Slicer Wiki - User contributions [en]

Documentation/Nightly/Modules/BodyCentricCubicMesh

2018-08-07T14:08:54Z

Jbest: changed logo

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/CBC_3D_I2MConversion |CBC 3D I2MConversion]] 
Acknowledgments:
*This work was partially supported by NIH R44 OD018334-03A, grant CCF-1439079 and by the Richard T.Cheng Endowment.

Author: Fotis Drakopoulos 
Contributors: Joi Best (CRTC), Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andrey Fedorov (CRTC), Nikos Chrisochoides (CRTC) 
Contact: Nikos Chrisochoides: <email>npchris@gmail.com</email> , Joi Best: <email>jbest002@odu.edu</email> 
Website: https://crtc.cs.odu.edu
 
License: BSD 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|Image:Crtc logo.png|Center for Real-time Computing
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
The module generates a Body Centric Cubic (BCC) mesh from a labeled image. Initially the generated mesh is homogeneous, that means does not distinguish different tissues. Later the module specifies which tissue each tetrahedron belongs to. Each tissue is capable of automatically adjusting its resolution based on its geometric complexity and the predefined subdivision criterion. The current version of the module supports a single-tissue input labeled image.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{|
|[[File:brain.jpg|thumb|280px|Brain BCC mesh]]
|[[File:nidus.jpg|thumb|280px|Nidus BCC mesh]]
|[[File:ventricles.jpg|thumb|280px|Ventricles BCC mesh]]
|}
{|
|[[File:brain_section.jpg|thumb|280px|Brain BCC mesh cross-section]]
|[[File:nidus_section.jpg|thumb|280px|Nidus BCC mesh cross-section]]
|[[File:ventricles_section.jpg|thumb|280px|Ventricles BCC mesh cross-section]]
|}

{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

{|
|
* '''Mesh Generation Parameters:'''
** '''Size:''' Controls the size of the mesh. The smaller the value the larger the mesh. Value should be between [1,20] (default: 8).
** '''Fidelity:''' Controls the subdivision of the elements that belong to more than one image labels. The larger the value the better the conformity of the mesh on the image label boundaries. Value should be between [0.1,1] (default: 0.8).
** '''Resample Resolution:''' Controls the image resampling. Suggested value is 0 (no-resampling) for large tissues and 1 or 2 for smaller tissues. Value should be 0 or 1 or 2 (default: 0).
* '''Input/Output:'''
** '''Input Labeled Image:''' The input labeled image.
** '''Output Mesh File:''' The output tetrahedral mesh in vtk file format. (default: outputMesh.vtk)
|[[Image:BCCPanel.jpg|thumb|320px|User Interface]]
|}

'''Note: this module will only work if the input image has identity orientation!'''


{{documentation/{{documentation/version}}/module-section|Similar Modules}}
*[[Documentation/Nightly/Modules/MeshCompression]]


{{documentation/{{documentation/version}}/module-section|References}}
* Fedorov A., Chrisochoides N., Kikinis R., Warfield S, "Tetrahedral mesh generation for medical imaging", The Insight Journal-2005 MICCAI Open-Source Workshop, 2005
* Yixun Liu, Panagiotis Foteinos, Andrey Chernikov and Nikos Chrisochoides, "Mesh Deformation-based Multi-tissue Mesh Generