{documentation/version}}/module-section|Extension Description}}<br />
[[File:SlicerVirtualReality.png|x200px]]<br />
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This extension enables user to interact with a Slicer scene using virtual reality. It integrates the [https://vtk.org VTK OpenVR] module and allow to support devices implementing [https://github.com/ValveSoftware/openvr/wiki/API-Documentation OpenVR interface].<br />
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This extension allows to modify the scene from Slicer's 3D View (left) and the VR View (right)<br />
{|<br />
|[[Image:SlicerVirtualReality_Screenshot1.png|thumb|700px|Modification of the scene from the 3D View]]<br />
|[[Image:SlicerVirtualReality_Screenshot2.png|thumb|700px|Modification of the scene from the VR View]]<br />
|}<br />
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{{documentation/{{documentation/version}}/module-section|Similar Extensions}}<br />
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* The [[Documentation/{{documentation/version}}/Extensions/OpenCVExample | OpenCVExample]] extension depends on this module and provides a template for linking and using OpenCV.<br />
* The [https://github.com/SBU-BMI/SlicerPathology Slicer Pathology] extension uses the SlicerOpenCV extension <br />
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{{documentation/{{documentation/version}}/module-section|References}}<br />
* [https://vtk.org Visualization Toolkit (VTK)]<br />
* [https://github.com/ValveSoftware/openvr#readme OpenVR] <br />
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[[Category:Documentation/{{documentation/version}}/Modules/Libraries]]<br />
<!-- ---------------------------- --></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=File:SlicerVirtualReality_Screenshot2.png&diff=58512File:SlicerVirtualReality Screenshot2.png2018-02-07T21:29:28Z<p>Jb.vimort: </p>
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<div></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=File:SlicerVirtualReality_Screenshot1.png&diff=58511File:SlicerVirtualReality Screenshot1.png2018-02-07T21:28:56Z<p>Jb.vimort: </p>
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<div></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/BoneTextureSerializer&diff=55145Documentation/Nightly/Modules/BoneTextureSerializer2017-10-17T21:58:05Z<p>Jb.vimort: </p>
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'''''Extensions:''''' [https://www.slicer.org/wiki/Documentation/Nightly/Extensions/BoneTextureExtesion BoneTextureExtesion]<br><br />
'''''Author:''''' Jean-Baptise Vimort, Kitware Inc.<br><br />
'''''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)<br><br />
'''''Contact:''''' Jean-Baptiste Vimort, <email>jb.vimort@kitware.com</email><br><br />
'''''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<br />
Temporomandibular Joint Osteoarthritis) and National Institute of Biomedical Imaging and Bioengineering NIBIB) grant R01EB021391 (Shape Analysis Toolbox for Medical Image Computing Projects).<br><br />
'''''License:''''' [http://www.apache.org/licenses/LICENSE-2.0.html Apache License, Version 2.0]<br />
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<gallery><br />
Image:Kitware-logo.png|Kitware Inc.<br />
Image:UofM-logo.png|University of Michigan<br />
</gallery><br />
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{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
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This module provides a simple way to serialize the BoneTexture module.<br><br />
In order to make it work, all the input data should be in the same folder and named as following:<br />
* The input scan should be named ScanXXX.nrrd, where XXX is the ID of the case<br />
* If it exists, the input mask should be named SegmCXXX.nrrd, where XXX is the ID corresponding to the the input scan<br />
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{{documentation/{{documentation/version}}/module-section|Interface}}<br />
{|<br />
|[[Image:BoneTextureSerializer-Interface.png|thumb|500px]]<br />
|<br />
|}<br />
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{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
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==Inputs==<br />
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{|<br />
|[[Image:BoneTextureSerealizer-Input.png|thumb|500px|BoneTextureSerializer Input]]<br />
| This section allows the user to specify the input folder, the folder specified should contain all the inputs (scans and segmentations) as described previously.<br />
|}<br />
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==Parameters==<br />
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{|<br />
|[[Image:BoneTexture-Parameter.png|thumb|500px|BoneTextureSerializer parameters]]<br />
|This section allows the user to choose:<br />
* The Type of features wanted: Run length features or co-occurrence features<br />
* All the parameters necessary to run each algorithms<br />
* The type of outputs wanted: texture features or texture maps<br />
|}<br />
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{|<br />
|[[Image:BoneTexture-GLCMParam.png|thumb|500px|GLCM Parameters]]<br />
|[[Image:BoneTexture-GLRLMParam.png|thumb|500px| GLRLM Parameters]]<br />
|[[Image:BoneTexture-BMParam.png|thumb|500px| BM Parameters]]<br />
|}<br />
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==Exportation==<br />
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{|<br />
|[[Image:BoneTextureSerializer-Exportation.png|thumb|500px|Image:BoneTextureSerializer Image:BoneTextureSerializer]]<br />
|This section allows the user to specify the folder where all the results will be saved:<br />
* The texture features for the whole image will be saved in a csv file<br />
* 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)<br />
|}<br />
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{{documentation/{{documentation/version}}/module-section|Additional Information}}<br />
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* [http://www.insight-journal.org/browse/publication/985 InsightJournal article]<br />
* [https://github.com/InsightSoftwareC BoneTextureExtension Tutorial]<br />
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{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
The source code is available on [https://github.com/Kitware/BoneTextureExtension/tree/master/BoneTextureSerializer github]<br />
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{{documentation/{{documentation/version}}/module-footer}}<br />
[[Category:Documentation/{{documentation/version}}/Modules/ShapeAnalysis]]<br />
<!-- ---------------------------- --></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=File:BoneTexture-BMParam.png&diff=55144File:BoneTexture-BMParam.png2017-10-17T21:57:20Z<p>Jb.vimort: </p>
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<div></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/BoneTexture&diff=55143Documentation/Nightly/Modules/BoneTexture2017-10-17T21:57:01Z<p>Jb.vimort: </p>
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<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
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{{documentation/{{documentation/version}}/module-header}}<br />
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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
<br />
'''''Extensions:''''' [https://www.slicer.org/wiki/Documentation/Nightly/Extensions/BoneTextureExtesion BoneTextureExtesion]<br><br />
'''''Author:''''' Jean-Baptise Vimort, Kitware Inc.<br><br />
'''''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)<br><br />
'''''Contact:''''' Jean-Baptiste Vimort, <email>jb.vimort@kitware.com</email><br><br />
'''''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<br />
Temporomandibular Joint Osteoarthritis) and National Institute of Biomedical Imaging and Bioengineering NIBIB) grant R01EB021391 (Shape Analysis Toolbox for Medical Image Computing Projects).<br><br />
'''''License:''''' [http://www.apache.org/licenses/LICENSE-2.0.html Apache License, Version 2.0]<br />
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<gallery><br />
Image:Kitware-logo.png|Kitware Inc.<br />
Image:UofM-logo.png|University of Michigan<br />
</gallery><br />
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This module provide a simple and dynamic user interface that allows:<br />
* to use [[Documentation/{{documentation/version}}/Modules/ComputeGLCMFeatureMaps|ComputeGLCMFeatureMaps]], [[Documentation/{{documentation/version}}/Modules/ComputeGLCMFeatures|ComputeGLCMFeatures]], [[Documentation/{{documentation/version}}/Modules/ComputeGLRLMFeatureMaps|ComputeGLRLMFeatureMaps]] and [[Documentation/{{documentation/version}}/Modules/ComputeGLRLMFeatures|ComputeGLRLMFeatures]].<br><br />
* to easily modify the parameters and choose the wanted outputs in order to fit to each case studied in the best way possible.<br />
* to observe each outputs generated to be able to verify their consistency and hypothetically re-run the algorithm with a different parameter set. <br />
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{|<br />
|[[Image:BoneTexture-Interface.png|thumb|500px]]<br />
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{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
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==Inputs==<br />
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{|<br />
|[[Image:BoneTexture-Input.png|thumb|500px|BoneTexture Inputs]]<br />
| This section allows the user to specify:<br />
* The input scan: it's interesting to notice that the computation time will improve if the useful data is taking as much space as possible in the input scan (a preliminary cropping step might be considered in order to erase the useless data on the boundaries)<br />
* An input mask: the mask is optional, therefore it will reduce the computation time of the algorithms<br />
|}<br />
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==Parameters==<br />
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{|<br />
|[[Image:BoneTexture-Parameter.png|thumb|500px|BoneTexture parameters]]<br />
|This section allows the user to choose:<br />
* The Type of features wanted: Run length features or co-occurrence features<br />
* All the parameters necessary to run each algorithms<br />
* The type of outputs wanted: texture features or texture maps<br />
|}<br />
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{|<br />
|[[Image:BoneTexture-GLCMParam.png|thumb|500px|GLCM Parameters]]<br />
|[[Image:BoneTexture-GLRLMParam.png|thumb|500px| GLRLM Parameters]]<br />
|[[Image:BoneTexture-BMParam.png|thumb|500px| BM Parameters]]<br />
|}<br />
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==Result display==<br />
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===Texture features===<br />
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{|<br />
|[[Image:BoneTexture-FeatureValues.png|thumb|500px|Texture features result]]<br />
|The texture features computed over the whole input scan will be displayed in this table. <br />
|}<br />
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===Texture Maps===<br />
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{|<br />
|[[Image:BoneTexture-DisplayColormaps.png|thumb|500px|Texture map choice]]<br />
|This section allows the user to easily observe the texture maps generated. <br><br />
The first drop down menu allow to choose the texture map set (usually GLCM or CLRLM).<br />
|}<br />
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{|<br />
|[[Image:BoneTexture-FeatureSelection.png|thumb|500px|Feature choice]]<br />
|The second drop down menu allow to choose the feature displayed in the 3D view of Slicer. <br />
|}<br />
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{{documentation/{{documentation/version}}/module-section|Additional Information}}<br />
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* [http://www.insight-journal.org/browse/publication/985 InsightJournal article]<br />
* [https://github.com/InsightSoftwareC BoneTextureExtension Tutorial]<br />
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{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
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{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
The source code is available on [https://github.com/Kitware/BoneTextureExtension/tree/master/BoneTexture github]<br />
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{{documentation/{{documentation/version}}/module-footer}}<br />
[[Category:Documentation/{{documentation/version}}/Modules/ShapeAnalysis]]<br />
<!-- ---------------------------- --></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=File:BoneTexture-Parameter.png&diff=55142File:BoneTexture-Parameter.png2017-10-17T21:56:15Z<p>Jb.vimort: Jb.vimort uploaded a new version of File:BoneTexture-Parameter.png</p>
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<div></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=File:BoneTextureSerializer-Interface.png&diff=55141File:BoneTextureSerializer-Interface.png2017-10-17T21:49:36Z<p>Jb.vimort: Jb.vimort uploaded a new version of File:BoneTextureSerializer-Interface.png</p>
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<div></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=File:BoneTexture-Interface.png&diff=55140File:BoneTexture-Interface.png2017-10-17T21:49:17Z<p>Jb.vimort: Jb.vimort uploaded a new version of File:BoneTexture-Interface.png</p>
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<div></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=File:BSBV.eps&diff=55139File:BSBV.eps2017-10-17T21:48:23Z<p>Jb.vimort: </p>
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<div></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=File:TbN.eps&diff=55138File:TbN.eps2017-10-17T21:48:10Z<p>Jb.vimort: </p>
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<div></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=File:TbSp.eps&diff=55137File:TbSp.eps2017-10-17T21:47:56Z<p>Jb.vimort: </p>
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<div></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=File:TbTh.eps&diff=55136File:TbTh.eps2017-10-17T21:47:41Z<p>Jb.vimort: </p>
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<div></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=File:BVTV.eps&diff=55135File:BVTV.eps2017-10-17T21:47:21Z<p>Jb.vimort: Jb.vimort uploaded a new version of File:BVTV.eps</p>
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<div></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=File:BVTV.eps&diff=55134File:BVTV.eps2017-10-17T21:42:18Z<p>Jb.vimort: </p>
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<div></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/BoneTextureExtension&diff=55133Documentation/Nightly/Extensions/BoneTextureExtension2017-10-17T21:42:08Z<p>Jb.vimort: </p>
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<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
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{{documentation/{{documentation/version}}/module-header}}<br />
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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
'''''Author:''''' Jean-Baptise Vimort, Kitware Inc.<br><br />
'''''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)<br><br />
'''''Contact:''''' Jean-Baptiste Vimort, <email>jb.vimort@kitware.com</email><br><br />
'''''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<br />
Temporomandibular Joint Osteoarthritis) and National Institute of Biomedical Imaging and Bioengineering NIBIB) grant R01EB021391 (Shape Analysis Toolbox for Medical Image Computing Projects).<br><br />
'''''License:''''' [http://www.apache.org/licenses/LICENSE-2.0.html Apache License, Version 2.0]<br />
<gallery><br />
Image:Kitware-logo.png|Kitware Inc.<br />
Image:UofM-logo.png|University of Michigan<br />
</gallery><br />
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{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
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{|<br />
|[[Image:Logo-BoneTextureExtension.png|250px]]<br />
|<br />
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 [http://www.insight-journal.org/browse/publication/985 itkTextureFeatures]<br />
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Key Features:<br />
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* Estimated texture features:<br />
** 8 co-occurrence textural features: energy, entropy, correlation, inverse difference moment, inertia, cluster shade, cluster prominence and Haralick correlation<br />
** 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.<br />
* 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.<br />
|}<br />
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{{documentation/{{documentation/version}}/module-section|Usage}}<br />
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==Main modules interface==<br />
{|<br />
|[[Image:BoneTexture-Interface.png|thumb|400px|BoneTexture User Interface]]<br />
|[[Image:BoneTextureSerializer-Interface.png|thumb|400px|BoneTextureSerializer User Interface]]<br />
|}<br />
==Input example==<br />
{|<br />
|[[Image:Scan.eps|thumb|400px|Input scan]]<br />
|[[Image:CondileMask.eps|thumb|345px|Input mask]]<br />
|}<br />
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==Texture features==<br />
{|<br />
|[[Image:TextureFeaturesTab.png|thumb|600px|Texture feature result table]]<br />
|}<br />
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==Texture feature maps==<br />
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===Co-occurrence texture feature maps===<br />
{|<br />
|[[Image:Energy.eps|thumb|200px|Energy]]<br />
|[[Image:Entropy.eps|thumb|200px|Entropy]]<br />
|[[Image:Correlation.eps|thumb|200px|Correlation]]<br />
|[[Image:InverseDifferenceMoment.eps|thumb|200px|Inverse difference moment]]<br />
|[[Image:ColorBar.jpg|thumb|112px]]<br />
|}<br />
{|<br />
|[[Image:Inertia.eps|thumb|200px|Inertia]]<br />
|[[Image:ClusterShade.eps|thumb|200px|Cluster shade]]<br />
|[[Image:ClusterProminence.eps|thumb|200px|Cluster prominence]]<br />
|[[Image:HaralickCorrelation.eps|thumb|200px|Haralick correlation]]<br />
|[[Image:ColorBar.jpg|thumb|112px]]<br />
|}<br />
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===Run Length texture feature maps===<br />
{|<br />
|[[Image:ShortRunEmphasis.eps|thumb|200px|Short run emphasis]]<br />
|[[Image:LongRunEmphasis.eps|thumb|200px|Long run emphasis]]<br />
|[[Image:GreyLevelnonUniformity.eps|thumb|200px|Grey level non uniformity]]<br />
|[[Image:RunLengthnonUniformity.eps|thumb|200px|Run length non uniformity]]<br />
|[[Image:LowGreyLevelRunEmphasis.eps|thumb|200px|Low grey level run emphasis]]<br />
|[[Image:ColorBar.jpg|thumb|112px]]<br />
|}<br />
{|<br />
|[[Image:HighGreyLevelRunEmphasis.eps|thumb|200px|High grey level run emphasis]]<br />
|[[Image:ShortRunLowGreyLevelEmphasis.eps|thumb|200px|Short run low grey level emphasis]]<br />
|[[Image:ShortRunHighGreyLevelEmphasis.eps|thumb|200px|Short run high grey level emphasis]]<br />
|[[Image:LongRunLowGreyLevelEmphasis.eps|thumb|200px|Long run low grey level emphasis]]<br />
|[[Image:LongRunHighGreyLevelEmphasis.eps|thumb|200px|Long run high grey level emphasis]]<br />
|[[Image:ColorBar.jpg|thumb|112px]]<br />
|}<br />
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===Bone Morphometry feature maps===<br />
{|<br />
|[[Image:BVTV.eps|thumb|200px|BVTV]]<br />
|[[Image:TbTh.eps|thumb|200px|TbTh]]<br />
|[[Image:TbSp.eps|thumb|200px|TbSp]]<br />
|[[Image:TbN.eps|thumb|200px|TbN]]<br />
|[[Image:BSBV.eps|thumb|200px|BSBV]]<br />
|[[Image:ColorBar.jpg|thumb|112px]]<br />
|}<br />
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{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
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*[[Documentation/{{documentation/version}}/Modules/BoneTexture|BoneTexture]]<br />
*[[Documentation/{{documentation/version}}/Modules/BoneTextureSerializer|BoneTextureSerializer]]<br />
*[[Documentation/{{documentation/version}}/Modules/ComputeGLCMFeatureMaps|ComputeGLCMFeatureMaps]]<br />
*[[Documentation/{{documentation/version}}/Modules/ComputeGLCMFeatures|ComputeGLCMFeatures]]<br />
*[[Documentation/{{documentation/version}}/Modules/ComputeGLRLMFeatureMaps|ComputeGLRLMFeatureMaps]]<br />
*[[Documentation/{{documentation/version}}/Modules/ComputeGLRLMFeatures|ComputeGLRLMFeatures]]<br />
*[[Documentation/{{documentation/version}}/Modules/ComputeBMFeatureMaps|ComputeBMFeatureMaps]]<br />
*[[Documentation/{{documentation/version}}/Modules/ComputeBMFeatures|ComputeBMFeatures]]<br />
*[[Documentation/{{documentation/version}}/Modules/SeparateVectorImage|SeparateVectorImage]]<br />
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{{documentation/{{documentation/version}}/module-section|Additional Information}}<br />
<br />
* [http://www.insight-journal.org/browse/publication/985 InsightJournal article]<br />
* [https://github.com/InsightSoftwareC BoneTextureExtension Tutorial]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
N/A<br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
<br />
The source code is available on [https://github.com/Kitware/BoneTextureExtension github]<br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=File:TextureFeaturesTab.png&diff=55132File:TextureFeaturesTab.png2017-10-17T21:25:54Z<p>Jb.vimort: Jb.vimort uploaded a new version of File:TextureFeaturesTab.png</p>
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<div></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=File:TextureFeaturesTab.png&diff=55131File:TextureFeaturesTab.png2017-10-17T21:24:56Z<p>Jb.vimort: Jb.vimort uploaded a new version of File:TextureFeaturesTab.png</p>
<hr />
<div></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=File:ComputeBMFeatures-Interface.png&diff=55130File:ComputeBMFeatures-Interface.png2017-10-17T21:23:36Z<p>Jb.vimort: </p>
<hr />
<div></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=File:ComputeBMFeatureMaps-Interface.png&diff=55129File:ComputeBMFeatureMaps-Interface.png2017-10-17T21:23:12Z<p>Jb.vimort: </p>
<hr />
<div></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/ComputeBMFeatureMaps&diff=55115Documentation/Nightly/Modules/ComputeBMFeatureMaps2017-10-16T23:50:35Z<p>Jb.vimort: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
<br />
'''''Extensions:''''' [https://www.slicer.org/wiki/Documentation/Nightly/Extensions/BoneTextureExtesion BoneTextureExtesion]<br><br />
'''''Author:''''' Jean-Baptise Vimort, Kitware Inc.<br><br />
'''''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)<br><br />
'''''Contact:''''' Jean-Baptiste Vimort, <email>jb.vimort@kitware.com</email><br><br />
'''''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<br />
Temporomandibular Joint Osteoarthritis) and National Institute of Biomedical Imaging and Bioengineering NIBIB) grant R01EB021391 (Shape Analysis Toolbox for Medical Image Computing Projects).<br><br />
'''''License:''''' [http://www.apache.org/licenses/LICENSE-2.0.html Apache License, Version 2.0]<br />
<br />
<gallery><br />
Image:Kitware-logo.png|Kitware Inc.<br />
Image:UofM-logo.png|University of Michigan<br />
</gallery><br />
<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<!-- ---------------------------- --><br />
This module can be used in order to compute bone morphometry feature maps of an input image. The computation of the bone morphometry features is based on a binary segmentation of the whole image and it based on the itk remote module: itkBoneMorphometry [https://github.com/InsightSoftwareConsortium/ITKBoneMorphometry itkBoneMorphometry].<br><br />
The following Bone Morphompetry Features are computed: <br />
* percent bone volume [BVTV]<br />
* trabecular thickness [TbTh]<br />
* trabecular separation [TbSp]<br />
* trabecular number [TbN]<br />
* Bone Surface to Bone Volume ratio [BSBV]<br />
<br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
{|<br />
|[[Image:ComputeBMFeatureMaps-Interface.png|500px]]<br />
|<br />
* <span style="color:blue">'''''Inputs'''''</span>: <br />
** <span style="color:green">'''Input volume'''</span> [<span style="color:orange">index: 0</span>] : Input Volume<br />
** <span style="color:green">'''Output volume'''</span> [<span style="color:orange">index: 1</span>] : Output diffusion-weighted volume where the 8 feature maps will be stored<br />
** <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<br />
** <span style="color:green">'''Threshold'''</span> [<span style="color:orange">-i --inputMask</span>] (<span style="color:purple">0</span>) : The threshold value that will be used for the binary segmentation of the image<br />
** <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<br />
<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Additional Information}}<br />
<br />
* [https://github.com/InsightSoftwareC BoneTextureExtension Tutorial]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
The source code is available on [https://github.com/Kitware/BoneTextureExtension/tree/master/ComputeBMFeatureMaps github]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
[[Category:Documentation/{{documentation/version}}/Modules/ShapeAnalysis]]<br />
<!-- ---------------------------- --></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/ComputeBMFeatures&diff=55114Documentation/Nightly/Modules/ComputeBMFeatures2017-10-16T23:49:34Z<p>Jb.vimort: Created page with "<noinclude>{{documentation/versioncheck}}</noinclude> <!-- ---------------------------- --> {{documentation/{{documentation/version}}/module-header}} <!-- --------------------..."</p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
<br />
'''''Extensions:''''' [https://www.slicer.org/wiki/Documentation/Nightly/Extensions/BoneTextureExtesion BoneTextureExtesion]<br><br />
'''''Author:''''' Jean-Baptise Vimort, Kitware Inc.<br><br />
'''''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)<br><br />
'''''Contact:''''' Jean-Baptiste Vimort, <email>jb.vimort@kitware.com</email><br><br />
'''''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<br />
Temporomandibular Joint Osteoarthritis) and National Institute of Biomedical Imaging and Bioengineering NIBIB) grant R01EB021391 (Shape Analysis Toolbox for Medical Image Computing Projects).<br><br />
'''''License:''''' [http://www.apache.org/licenses/LICENSE-2.0.html Apache License, Version 2.0]<br />
<br />
<gallery><br />
Image:Kitware-logo.png|Kitware Inc.<br />
Image:UofM-logo.png|University of Michigan<br />
</gallery><br />
<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<!-- ---------------------------- --><br />
This module can be used in order to compute bone morphometry features of an input image. The computation of the bone morphometry features is based on a binary segmentation of the whole image and it based on the itk remote module: itkBoneMorphometry [https://github.com/InsightSoftwareConsortium/ITKBoneMorphometry itkBoneMorphometry].<br><br />
The following Bone Morphompetry Features are computed: <br />
* percent bone volume [BVTV]<br />
* trabecular thickness [TbTh]<br />
* trabecular separation [TbSp]<br />
* trabecular number [TbN]<br />
* Bone Surface to Bone Volume ratio [BSBV]<br />
<br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
{|<br />
|[[Image:ComputeBMFeatures-Interface.png|500px]]<br />
|<br />
* <span style="color:blue">'''''Inputs'''''</span>: <br />
** <span style="color:green">'''Input volume'''</span> [<span style="color:orange">index: 0</span>] : Input Volume<br />
** <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<br />
** <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<br />
** <span style="color:green">'''Threshold'''</span> [<span style="color:orange">-i --inputMask</span>] (<span style="color:purple">0</span>) : The threshold value that will be used for the binary segmentation of the image<br />
** <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<br />
* <span style="color:blue">'''''Outputs'''''</span>: <br />
** <span style="color:green">'''BVTV'''</span> [<span style="color:orange">output</span>] : percent bone volume feature value<br />
** <span style="color:green">'''TbTh'''</span> [<span style="color:orange">output</span>] : trabecular thickness feature value<br />
** <span style="color:green">'''TbSp'''</span> [<span style="color:orange">output</span>] : trabecular separation feature value<br />
** <span style="color:green">'''TbN'''</span> [<span style="color:orange">output</span>] :trabecular number feature value<br />
** <span style="color:green">'''BSBV'''</span> [<span style="color:orange">output</span>] : Bone Surface to Bone Volume ratio feature value<br />
* <span style="color:blue">'''''Advanced'''''</span>: <br />
** <span style="color:green">'''Output Vector'''</span> [<span style="color:orange">output</span>] : Output vector containing all the feature value stored in the same order than previously <br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Additional Information}}<br />
<br />
* [https://github.com/InsightSoftwareC BoneTextureExtension Tutorial]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
The source code is available on [https://github.com/Kitware/BoneTextureExtension/tree/master/ComputeBMFeatures github]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
[[Category:Documentation/{{documentation/version}}/Modules/ShapeAnalysis]]<br />
<!-- ---------------------------- --></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/ComputeBMFeatureMaps&diff=55113Documentation/Nightly/Modules/ComputeBMFeatureMaps2017-10-16T23:20:35Z<p>Jb.vimort: Created page with "<noinclude>{{documentation/versioncheck}}</noinclude> <!-- ---------------------------- --> {{documentation/{{documentation/version}}/module-header}} <!-- --------------------..."</p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
<br />
'''''Extensions:''''' [https://www.slicer.org/wiki/Documentation/Nightly/Extensions/BoneTextureExtesion BoneTextureExtesion]<br><br />
'''''Author:''''' Jean-Baptise Vimort, Kitware Inc.<br><br />
'''''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)<br><br />
'''''Contact:''''' Jean-Baptiste Vimort, <email>jb.vimort@kitware.com</email><br><br />
'''''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<br />
Temporomandibular Joint Osteoarthritis) and National Institute of Biomedical Imaging and Bioengineering NIBIB) grant R01EB021391 (Shape Analysis Toolbox for Medical Image Computing Projects).<br><br />
'''''License:''''' [http://www.apache.org/licenses/LICENSE-2.0.html Apache License, Version 2.0]<br />
<br />
<gallery><br />
Image:Kitware-logo.png|Kitware Inc.<br />
Image:UofM-logo.png|University of Michigan<br />
</gallery><br />
<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<!-- ---------------------------- --><br />
This module can be used in order to compute bone morphometry features maps of an input image. The computation of the bone morphometry features is based on a binary segmentation of the whole image and it based on the itk remote module: itkBoneMorphometry [https://github.com/InsightSoftwareConsortium/ITKBoneMorphometry itkBoneMorphometry].<br><br />
The following Bone Morphompetry Features are computed: <br />
* percent bone volume [BVTV]<br />
* trabecular thickness [TbTh]<br />
* trabecular separation [TbSp]<br />
* trabecular number [TbN]<br />
* Bone Surface to Bone Volume ratio [BSBV]<br />
<br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
{|<br />
|[[Image:ComputeBMFeatureMaps-Interface.png|500px]]<br />
|<br />
* <span style="color:blue">'''''Inputs'''''</span>: <br />
** <span style="color:green">'''Input volume'''</span> [<span style="color:orange">index: 0</span>] : Input Volume<br />
** <span style="color:green">'''Output volume'''</span> [<span style="color:orange">index: 1</span>] : Output diffusion-weighted volume where the 8 feature maps will be stored<br />
** <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<br />
** <span style="color:green">'''Threshold'''</span> [<span style="color:orange">-i --inputMask</span>] (<span style="color:purple">0</span>) : The threshold value that will be used for the binary segmentation of the image<br />
** <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<br />
<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Additional Information}}<br />
<br />
* [https://github.com/InsightSoftwareC BoneTextureExtension Tutorial]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
The source code is available on [https://github.com/Kitware/BoneTextureExtension/tree/master/ComputeBMFeatureMaps github]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
[[Category:Documentation/{{documentation/version}}/Modules/ShapeAnalysis]]<br />
<!-- ---------------------------- --></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/ComputeGLRLMFeatureMaps&diff=53017Documentation/Nightly/Modules/ComputeGLRLMFeatureMaps2017-07-13T14:36:43Z<p>Jb.vimort: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
<br />
'''''Extensions:''''' [https://www.slicer.org/wiki/Documentation/Nightly/Extensions/BoneTextureExtesion BoneTextureExtesion]<br><br />
'''''Author:''''' Jean-Baptise Vimort, Kitware Inc.<br><br />
'''''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)<br><br />
'''''Contact:''''' Jean-Baptiste Vimort, <email>jb.vimort@kitware.com</email><br><br />
'''''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<br />
Temporomandibular Joint Osteoarthritis) and National Institute of Biomedical Imaging and Bioengineering NIBIB) grant R01EB021391 (Shape Analysis Toolbox for Medical Image Computing Projects).<br><br />
'''''License:''''' [http://www.apache.org/licenses/LICENSE-2.0.html Apache License, Version 2.0]<br />
<br />
<gallery><br />
Image:Kitware-logo.png|Kitware Inc.<br />
Image:UofM-logo.png|University of Michigan<br />
</gallery><br />
<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<!-- ---------------------------- --><br />
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><br />
The GLRLM matrix describes each neighborhood local texture, it is then used to compute the following run length texture features: <br />
* short run emphasis<br />
* long run emphasis<br />
* grey level non uniformity<br />
* run length non uniformity<br />
* low grey level run emphasis<br />
* high grey level run emphasis<br />
* short run low grey level emphasis<br />
* short run high grey level emphasis<br />
* long run low grey level emphasis<br />
* long run high grey level emphasis<br />
<br />
<br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
{|<br />
|[[Image:ComputeGLRLMFeatureMaps-Interface.png|500px]]<br />
|<br />
* <span style="color:blue">'''''Inputs'''''</span>: <br />
** <span style="color:green">'''Input volume'''</span> [<span style="color:orange">index: 0</span>] : Input Volume<br />
** <span style="color:green">'''Output volume'''</span> [<span style="color:orange">index: 1</span>] : Output diffusion-weighted volume where the 10 feature maps will be stored<br />
** <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<br />
** <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<br />
** <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<br />
** <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<br />
** <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<br />
** <span style="color:green">'''Pixel Intensity Max'''</span> [<span style="color:orange">-P --pixelIntensityMax</span>] (<span style="color:purple">4000</span>) : Maximum of the pixel intensity range over which the features will be calculated<br />
** <span style="color:green">'''Distance Min'''</span> [<span style="color:orange">-d --distanceMin</span>] (<span style="color:purple">0.0</span>) : Minnimum of the distance range over which the features will be calculated<br />
** <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<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Additional Information}}<br />
<br />
* [http://www.insight-journal.org/browse/publication/985 InsightJournal article]<br />
* [https://github.com/InsightSoftwareC BoneTextureExtension Tutorial]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
The source code is available on [https://github.com/Kitware/BoneTextureExtension/tree/master/ComputeGLRLMFeatureMaps github]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
[[Category:Documentation/{{documentation/version}}/Modules/ShapeAnalysis]]<br />
<!-- ---------------------------- --></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/ComputeGLCMFeatureMaps&diff=53014Documentation/Nightly/Modules/ComputeGLCMFeatureMaps2017-07-13T14:35:48Z<p>Jb.vimort: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
<br />
'''''Extensions:''''' [https://www.slicer.org/wiki/Documentation/Nightly/Extensions/BoneTextureExtesion BoneTextureExtesion]<br><br />
'''''Author:''''' Jean-Baptise Vimort, Kitware Inc.<br><br />
'''''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)<br><br />
'''''Contact:''''' Jean-Baptiste Vimort, <email>jb.vimort@kitware.com</email><br><br />
'''''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<br />
Temporomandibular Joint Osteoarthritis) and National Institute of Biomedical Imaging and Bioengineering NIBIB) grant R01EB021391 (Shape Analysis Toolbox for Medical Image Computing Projects).<br><br />
'''''License:''''' [http://www.apache.org/licenses/LICENSE-2.0.html Apache License, Version 2.0]<br />
<br />
<gallery><br />
Image:Kitware-logo.png|Kitware Inc.<br />
Image:UofM-logo.png|University of Michigan<br />
</gallery><br />
<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<!-- ---------------------------- --><br />
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 co-occurrence matrix (GLCM) computed with [https://itk.org/Doxygen/html/classitk_1_1Statistics_1_1ScalarImageToTextureFeaturesFilter.html itk::itkCooccurrenceTextureFeaturesImageFilter] for each pixel’s neighborhood.<br><br />
The GLCM matrix describes each neighborhood local texture, it is then used to compute the following co-occurrence texture features: <br />
* Energy<br />
* Entropy<br />
* Correlation<br />
* Inverse difference moment<br />
* Inertia<br />
* Cluster shade<br />
* Cluster prominence<br />
* Haralick correlation<br />
<br />
<br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
{|<br />
|[[Image:ComputeGLCMFeatureMaps-Interface.png|500px]]<br />
|<br />
* <span style="color:blue">'''''Inputs'''''</span>: <br />
** <span style="color:green">'''Input volume'''</span> [<span style="color:orange">index: 0</span>] : Input Volume<br />
** <span style="color:green">'''Output volume'''</span> [<span style="color:orange">index: 1</span>] : Output diffusion-weighted volume where the 8 feature maps will be stored<br />
** <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<br />
** <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<br />
** <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<br />
** <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<br />
** <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<br />
** <span style="color:green">'''Pixel Intensity Max'''</span> [<span style="color:orange">-P --pixelIntensityMax</span>] (<span style="color:purple">4000</span>) : Maximum of the pixel intensity range over which the features will be calculated<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Additional Information}}<br />
<br />
* [http://www.insight-journal.org/browse/publication/985 InsightJournal article]<br />
* [https://github.com/InsightSoftwareC BoneTextureExtension Tutorial]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
The source code is available on [https://github.com/Kitware/BoneTextureExtension/tree/master/ComputeGLCMFeatureMaps github]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
[[Category:Documentation/{{documentation/version}}/Modules/ShapeAnalysis]]<br />
<!-- ---------------------------- --></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/BoneTextureExtension&diff=52940Documentation/Nightly/Extensions/BoneTextureExtension2017-07-10T19:58:12Z<p>Jb.vimort: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
'''''Author:''''' Jean-Baptise Vimort, Kitware Inc.<br><br />
'''''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)<br><br />
'''''Contact:''''' Jean-Baptiste Vimort, <email>jb.vimort@kitware.com</email><br><br />
'''''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<br />
Temporomandibular Joint Osteoarthritis) and National Institute of Biomedical Imaging and Bioengineering NIBIB) grant R01EB021391 (Shape Analysis Toolbox for Medical Image Computing Projects).<br><br />
'''''License:''''' [http://www.apache.org/licenses/LICENSE-2.0.html Apache License, Version 2.0]<br />
<gallery><br />
Image:Kitware-logo.png|Kitware Inc.<br />
Image:UofM-logo.png|University of Michigan<br />
</gallery><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
<br />
{|<br />
|[[Image:Logo-BoneTextureExtension.png|250px]]<br />
|<br />
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 [http://www.insight-journal.org/browse/publication/985 itkTextureFeatures]<br />
<br />
Key Features:<br />
<br />
* Estimated texture features:<br />
** 8 co-occurrence textural features: energy, entropy, correlation, inverse difference moment, inertia, cluster shade, cluster prominence and Haralick correlation<br />
** 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.<br />
* 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.<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Usage}}<br />
<br />
==Main modules interface==<br />
{|<br />
|[[Image:BoneTexture-Interface.png|thumb|400px|BoneTexture User Interface]]<br />
|[[Image:BoneTextureSerializer-Interface.png|thumb|400px|BoneTextureSerializer User Interface]]<br />
|}<br />
==Input example==<br />
{|<br />
|[[Image:Scan.eps|thumb|400px|Input scan]]<br />
|[[Image:CondileMask.eps|thumb|345px|Input mask]]<br />
|}<br />
<br />
==Texture features==<br />
{|<br />
|[[Image:TextureFeaturesTab.png|thumb|600px|Texture feature result table]]<br />
|}<br />
<br />
==Texture feature maps==<br />
<br />
===Co-occurrence texture feature maps===<br />
{|<br />
|[[Image:Energy.eps|thumb|200px|Energy]]<br />
|[[Image:Entropy.eps|thumb|200px|Entropy]]<br />
|[[Image:Correlation.eps|thumb|200px|Correlation]]<br />
|[[Image:InverseDifferenceMoment.eps|thumb|200px|Inverse difference moment]]<br />
|[[Image:ColorBar.jpg|thumb|112px]]<br />
|}<br />
{|<br />
|[[Image:Inertia.eps|thumb|200px|Inertia]]<br />
|[[Image:ClusterShade.eps|thumb|200px|Cluster shade]]<br />
|[[Image:ClusterProminence.eps|thumb|200px|Cluster prominence]]<br />
|[[Image:HaralickCorrelation.eps|thumb|200px|Haralick correlation]]<br />
|[[Image:ColorBar.jpg|thumb|112px]]<br />
|}<br />
<br />
===Run Length texture feature maps===<br />
{|<br />
|[[Image:ShortRunEmphasis.eps|thumb|200px|Short run emphasis]]<br />
|[[Image:LongRunEmphasis.eps|thumb|200px|Long run emphasis]]<br />
|[[Image:GreyLevelnonUniformity.eps|thumb|200px|Grey level non uniformity]]<br />
|[[Image:RunLengthnonUniformity.eps|thumb|200px|Run length non uniformity]]<br />
|[[Image:LowGreyLevelRunEmphasis.eps|thumb|200px|Low grey level run emphasis]]<br />
|[[Image:ColorBar.jpg|thumb|112px]]<br />
|}<br />
{|<br />
|[[Image:HighGreyLevelRunEmphasis.eps|thumb|200px|High grey level run emphasis]]<br />
|[[Image:ShortRunLowGreyLevelEmphasis.eps|thumb|200px|Short run low grey level emphasis]]<br />
|[[Image:ShortRunHighGreyLevelEmphasis.eps|thumb|200px|Short run high grey level emphasis]]<br />
|[[Image:LongRunLowGreyLevelEmphasis.eps|thumb|200px|Long run low grey level emphasis]]<br />
|[[Image:LongRunHighGreyLevelEmphasis.eps|thumb|200px|Long run high grey level emphasis]]<br />
|[[Image:ColorBar.jpg|thumb|112px]]<br />
|}<br />
<br />
<br />
<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
*[[Documentation/{{documentation/version}}/Modules/BoneTexture|BoneTexture]]<br />
*[[Documentation/{{documentation/version}}/Modules/BoneTextureSerializer|BoneTextureSerializer]]<br />
*[[Documentation/{{documentation/version}}/Modules/ComputeGLCMFeatureMaps|ComputeGLCMFeatureMaps]]<br />
*[[Documentation/{{documentation/version}}/Modules/ComputeGLCMFeatures|ComputeGLCMFeatures]]<br />
*[[Documentation/{{documentation/version}}/Modules/ComputeGLRLMFeatureMaps|ComputeGLRLMFeatureMaps]]<br />
*[[Documentation/{{documentation/version}}/Modules/ComputeGLRLMFeatures|ComputeGLRLMFeatures]]<br />
*[[Documentation/{{documentation/version}}/Modules/SeparateVectorImage|SeparateVectorImage]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Additional Information}}<br />
<br />
* [http://www.insight-journal.org/browse/publication/985 InsightJournal article]<br />
* [https://github.com/InsightSoftwareC BoneTextureExtension Tutorial]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
<br />
The source code is available on [https://github.com/Kitware/BoneTextureExtension github]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=File:ColorBar.jpg&diff=52939File:ColorBar.jpg2017-07-10T19:54:22Z<p>Jb.vimort: </p>
<hr />
<div></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/BoneTextureExtension&diff=52936Documentation/Nightly/Extensions/BoneTextureExtension2017-07-10T19:54:07Z<p>Jb.vimort: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
'''''Author:''''' Jean-Baptise Vimort, Kitware Inc.<br><br />
'''''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)<br><br />
'''''Contact:''''' Jean-Baptiste Vimort, <email>jb.vimort@kitware.com</email><br><br />
'''''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<br />
Temporomandibular Joint Osteoarthritis) and National Institute of Biomedical Imaging and Bioengineering NIBIB) grant R01EB021391 (Shape Analysis Toolbox for Medical Image Computing Projects).<br><br />
'''''License:''''' [http://www.apache.org/licenses/LICENSE-2.0.html Apache License, Version 2.0]<br />
<gallery><br />
Image:Kitware-logo.png|Kitware Inc.<br />
Image:UofM-logo.png|University of Michigan<br />
</gallery><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
<br />
{|<br />
|[[Image:Logo-BoneTextureExtension.png|250px]]<br />
|<br />
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 [http://www.insight-journal.org/browse/publication/985 itkTextureFeatures]<br />
<br />
Key Features:<br />
<br />
* Estimated texture features:<br />
** 8 co-occurrence textural features: energy, entropy, correlation, inverse difference moment, inertia, cluster shade, cluster prominence and Haralick correlation<br />
** 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.<br />
* 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.<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Usage}}<br />
<br />
==Main modules interface==<br />
{|<br />
|[[Image:BoneTexture-Interface.png|thumb|400px|BoneTexture User Interface]]<br />
|[[Image:BoneTextureSerializer-Interface.png|thumb|400px|BoneTextureSerializer User Interface]]<br />
|}<br />
==Input example==<br />
{|<br />
|[[Image:Scan.eps|thumb|400px|Input scan]]<br />
|[[Image:CondileMask.eps|thumb|345px|Input mask]]<br />
|}<br />
<br />
==Texture features==<br />
{|<br />
|[[Image:TextureFeaturesTab.png|thumb|600px|Texture feature result table]]<br />
|}<br />
<br />
==Texture feature maps==<br />
<br />
===Co-occurrence texture feature maps===<br />
{|<br />
|[[Image:Energy.eps|thumb|200px|Energy]]<br />
|[[Image:Entropy.eps|thumb|200px|Entropy]]<br />
|[[Image:Correlation.eps|thumb|200px|Correlation]]<br />
|[[Image:InverseDifferenceMoment.eps|thumb|200px|Inverse difference moment]]<br />
|[[Image:ColorBar.jpg|thumb|200px|Inverse difference moment]]<br />
|}<br />
{|<br />
|[[Image:Inertia.eps|thumb|200px|Inertia]]<br />
|[[Image:ClusterShade.eps|thumb|200px|Cluster shade]]<br />
|[[Image:ClusterProminence.eps|thumb|200px|Cluster prominence]]<br />
|[[Image:HaralickCorrelation.eps|thumb|200px|Haralick correlation]]<br />
|[[Image:ColorBar.jpg|thumb|200px|Inverse difference moment]]<br />
|}<br />
<br />
===Run Length texture feature maps===<br />
{|<br />
|[[Image:ShortRunEmphasis.eps|thumb|200px|Short run emphasis]]<br />
|[[Image:LongRunEmphasis.eps|thumb|200px|Long run emphasis]]<br />
|[[Image:GreyLevelnonUniformity.eps|thumb|200px|Grey level non uniformity]]<br />
|[[Image:RunLengthnonUniformity.eps|thumb|200px|Run length non uniformity]]<br />
|[[Image:LowGreyLevelRunEmphasis.eps|thumb|200px|Low grey level run emphasis]]<br />
|}<br />
{|<br />
|[[Image:HighGreyLevelRunEmphasis.eps|thumb|200px|High grey level run emphasis]]<br />
|[[Image:ShortRunLowGreyLevelEmphasis.eps|thumb|200px|Short run low grey level emphasis]]<br />
|[[Image:ShortRunHighGreyLevelEmphasis.eps|thumb|200px|Short run high grey level emphasis]]<br />
|[[Image:LongRunLowGreyLevelEmphasis.eps|thumb|200px|Long run low grey level emphasis]]<br />
|[[Image:LongRunHighGreyLevelEmphasis.eps|thumb|200px|Long run high grey level emphasis]]<br />
|}<br />
<br />
<br />
<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
*[[Documentation/{{documentation/version}}/Modules/BoneTexture|BoneTexture]]<br />
*[[Documentation/{{documentation/version}}/Modules/BoneTextureSerializer|BoneTextureSerializer]]<br />
*[[Documentation/{{documentation/version}}/Modules/ComputeGLCMFeatureMaps|ComputeGLCMFeatureMaps]]<br />
*[[Documentation/{{documentation/version}}/Modules/ComputeGLCMFeatures|ComputeGLCMFeatures]]<br />
*[[Documentation/{{documentation/version}}/Modules/ComputeGLRLMFeatureMaps|ComputeGLRLMFeatureMaps]]<br />
*[[Documentation/{{documentation/version}}/Modules/ComputeGLRLMFeatures|ComputeGLRLMFeatures]]<br />
*[[Documentation/{{documentation/version}}/Modules/SeparateVectorImage|SeparateVectorImage]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Additional Information}}<br />
<br />
* [http://www.insight-journal.org/browse/publication/985 InsightJournal article]<br />
* [https://github.com/InsightSoftwareC BoneTextureExtension Tutorial]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
<br />
The source code is available on [https://github.com/Kitware/BoneTextureExtension github]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/BoneTextureExtension&diff=52901Documentation/Nightly/Extensions/BoneTextureExtension2017-07-10T17:28:23Z<p>Jb.vimort: Created page with "<noinclude>{{documentation/versioncheck}}</noinclude> <!-- ---------------------------- --> {{documentation/{{documentation/version}}/module-header}} <!-- -------------------..."</p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
'''''Author:''''' Jean-Baptise Vimort, Kitware Inc.<br><br />
'''''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)<br><br />
'''''Contact:''''' Jean-Baptiste Vimort, <email>jb.vimort@kitware.com</email><br><br />
'''''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<br />
Temporomandibular Joint Osteoarthritis) and National Institute of Biomedical Imaging and Bioengineering NIBIB) grant R01EB021391 (Shape Analysis Toolbox for Medical Image Computing Projects).<br><br />
'''''License:''''' [http://www.apache.org/licenses/LICENSE-2.0.html Apache License, Version 2.0]<br />
<gallery><br />
Image:Kitware-logo.png|Kitware Inc.<br />
Image:UofM-logo.png|University of Michigan<br />
</gallery><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
<br />
{|<br />
|[[Image:Logo-BoneTextureExtension.png|250px]]<br />
|<br />
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 [http://www.insight-journal.org/browse/publication/985 itkTextureFeatures]<br />
<br />
Key Features:<br />
<br />
* Estimated texture features:<br />
** 8 co-occurrence textural features: energy, entropy, correlation, inverse difference moment, inertia, cluster shade, cluster prominence and Haralick correlation<br />
** 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.<br />
* 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.<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Usage}}<br />
<br />
==Main modules interface==<br />
{|<br />
|[[Image:BoneTexture-Interface.png|thumb|400px|BoneTexture User Interface]]<br />
|[[Image:BoneTextureSerializer-Interface.png|thumb|400px|BoneTextureSerializer User Interface]]<br />
|}<br />
==Input example==<br />
{|<br />
|[[Image:Scan.eps|thumb|400px|Input scan]]<br />
|[[Image:CondileMask.eps|thumb|345px|Input mask]]<br />
|}<br />
<br />
==Texture features==<br />
{|<br />
|[[Image:TextureFeaturesTab.png|thumb|600px|Texture feature result table]]<br />
|}<br />
<br />
==Texture feature maps==<br />
<br />
===Co-occurrence texture feature maps===<br />
{|<br />
|[[Image:Energy.eps|thumb|200px|Energy]]<br />
|[[Image:Entropy.eps|thumb|200px|Entropy]]<br />
|[[Image:Correlation.eps|thumb|200px|Correlation]]<br />
|[[Image:InverseDifferenceMoment.eps|thumb|200px|Inverse difference moment]]<br />
|}<br />
{|<br />
|[[Image:Inertia.eps|thumb|200px|Inertia]]<br />
|[[Image:ClusterShade.eps|thumb|200px|Cluster shade]]<br />
|[[Image:ClusterProminence.eps|thumb|200px|Cluster prominence]]<br />
|[[Image:HaralickCorrelation.eps|thumb|200px|Haralick correlation]]<br />
|}<br />
<br />
===Run Length texture feature maps===<br />
{|<br />
|[[Image:ShortRunEmphasis.eps|thumb|200px|Short run emphasis]]<br />
|[[Image:LongRunEmphasis.eps|thumb|200px|Long run emphasis]]<br />
|[[Image:GreyLevelnonUniformity.eps|thumb|200px|Grey level non uniformity]]<br />
|[[Image:RunLengthnonUniformity.eps|thumb|200px|Run length non uniformity]]<br />
|[[Image:LowGreyLevelRunEmphasis.eps|thumb|200px|Low grey level run emphasis]]<br />
|}<br />
{|<br />
|[[Image:HighGreyLevelRunEmphasis.eps|thumb|200px|High grey level run emphasis]]<br />
|[[Image:ShortRunLowGreyLevelEmphasis.eps|thumb|200px|Short run low grey level emphasis]]<br />
|[[Image:ShortRunHighGreyLevelEmphasis.eps|thumb|200px|Short run high grey level emphasis]]<br />
|[[Image:LongRunLowGreyLevelEmphasis.eps|thumb|200px|Long run low grey level emphasis]]<br />
|[[Image:LongRunHighGreyLevelEmphasis.eps|thumb|200px|Long run high grey level emphasis]]<br />
|}<br />
<br />
<br />
<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
*[[Documentation/{{documentation/version}}/Modules/BoneTexture|BoneTexture]]<br />
*[[Documentation/{{documentation/version}}/Modules/BoneTextureSerializer|BoneTextureSerializer]]<br />
*[[Documentation/{{documentation/version}}/Modules/ComputeGLCMFeatureMaps|ComputeGLCMFeatureMaps]]<br />
*[[Documentation/{{documentation/version}}/Modules/ComputeGLCMFeatures|ComputeGLCMFeatures]]<br />
*[[Documentation/{{documentation/version}}/Modules/ComputeGLRLMFeatureMaps|ComputeGLRLMFeatureMaps]]<br />
*[[Documentation/{{documentation/version}}/Modules/ComputeGLRLMFeatures|ComputeGLRLMFeatures]]<br />
*[[Documentation/{{documentation/version}}/Modules/SeparateVectorImage|SeparateVectorImage]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Additional Information}}<br />
<br />
* [http://www.insight-journal.org/browse/publication/985 InsightJournal article]<br />
* [https://github.com/InsightSoftwareC BoneTextureExtension Tutorial]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
<br />
The source code is available on [https://github.com/Kitware/BoneTextureExtension github]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=File:BoneTextureExtension-Slicer.png&diff=52900File:BoneTextureExtension-Slicer.png2017-07-10T15:53:08Z<p>Jb.vimort: </p>
<hr />
<div></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/BoneTextureSerializer&diff=52852Documentation/Nightly/Modules/BoneTextureSerializer2017-07-07T18:07:14Z<p>Jb.vimort: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
<br />
'''''Extensions:''''' [https://www.slicer.org/wiki/Documentation/Nightly/Extensions/BoneTextureExtesion BoneTextureExtesion]<br><br />
'''''Author:''''' Jean-Baptise Vimort, Kitware Inc.<br><br />
'''''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)<br><br />
'''''Contact:''''' Jean-Baptiste Vimort, <email>jb.vimort@kitware.com</email><br><br />
'''''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<br />
Temporomandibular Joint Osteoarthritis) and National Institute of Biomedical Imaging and Bioengineering NIBIB) grant R01EB021391 (Shape Analysis Toolbox for Medical Image Computing Projects).<br><br />
'''''License:''''' [http://www.apache.org/licenses/LICENSE-2.0.html Apache License, Version 2.0]<br />
<br />
<gallery><br />
Image:Kitware-logo.png|Kitware Inc.<br />
Image:UofM-logo.png|University of Michigan<br />
</gallery><br />
<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<!-- ---------------------------- --><br />
<br />
This module provides a simple way to serialize the BoneTexture module.<br><br />
In order to make it work, all the input data should be in the same folder and named as following:<br />
* The input scan should be named ScanXXX.nrrd, where XXX is the ID of the case<br />
* If it exists, the input mask should be named SegmCXXX.nrrd, where XXX is the ID corresponding to the the input scan<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Interface}}<br />
{|<br />
|[[Image:BoneTextureSerializer-Interface.png|thumb|500px]]<br />
|<br />
|}<br />
<br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
<br />
==Inputs==<br />
<br />
{|<br />
|[[Image:BoneTextureSerealizer-Input.png|thumb|500px|BoneTextureSerializer Input]]<br />
| This section allows the user to specify the input folder, the folder specified should contain all the inputs (scans and segmentations) as described previously.<br />
|}<br />
<br />
==Parameters==<br />
<br />
{|<br />
|[[Image:BoneTexture-Parameter.png|thumb|500px|BoneTextureSerializer parameters]]<br />
|This section allows the user to choose:<br />
* The Type of features wanted: Run length features or co-occurrence features<br />
* All the parameters necessary to run each algorithms<br />
* The type of outputs wanted: texture features or texture maps<br />
|}<br />
<br />
{|<br />
|[[Image:BoneTexture-GLCMParam.png|thumb|500px|GLCM Parameters]]<br />
|[[Image:BoneTexture-GLRLMParam.png|thumb|500px| GLRLM Parameters]]<br />
|}<br />
<br />
==Exportation==<br />
<br />
{|<br />
|[[Image:BoneTextureSerializer-Exportation.png|thumb|500px|Image:BoneTextureSerializer Image:BoneTextureSerializer]]<br />
|This section allows the user to specify the folder where all the results will be saved:<br />
* The texture features for the whole image will be saved in a csv file<br />
* 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)<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Additional Information}}<br />
<br />
* [http://www.insight-journal.org/browse/publication/985 InsightJournal article]<br />
* [https://github.com/InsightSoftwareC BoneTextureExtension Tutorial]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
The source code is available on [https://github.com/Kitware/BoneTextureExtension/tree/master/BoneTextureSerializer github]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
[[Category:Documentation/{{documentation/version}}/Modules/ShapeAnalysis]]<br />
<!-- ---------------------------- --></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/BoneTexture&diff=52849Documentation/Nightly/Modules/BoneTexture2017-07-07T16:46:17Z<p>Jb.vimort: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
<br />
'''''Extensions:''''' [https://www.slicer.org/wiki/Documentation/Nightly/Extensions/BoneTextureExtesion BoneTextureExtesion]<br><br />
'''''Author:''''' Jean-Baptise Vimort, Kitware Inc.<br><br />
'''''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)<br><br />
'''''Contact:''''' Jean-Baptiste Vimort, <email>jb.vimort@kitware.com</email><br><br />
'''''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<br />
Temporomandibular Joint Osteoarthritis) and National Institute of Biomedical Imaging and Bioengineering NIBIB) grant R01EB021391 (Shape Analysis Toolbox for Medical Image Computing Projects).<br><br />
'''''License:''''' [http://www.apache.org/licenses/LICENSE-2.0.html Apache License, Version 2.0]<br />
<br />
<gallery><br />
Image:Kitware-logo.png|Kitware Inc.<br />
Image:UofM-logo.png|University of Michigan<br />
</gallery><br />
<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<!-- ---------------------------- --><br />
<br />
This module provide a simple and dynamic user interface that allows:<br />
* to use [[Documentation/{{documentation/version}}/Modules/ComputeGLCMFeatureMaps|ComputeGLCMFeatureMaps]], [[Documentation/{{documentation/version}}/Modules/ComputeGLCMFeatures|ComputeGLCMFeatures]], [[Documentation/{{documentation/version}}/Modules/ComputeGLRLMFeatureMaps|ComputeGLRLMFeatureMaps]] and [[Documentation/{{documentation/version}}/Modules/ComputeGLRLMFeatures|ComputeGLRLMFeatures]].<br><br />
* to easily modify the parameters and choose the wanted outputs in order to fit to each case studied in the best way possible.<br />
* to observe each outputs generated to be able to verify their consistency and hypothetically re-run the algorithm with a different parameter set. <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Interface}}<br />
{|<br />
|[[Image:BoneTexture-Interface.png|thumb|500px]]<br />
|<br />
|}<br />
<br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
<br />
==Inputs==<br />
<br />
{|<br />
|[[Image:BoneTexture-Input.png|thumb|500px|BoneTexture Inputs]]<br />
| This section allows the user to specify:<br />
* The input scan: it's interesting to notice that the computation time will improve if the useful data is taking as much space as possible in the input scan (a preliminary cropping step might be considered in order to erase the useless data on the boundaries)<br />
* An input mask: the mask is optional, therefore it will reduce the computation time of the algorithms<br />
|}<br />
<br />
==Parameters==<br />
<br />
{|<br />
|[[Image:BoneTexture-Parameter.png|thumb|500px|BoneTexture parameters]]<br />
|This section allows the user to choose:<br />
* The Type of features wanted: Run length features or co-occurrence features<br />
* All the parameters necessary to run each algorithms<br />
* The type of outputs wanted: texture features or texture maps<br />
|}<br />
<br />
{|<br />
|[[Image:BoneTexture-GLCMParam.png|thumb|500px|GLCM Parameters]]<br />
|[[Image:BoneTexture-GLRLMParam.png|thumb|500px| GLRLM Parameters]]<br />
|}<br />
<br />
==Result display==<br />
<br />
===Texture features===<br />
<br />
{|<br />
|[[Image:BoneTexture-FeatureValues.png|thumb|500px|Texture features result]]<br />
|The texture features computed over the whole input scan will be displayed in this table. <br />
|}<br />
<br />
===Texture Maps===<br />
<br />
{|<br />
|[[Image:BoneTexture-DisplayColormaps.png|thumb|500px|Texture map choice]]<br />
|This section allows the user to easily observe the texture maps generated. <br><br />
The first drop down menu allow to choose the texture map set (usually GLCM or CLRLM).<br />
|}<br />
<br />
{|<br />
|[[Image:BoneTexture-FeatureSelection.png|thumb|500px|Feature choice]]<br />
|The second drop down menu allow to choose the feature displayed in the 3D view of Slicer. <br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Additional Information}}<br />
<br />
* [http://www.insight-journal.org/browse/publication/985 InsightJournal article]<br />
* [https://github.com/InsightSoftwareC BoneTextureExtension Tutorial]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
The source code is available on [https://github.com/Kitware/BoneTextureExtension/tree/master/BoneTexture github]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
[[Category:Documentation/{{documentation/version}}/Modules/ShapeAnalysis]]<br />
<!-- ---------------------------- --></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/BoneTextureExtesion&diff=52846Documentation/Nightly/Extensions/BoneTextureExtesion2017-07-07T15:12:56Z<p>Jb.vimort: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
'''''Author:''''' Jean-Baptise Vimort, Kitware Inc.<br><br />
'''''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)<br><br />
'''''Contact:''''' Jean-Baptiste Vimort, <email>jb.vimort@kitware.com</email><br><br />
'''''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<br />
Temporomandibular Joint Osteoarthritis) and National Institute of Biomedical Imaging and Bioengineering NIBIB) grant R01EB021391 (Shape Analysis Toolbox for Medical Image Computing Projects).<br><br />
'''''License:''''' [http://www.apache.org/licenses/LICENSE-2.0.html Apache License, Version 2.0]<br />
<gallery><br />
Image:Kitware-logo.png|Kitware Inc.<br />
Image:UofM-logo.png|University of Michigan<br />
</gallery><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
<br />
{|<br />
|[[Image:Logo-BoneTextureExtension.png|250px]]<br />
|<br />
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 [http://www.insight-journal.org/browse/publication/985 itkTextureFeatures]<br />
<br />
Key Features:<br />
<br />
* Estimated texture features:<br />
** 8 co-occurrence textural features: energy, entropy, correlation, inverse difference moment, inertia, cluster shade, cluster prominence and Haralick correlation<br />
** 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.<br />
* 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.<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Usage}}<br />
<br />
==Main modules interface==<br />
{|<br />
|[[Image:BoneTexture-Interface.png|thumb|400px|BoneTexture User Interface]]<br />
|[[Image:BoneTextureSerializer-Interface.png|thumb|400px|BoneTextureSerializer User Interface]]<br />
|}<br />
==Input example==<br />
{|<br />
|[[Image:Scan.eps|thumb|400px|Input scan]]<br />
|[[Image:CondileMask.eps|thumb|345px|Input mask]]<br />
|}<br />
<br />
==Texture features==<br />
{|<br />
|[[Image:TextureFeaturesTab.png|thumb|600px|Texture feature result table]]<br />
|}<br />
<br />
==Texture feature maps==<br />
<br />
===Co-occurrence texture feature maps===<br />
{|<br />
|[[Image:Energy.eps|thumb|200px|Energy]]<br />
|[[Image:Entropy.eps|thumb|200px|Entropy]]<br />
|[[Image:Correlation.eps|thumb|200px|Correlation]]<br />
|[[Image:InverseDifferenceMoment.eps|thumb|200px|Inverse difference moment]]<br />
|}<br />
{|<br />
|[[Image:Inertia.eps|thumb|200px|Inertia]]<br />
|[[Image:ClusterShade.eps|thumb|200px|Cluster shade]]<br />
|[[Image:ClusterProminence.eps|thumb|200px|Cluster prominence]]<br />
|[[Image:HaralickCorrelation.eps|thumb|200px|Haralick correlation]]<br />
|}<br />
<br />
===Run Length texture feature maps===<br />
{|<br />
|[[Image:ShortRunEmphasis.eps|thumb|200px|Short run emphasis]]<br />
|[[Image:LongRunEmphasis.eps|thumb|200px|Long run emphasis]]<br />
|[[Image:GreyLevelnonUniformity.eps|thumb|200px|Grey level non uniformity]]<br />
|[[Image:RunLengthnonUniformity.eps|thumb|200px|Run length non uniformity]]<br />
|[[Image:LowGreyLevelRunEmphasis.eps|thumb|200px|Low grey level run emphasis]]<br />
|}<br />
{|<br />
|[[Image:HighGreyLevelRunEmphasis.eps|thumb|200px|High grey level run emphasis]]<br />
|[[Image:ShortRunLowGreyLevelEmphasis.eps|thumb|200px|Short run low grey level emphasis]]<br />
|[[Image:ShortRunHighGreyLevelEmphasis.eps|thumb|200px|Short run high grey level emphasis]]<br />
|[[Image:LongRunLowGreyLevelEmphasis.eps|thumb|200px|Long run low grey level emphasis]]<br />
|[[Image:LongRunHighGreyLevelEmphasis.eps|thumb|200px|Long run high grey level emphasis]]<br />
|}<br />
<br />
<br />
<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
*[[Documentation/{{documentation/version}}/Modules/BoneTexture|BoneTexture]]<br />
*[[Documentation/{{documentation/version}}/Modules/BoneTextureSerializer|BoneTextureSerializer]]<br />
*[[Documentation/{{documentation/version}}/Modules/ComputeGLCMFeatureMaps|ComputeGLCMFeatureMaps]]<br />
*[[Documentation/{{documentation/version}}/Modules/ComputeGLCMFeatures|ComputeGLCMFeatures]]<br />
*[[Documentation/{{documentation/version}}/Modules/ComputeGLRLMFeatureMaps|ComputeGLRLMFeatureMaps]]<br />
*[[Documentation/{{documentation/version}}/Modules/ComputeGLRLMFeatures|ComputeGLRLMFeatures]]<br />
*[[Documentation/{{documentation/version}}/Modules/SeparateVectorImage|SeparateVectorImage]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Additional Information}}<br />
<br />
* [http://www.insight-journal.org/browse/publication/985 InsightJournal article]<br />
* [https://github.com/InsightSoftwareC BoneTextureExtension Tutorial]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
<br />
The source code is available on [https://github.com/Kitware/BoneTextureExtension github]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/BoneTextureExtesion&diff=52843Documentation/Nightly/Extensions/BoneTextureExtesion2017-07-07T15:11:40Z<p>Jb.vimort: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
'''''Author:''''' Jean-Baptise Vimort, Kitware Inc.<br><br />
'''''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)<br><br />
'''''Contact:''''' Jean-Baptiste Vimort, <email>jb.vimort@kitware.com</email><br><br />
'''''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<br />
Temporomandibular Joint Osteoarthritis) and National Institute of Biomedical Imaging and Bioengineering NIBIB) grant R01EB021391 (Shape Analysis Toolbox for Medical Image Computing Projects).<br><br />
'''''License:''''' [http://www.apache.org/licenses/LICENSE-2.0.html Apache License, Version 2.0]<br />
<gallery><br />
Image:Kitware-logo.png|Kitware Inc.<br />
Image:UofM-logo.png|University of Michigan<br />
</gallery><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
<br />
{|<br />
|[[Image:Logo-BoneTextureExtension.png|250px]]<br />
|<br />
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 [http://www.insight-journal.org/browse/publication/985 itkTextureFeatures]<br />
<br />
Key Features:<br />
<br />
* Estimated texture features:<br />
** 8 co-occurrence textural features: energy, entropy, correlation, inverse difference moment, inertia, cluster shade, cluster prominence and Haralick correlation<br />
** 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.<br />
* 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."<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Usage}}<br />
<br />
==Main modules interface==<br />
{|<br />
|[[Image:BoneTexture-Interface.png|thumb|400px|BoneTexture User Interface]]<br />
|[[Image:BoneTextureSerializer-Interface.png|thumb|400px|BoneTextureSerializer User Interface]]<br />
|}<br />
==Input example==<br />
{|<br />
|[[Image:Scan.eps|thumb|400px|Input scan]]<br />
|[[Image:CondileMask.eps|thumb|345px|Input mask]]<br />
|}<br />
<br />
==Texture features==<br />
{|<br />
|[[Image:TextureFeaturesTab.png|thumb|600px|Texture feature result table]]<br />
|}<br />
<br />
==Texture feature maps==<br />
<br />
===Co-occurrence texture feature maps===<br />
{|<br />
|[[Image:Energy.eps|thumb|200px|Energy]]<br />
|[[Image:Entropy.eps|thumb|200px|Entropy]]<br />
|[[Image:Correlation.eps|thumb|200px|Correlation]]<br />
|[[Image:InverseDifferenceMoment.eps|thumb|200px|Inverse difference moment]]<br />
|}<br />
{|<br />
|[[Image:Inertia.eps|thumb|200px|Inertia]]<br />
|[[Image:ClusterShade.eps|thumb|200px|Cluster shade]]<br />
|[[Image:ClusterProminence.eps|thumb|200px|Cluster prominence]]<br />
|[[Image:HaralickCorrelation.eps|thumb|200px|Haralick correlation]]<br />
|}<br />
<br />
===Run Length texture feature maps===<br />
{|<br />
|[[Image:ShortRunEmphasis.eps|thumb|200px|Short run emphasis]]<br />
|[[Image:LongRunEmphasis.eps|thumb|200px|Long run emphasis]]<br />
|[[Image:GreyLevelnonUniformity.eps|thumb|200px|Grey level non uniformity]]<br />
|[[Image:RunLengthnonUniformity.eps|thumb|200px|Run length non uniformity]]<br />
|[[Image:LowGreyLevelRunEmphasis.eps|thumb|200px|Low grey level run emphasis]]<br />
|}<br />
{|<br />
|[[Image:HighGreyLevelRunEmphasis.eps|thumb|200px|High grey level run emphasis]]<br />
|[[Image:ShortRunLowGreyLevelEmphasis.eps|thumb|200px|Short run low grey level emphasis]]<br />
|[[Image:ShortRunHighGreyLevelEmphasis.eps|thumb|200px|Short run high grey level emphasis]]<br />
|[[Image:LongRunLowGreyLevelEmphasis.eps|thumb|200px|Long run low grey level emphasis]]<br />
|[[Image:LongRunHighGreyLevelEmphasis.eps|thumb|200px|Long run high grey level emphasis]]<br />
|}<br />
<br />
<br />
<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
*[[Documentation/{{documentation/version}}/Modules/BoneTexture|BoneTexture]]<br />
*[[Documentation/{{documentation/version}}/Modules/BoneTextureSerializer|BoneTextureSerializer]]<br />
*[[Documentation/{{documentation/version}}/Modules/ComputeGLCMFeatureMaps|ComputeGLCMFeatureMaps]]<br />
*[[Documentation/{{documentation/version}}/Modules/ComputeGLCMFeatures|ComputeGLCMFeatures]]<br />
*[[Documentation/{{documentation/version}}/Modules/ComputeGLRLMFeatureMaps|ComputeGLRLMFeatureMaps]]<br />
*[[Documentation/{{documentation/version}}/Modules/ComputeGLRLMFeatures|ComputeGLRLMFeatures]]<br />
*[[Documentation/{{documentation/version}}/Modules/SeparateVectorImage|SeparateVectorImage]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Additional Information}}<br />
<br />
* [http://www.insight-journal.org/browse/publication/985 InsightJournal article]<br />
* [https://github.com/InsightSoftwareC BoneTextureExtension Tutorial]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
<br />
The source code is available on [https://github.com/Kitware/BoneTextureExtension github]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/BoneTextureSerializer&diff=52835Documentation/Nightly/Modules/BoneTextureSerializer2017-07-06T20:21:21Z<p>Jb.vimort: Created page with "<noinclude>{{documentation/versioncheck}}</noinclude> <!-- ---------------------------- --> {{documentation/{{documentation/version}}/module-header}} <!-- --------------------..."</p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
<br />
'''''Extensions:''''' [https://www.slicer.org/wiki/Documentation/Nightly/Extensions/BoneTextureExtesion BoneTextureExtesion]<br><br />
'''''Author:''''' Jean-Baptise Vimort, Kitware Inc.<br><br />
'''''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)<br><br />
'''''Contact:''''' Jean-Baptiste Vimort, <email>jb.vimort@kitware.com</email><br><br />
'''''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<br />
Temporomandibular Joint Osteoarthritis) and National Institute of Biomedical Imaging and Bioengineering NIBIB) grant R01EB021391 (Shape Analysis Toolbox for Medical Image Computing Projects).<br><br />
'''''License:''''' [http://www.apache.org/licenses/LICENSE-2.0.html Apache License, Version 2.0]<br />
<br />
<gallery><br />
Image:Kitware-logo.png|Kitware Inc.<br />
Image:UofM-logo.png|University of Michigan<br />
</gallery><br />
<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<!-- ---------------------------- --><br />
<br />
This module provide a simple to serialize the BoneTexture module once the good set of parameters has been chosen.<br><br />
In order two make it work, all the input data should be in the same folder and named as following:<br />
* The input scan should be named ScanXXX.nrrd, where XXX is the ID of the case<br />
* If it exist, the input mask should be named SegmCXXX.nrrd, where XXX is the ID corresponding to the the input scan<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Interface}}<br />
{|<br />
|[[Image:BoneTextureSerializer-Interface.png|thumb|500px]]<br />
|<br />
|}<br />
<br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
<br />
==Inputs==<br />
<br />
{|<br />
|[[Image:BoneTextureSerealizer-Input.png|thumb|500px|Image:BoneTextureSerializer Input]]<br />
| This section allow the user to specify the input folder, the folder specified should contain all the inputs (scans and segmentation) has described previously.<br />
|}<br />
<br />
==Parameters==<br />
<br />
{|<br />
|[[Image:BoneTexture-Parameter.png|thumb|500px|Image:BoneTextureSerializer parameters]]<br />
|This section allow the user to choose:<br />
* The Type of features wanted: Run length features or co-occurrence features<br />
* All the parameters necessary to run each algorithms<br />
* The type of output wanted: texture features or texture maps<br />
|}<br />
<br />
{|<br />
|[[Image:BoneTexture-GLCMParam.png|thumb|500px|GLCM Parameters]]<br />
|[[Image:BoneTexture-GLRLMParam.png|thumb|500px| GLRLM Parameters]]<br />
|}<br />
<br />
==Exportation==<br />
<br />
{|<br />
|[[Image:BoneTextureSerializer-Exportation.png|thumb|500px|Image:BoneTextureSerializer Image:BoneTextureSerializer]]<br />
|This section allow the folder where all the results will be saved:<br />
* The texture features for the whole image will be saved in a csv file<br />
* 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)<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Additional Information}}<br />
<br />
* [http://www.insight-journal.org/browse/publication/985 InsightJournal article]<br />
* [https://github.com/InsightSoftwareC BoneTextureExtension Tutorial]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
The source code is available on [https://github.com/Kitware/BoneTextureExtension/tree/master/BoneTextureSerializer github]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
[[Category:Documentation/{{documentation/version}}/Modules/ShapeAnalysis]]<br />
<!-- ---------------------------- --></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=File:BoneTextureSerializer-Exportation.png&diff=52834File:BoneTextureSerializer-Exportation.png2017-07-06T19:49:48Z<p>Jb.vimort: </p>
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<div></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=File:BoneTextureSerealizer-Input.png&diff=52833File:BoneTextureSerealizer-Input.png2017-07-06T19:49:28Z<p>Jb.vimort: </p>
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<div></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/BoneTexture&diff=52830Documentation/Nightly/Modules/BoneTexture2017-07-06T19:40:05Z<p>Jb.vimort: Created page with "<noinclude>{{documentation/versioncheck}}</noinclude> <!-- ---------------------------- --> {{documentation/{{documentation/version}}/module-header}} <!-- --------------------..."</p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
<br />
'''''Extensions:''''' [https://www.slicer.org/wiki/Documentation/Nightly/Extensions/BoneTextureExtesion BoneTextureExtesion]<br><br />
'''''Author:''''' Jean-Baptise Vimort, Kitware Inc.<br><br />
'''''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)<br><br />
'''''Contact:''''' Jean-Baptiste Vimort, <email>jb.vimort@kitware.com</email><br><br />
'''''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<br />
Temporomandibular Joint Osteoarthritis) and National Institute of Biomedical Imaging and Bioengineering NIBIB) grant R01EB021391 (Shape Analysis Toolbox for Medical Image Computing Projects).<br><br />
'''''License:''''' [http://www.apache.org/licenses/LICENSE-2.0.html Apache License, Version 2.0]<br />
<br />
<gallery><br />
Image:Kitware-logo.png|Kitware Inc.<br />
Image:UofM-logo.png|University of Michigan<br />
</gallery><br />
<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<!-- ---------------------------- --><br />
<br />
This module provide a simple and dynamic user interface that allow:<br />
* to use [[Documentation/{{documentation/version}}/Modules/ComputeGLCMFeatureMaps|ComputeGLCMFeatureMaps]], [[Documentation/{{documentation/version}}/Modules/ComputeGLCMFeatures|ComputeGLCMFeatures]], [[Documentation/{{documentation/version}}/Modules/ComputeGLRLMFeatureMaps|ComputeGLRLMFeatureMaps]] and [[Documentation/{{documentation/version}}/Modules/ComputeGLRLMFeatures|ComputeGLRLMFeatures]].<br><br />
* to easily modify the parameters and choose the wanted outputs in order to fit to every case study in the best way possible.<br />
* to observe every output generated to be able to verify their consistency and hypothetically re-run the algorithm with a different parameter set. <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Interface}}<br />
{|<br />
|[[Image:BoneTexture-Interface.png|thumb|500px]]<br />
|<br />
|}<br />
<br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
<br />
==Inputs==<br />
<br />
{|<br />
|[[Image:BoneTexture-Input.png|thumb|500px|BoneTexture Inputs]]<br />
| This section allow the user to specify:<br />
* The input scan: it's interesting to notice that the computation time will improve if the useful data is taking as much space as possible in the input scan (a preliminary cropping step might be considered in order to erase the useless data on the boundaries)<br />
* An input mask: the mask is optional, therefore it will improve the computation time of the algorithms<br />
|}<br />
<br />
==Parameters==<br />
<br />
{|<br />
|[[Image:BoneTexture-Parameter.png|thumb|500px|BoneTexture parameters]]<br />
|This section allow the user to choose:<br />
* The Type of features wanted: Run length features or co-occurrence features<br />
* All the parameters necessary to run each algorithms<br />
* The type of output wanted: texture features or texture maps<br />
|}<br />
<br />
{|<br />
|[[Image:BoneTexture-GLCMParam.png|thumb|500px|GLCM Parameters]]<br />
|[[Image:BoneTexture-GLRLMParam.png|thumb|500px| GLRLM Parameters]]<br />
|}<br />
<br />
==Result display==<br />
<br />
===Texture features===<br />
<br />
{|<br />
|[[Image:BoneTexture-FeatureValues.png|thumb|500px|Texture features result]]<br />
|The texture features computed over the whole input scan will be displayed in this table. <br />
|}<br />
<br />
===Texture Maps===<br />
<br />
{|<br />
|[[Image:BoneTexture-DisplayColormaps.png|thumb|500px|Texture map choice]]<br />
|This section allow the user to easily observe the texture maps generated. <br><br />
The first drop down menu allow to choose the texture map set (usually GLCM or CLRLM).<br />
|}<br />
<br />
{|<br />
|[[Image:BoneTexture-FeatureSelection.png|thumb|500px|Feature choice]]<br />
|The second drop down menu allow to choose the feature displayed in the 3D view of Slicer. <br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Additional Information}}<br />
<br />
* [http://www.insight-journal.org/browse/publication/985 InsightJournal article]<br />
* [https://github.com/InsightSoftwareC BoneTextureExtension Tutorial]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
The source code is available on [https://github.com/Kitware/BoneTextureExtension/tree/master/BoneTexture github]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
[[Category:Documentation/{{documentation/version}}/Modules/ShapeAnalysis]]<br />
<!-- ---------------------------- --></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=File:BoneTexture-FeatureSelection.png&diff=52829File:BoneTexture-FeatureSelection.png2017-07-06T18:37:00Z<p>Jb.vimort: </p>
<hr />
<div></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=File:BoneTexture-DisplayColormaps.png&diff=52828File:BoneTexture-DisplayColormaps.png2017-07-06T18:36:48Z<p>Jb.vimort: </p>
<hr />
<div></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=File:BoneTexture-FeatureValues.png&diff=52827File:BoneTexture-FeatureValues.png2017-07-06T18:36:32Z<p>Jb.vimort: </p>
<hr />
<div></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=File:BoneTexture-GLRLMParam.png&diff=52826File:BoneTexture-GLRLMParam.png2017-07-06T18:36:11Z<p>Jb.vimort: </p>
<hr />
<div></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=File:BoneTexture-GLCMParam.png&diff=52825File:BoneTexture-GLCMParam.png2017-07-06T18:35:57Z<p>Jb.vimort: </p>
<hr />
<div></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=File:BoneTexture-Parameter.png&diff=52824File:BoneTexture-Parameter.png2017-07-06T18:35:39Z<p>Jb.vimort: </p>
<hr />
<div></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=File:BoneTexture-Input.png&diff=52823File:BoneTexture-Input.png2017-07-06T18:35:18Z<p>Jb.vimort: </p>
<hr />
<div></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/BoneTextureExtesion&diff=52820Documentation/Nightly/Extensions/BoneTextureExtesion2017-07-06T17:30:21Z<p>Jb.vimort: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
'''''Author:''''' Jean-Baptise Vimort, Kitware Inc.<br><br />
'''''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)<br><br />
'''''Contact:''''' Jean-Baptiste Vimort, <email>jb.vimort@kitware.com</email><br><br />
'''''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<br />
Temporomandibular Joint Osteoarthritis) and National Institute of Biomedical Imaging and Bioengineering NIBIB) grant R01EB021391 (Shape Analysis Toolbox for Medical Image Computing Projects).<br><br />
'''''License:''''' [http://www.apache.org/licenses/LICENSE-2.0.html Apache License, Version 2.0]<br />
<gallery><br />
Image:Kitware-logo.png|Kitware Inc.<br />
Image:UofM-logo.png|University of Michigan<br />
</gallery><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
<br />
{|<br />
|[[Image:Logo-BoneTextureExtension.png|250px]]<br />
|<br />
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 ITK called [http://www.insight-journal.org/browse/publication/985 itkTextureFeatures]<br />
<br />
Key Features:<br />
<br />
* Estimated texture features:<br />
** 8 co-occurrence textural features: energy, entropy, correlation, inverse difference moment, inertia, cluster shade, cluster prominence and Haralick correlation<br />
** 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.<br />
* 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.")<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Usage}}<br />
<br />
==Main modules interface==<br />
{|<br />
|[[Image:BoneTexture-Interface.png|thumb|400px|BoneTexture User Interface]]<br />
|[[Image:BoneTextureSerializer-Interface.png|thumb|400px|BoneTextureSerializer User Interface]]<br />
|}<br />
==Input example==<br />
{|<br />
|[[Image:Scan.eps|thumb|400px|Input scan]]<br />
|[[Image:CondileMask.eps|thumb|345px|Input mask]]<br />
|}<br />
<br />
==Texture features==<br />
{|<br />
|[[Image:TextureFeaturesTab.png|thumb|600px|Texture feature result table]]<br />
|}<br />
<br />
==Texture feature maps==<br />
<br />
===Co-occurrence texture feature maps===<br />
{|<br />
|[[Image:Energy.eps|thumb|200px|Energy]]<br />
|[[Image:Entropy.eps|thumb|200px|Entropy]]<br />
|[[Image:Correlation.eps|thumb|200px|Correlation]]<br />
|[[Image:InverseDifferenceMoment.eps|thumb|200px|Inverse difference moment]]<br />
|}<br />
{|<br />
|[[Image:Inertia.eps|thumb|200px|Inertia]]<br />
|[[Image:ClusterShade.eps|thumb|200px|Cluster shade]]<br />
|[[Image:ClusterProminence.eps|thumb|200px|Cluster prominence]]<br />
|[[Image:HaralickCorrelation.eps|thumb|200px|Haralick correlation]]<br />
|}<br />
<br />
===Run Length texture feature maps===<br />
{|<br />
|[[Image:ShortRunEmphasis.eps|thumb|200px|Short run emphasis]]<br />
|[[Image:LongRunEmphasis.eps|thumb|200px|Long run emphasis]]<br />
|[[Image:GreyLevelnonUniformity.eps|thumb|200px|Grey level non uniformity]]<br />
|[[Image:RunLengthnonUniformity.eps|thumb|200px|Run length non uniformity]]<br />
|[[Image:LowGreyLevelRunEmphasis.eps|thumb|200px|Low grey level run emphasis]]<br />
|}<br />
{|<br />
|[[Image:HighGreyLevelRunEmphasis.eps|thumb|200px|High grey level run emphasis]]<br />
|[[Image:ShortRunLowGreyLevelEmphasis.eps|thumb|200px|Short run low grey level emphasis]]<br />
|[[Image:ShortRunHighGreyLevelEmphasis.eps|thumb|200px|Short run high grey level emphasis]]<br />
|[[Image:LongRunLowGreyLevelEmphasis.eps|thumb|200px|Long run low grey level emphasis]]<br />
|[[Image:LongRunHighGreyLevelEmphasis.eps|thumb|200px|Long run high grey level emphasis]]<br />
|}<br />
<br />
<br />
<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
*[[Documentation/{{documentation/version}}/Modules/BoneTexture|BoneTexture]]<br />
*[[Documentation/{{documentation/version}}/Modules/BoneTextureSerializer|BoneTextureSerializer]]<br />
*[[Documentation/{{documentation/version}}/Modules/ComputeGLCMFeatureMaps|ComputeGLCMFeatureMaps]]<br />
*[[Documentation/{{documentation/version}}/Modules/ComputeGLCMFeatures|ComputeGLCMFeatures]]<br />
*[[Documentation/{{documentation/version}}/Modules/ComputeGLRLMFeatureMaps|ComputeGLRLMFeatureMaps]]<br />
*[[Documentation/{{documentation/version}}/Modules/ComputeGLRLMFeatures|ComputeGLRLMFeatures]]<br />
*[[Documentation/{{documentation/version}}/Modules/SeparateVectorImage|SeparateVectorImage]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Additional Information}}<br />
<br />
* [http://www.insight-journal.org/browse/publication/985 InsightJournal article]<br />
* [https://github.com/InsightSoftwareC BoneTextureExtension Tutorial]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
<br />
The source code is available on [https://github.com/Kitware/BoneTextureExtension github]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=File:TextureFeaturesTab.png&diff=52819File:TextureFeaturesTab.png2017-07-06T17:29:55Z<p>Jb.vimort: </p>
<hr />
<div></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/BoneTextureExtesion&diff=52816Documentation/Nightly/Extensions/BoneTextureExtesion2017-07-06T17:29:34Z<p>Jb.vimort: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
'''''Author:''''' Jean-Baptise Vimort, Kitware Inc.<br><br />
'''''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)<br><br />
'''''Contact:''''' Jean-Baptiste Vimort, <email>jb.vimort@kitware.com</email><br><br />
'''''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<br />
Temporomandibular Joint Osteoarthritis) and National Institute of Biomedical Imaging and Bioengineering NIBIB) grant R01EB021391 (Shape Analysis Toolbox for Medical Image Computing Projects).<br><br />
'''''License:''''' [http://www.apache.org/licenses/LICENSE-2.0.html Apache License, Version 2.0]<br />
<gallery><br />
Image:Kitware-logo.png|Kitware Inc.<br />
Image:UofM-logo.png|University of Michigan<br />
</gallery><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
<br />
{|<br />
|[[Image:Logo-BoneTextureExtension.png|250px]]<br />
|<br />
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 ITK called [http://www.insight-journal.org/browse/publication/985 itkTextureFeatures]<br />
<br />
Key Features:<br />
<br />
* Estimated texture features:<br />
** 8 co-occurrence textural features: energy, entropy, correlation, inverse difference moment, inertia, cluster shade, cluster prominence and Haralick correlation<br />
** 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.<br />
* 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.")<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Usage}}<br />
<br />
==Main modules interface==<br />
{|<br />
|[[Image:BoneTexture-Interface.png|thumb|400px|BoneTexture User Interface]]<br />
|[[Image:BoneTextureSerializer-Interface.png|thumb|400px|BoneTextureSerializer User Interface]]<br />
|}<br />
==Input example==<br />
{|<br />
|[[Image:Scan.eps|thumb|400px|Input scan]]<br />
|[[Image:CondileMask.eps|thumb|345px|Input mask]]<br />
|}<br />
<br />
==Texture features==<br />
{|<br />
|[[Image:TextureFeaturesTab.png|thumb|400px|Texture feature result table]]<br />
|}<br />
<br />
==Texture feature maps==<br />
<br />
===Co-occurrence texture feature maps===<br />
{|<br />
|[[Image:Energy.eps|thumb|200px|Energy]]<br />
|[[Image:Entropy.eps|thumb|200px|Entropy]]<br />
|[[Image:Correlation.eps|thumb|200px|Correlation]]<br />
|[[Image:InverseDifferenceMoment.eps|thumb|200px|Inverse difference moment]]<br />
|}<br />
{|<br />
|[[Image:Inertia.eps|thumb|200px|Inertia]]<br />
|[[Image:ClusterShade.eps|thumb|200px|Cluster shade]]<br />
|[[Image:ClusterProminence.eps|thumb|200px|Cluster prominence]]<br />
|[[Image:HaralickCorrelation.eps|thumb|200px|Haralick correlation]]<br />
|}<br />
<br />
===Run Length texture feature maps===<br />
{|<br />
|[[Image:ShortRunEmphasis.eps|thumb|200px|Short run emphasis]]<br />
|[[Image:LongRunEmphasis.eps|thumb|200px|Long run emphasis]]<br />
|[[Image:GreyLevelnonUniformity.eps|thumb|200px|Grey level non uniformity]]<br />
|[[Image:RunLengthnonUniformity.eps|thumb|200px|Run length non uniformity]]<br />
|[[Image:LowGreyLevelRunEmphasis.eps|thumb|200px|Low grey level run emphasis]]<br />
|}<br />
{|<br />
|[[Image:HighGreyLevelRunEmphasis.eps|thumb|200px|High grey level run emphasis]]<br />
|[[Image:ShortRunLowGreyLevelEmphasis.eps|thumb|200px|Short run low grey level emphasis]]<br />
|[[Image:ShortRunHighGreyLevelEmphasis.eps|thumb|200px|Short run high grey level emphasis]]<br />
|[[Image:LongRunLowGreyLevelEmphasis.eps|thumb|200px|Long run low grey level emphasis]]<br />
|[[Image:LongRunHighGreyLevelEmphasis.eps|thumb|200px|Long run high grey level emphasis]]<br />
|}<br />
<br />
<br />
<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
*[[Documentation/{{documentation/version}}/Modules/BoneTexture|BoneTexture]]<br />
*[[Documentation/{{documentation/version}}/Modules/BoneTextureSerializer|BoneTextureSerializer]]<br />
*[[Documentation/{{documentation/version}}/Modules/ComputeGLCMFeatureMaps|ComputeGLCMFeatureMaps]]<br />
*[[Documentation/{{documentation/version}}/Modules/ComputeGLCMFeatures|ComputeGLCMFeatures]]<br />
*[[Documentation/{{documentation/version}}/Modules/ComputeGLRLMFeatureMaps|ComputeGLRLMFeatureMaps]]<br />
*[[Documentation/{{documentation/version}}/Modules/ComputeGLRLMFeatures|ComputeGLRLMFeatures]]<br />
*[[Documentation/{{documentation/version}}/Modules/SeparateVectorImage|SeparateVectorImage]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Additional Information}}<br />
<br />
* [http://www.insight-journal.org/browse/publication/985 InsightJournal article]<br />
* [https://github.com/InsightSoftwareC BoneTextureExtension Tutorial]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
<br />
The source code is available on [https://github.com/Kitware/BoneTextureExtension github]<br />
<br />
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<!-- ---------------------------- --></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/BoneTextureExtesion&diff=52813Documentation/Nightly/Extensions/BoneTextureExtesion2017-07-06T17:28:46Z<p>Jb.vimort: </p>
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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
'''''Author:''''' Jean-Baptise Vimort, Kitware Inc.<br><br />
'''''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)<br><br />
'''''Contact:''''' Jean-Baptiste Vimort, <email>jb.vimort@kitware.com</email><br><br />
'''''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<br />
Temporomandibular Joint Osteoarthritis) and National Institute of Biomedical Imaging and Bioengineering NIBIB) grant R01EB021391 (Shape Analysis Toolbox for Medical Image Computing Projects).<br><br />
'''''License:''''' [http://www.apache.org/licenses/LICENSE-2.0.html Apache License, Version 2.0]<br />
<gallery><br />
Image:Kitware-logo.png|Kitware Inc.<br />
Image:UofM-logo.png|University of Michigan<br />
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{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
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{|<br />
|[[Image:Logo-BoneTextureExtension.png|250px]]<br />
|<br />
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 ITK called [http://www.insight-journal.org/browse/publication/985 itkTextureFeatures]<br />
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Key Features:<br />
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* Estimated texture features:<br />
** 8 co-occurrence textural features: energy, entropy, correlation, inverse difference moment, inertia, cluster shade, cluster prominence and Haralick correlation<br />
** 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.<br />
* 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.")<br />
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{{documentation/{{documentation/version}}/module-section|Usage}}<br />
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==Main modules interface==<br />
{|<br />
|[[Image:BoneTexture-Interface.png|thumb|400px|BoneTexture User Interface]]<br />
|[[Image:BoneTextureSerializer-Interface.png|thumb|400px|BoneTextureSerializer User Interface]]<br />
|}<br />
==Input example==<br />
{|<br />
|[[Image:Scan.eps|thumb|400px|Input scan]]<br />
|[[Image:CondileMask.eps|thumb|400px|Input mask]]<br />
|}<br />
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==Texture features==<br />
{|<br />
|[[Image:TextureFeaturesTab.png|thumb|400px|Texture feature result table]]<br />
|}<br />
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==Texture feature maps==<br />
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===Co-occurrence texture feature maps===<br />
{|<br />
|[[Image:Energy.eps|thumb|200px|Energy]]<br />
|[[Image:Entropy.eps|thumb|200px|Entropy]]<br />
|[[Image:Correlation.eps|thumb|200px|Correlation]]<br />
|[[Image:InverseDifferenceMoment.eps|thumb|200px|Inverse difference moment]]<br />
|}<br />
{|<br />
|[[Image:Inertia.eps|thumb|200px|Inertia]]<br />
|[[Image:ClusterShade.eps|thumb|200px|Cluster shade]]<br />
|[[Image:ClusterProminence.eps|thumb|200px|Cluster prominence]]<br />
|[[Image:HaralickCorrelation.eps|thumb|200px|Haralick correlation]]<br />
|}<br />
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===Run Length texture feature maps===<br />
{|<br />
|[[Image:ShortRunEmphasis.eps|thumb|200px|Short run emphasis]]<br />
|[[Image:LongRunEmphasis.eps|thumb|200px|Long run emphasis]]<br />
|[[Image:GreyLevelnonUniformity.eps|thumb|200px|Grey level non uniformity]]<br />
|[[Image:RunLengthnonUniformity.eps|thumb|200px|Run length non uniformity]]<br />
|[[Image:LowGreyLevelRunEmphasis.eps|thumb|200px|Low grey level run emphasis]]<br />
|}<br />
{|<br />
|[[Image:HighGreyLevelRunEmphasis.eps|thumb|200px|High grey level run emphasis]]<br />
|[[Image:ShortRunLowGreyLevelEmphasis.eps|thumb|200px|Short run low grey level emphasis]]<br />
|[[Image:ShortRunHighGreyLevelEmphasis.eps|thumb|200px|Short run high grey level emphasis]]<br />
|[[Image:LongRunLowGreyLevelEmphasis.eps|thumb|200px|Long run low grey level emphasis]]<br />
|[[Image:LongRunHighGreyLevelEmphasis.eps|thumb|200px|Long run high grey level emphasis]]<br />
|}<br />
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{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
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*[[Documentation/{{documentation/version}}/Modules/BoneTexture|BoneTexture]]<br />
*[[Documentation/{{documentation/version}}/Modules/BoneTextureSerializer|BoneTextureSerializer]]<br />
*[[Documentation/{{documentation/version}}/Modules/ComputeGLCMFeatureMaps|ComputeGLCMFeatureMaps]]<br />
*[[Documentation/{{documentation/version}}/Modules/ComputeGLCMFeatures|ComputeGLCMFeatures]]<br />
*[[Documentation/{{documentation/version}}/Modules/ComputeGLRLMFeatureMaps|ComputeGLRLMFeatureMaps]]<br />
*[[Documentation/{{documentation/version}}/Modules/ComputeGLRLMFeatures|ComputeGLRLMFeatures]]<br />
*[[Documentation/{{documentation/version}}/Modules/SeparateVectorImage|SeparateVectorImage]]<br />
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{{documentation/{{documentation/version}}/module-section|Additional Information}}<br />
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* [http://www.insight-journal.org/browse/publication/985 InsightJournal article]<br />
* [https://github.com/InsightSoftwareC BoneTextureExtension Tutorial]<br />
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{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
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{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
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The source code is available on [https://github.com/Kitware/BoneTextureExtension github]<br />
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<!-- ---------------------------- --></div>Jb.vimorthttps://www.slicer.org/w/index.php?title=File:CondileMask.eps&diff=52812File:CondileMask.eps2017-07-06T17:28:26Z<p>Jb.vimort: </p>
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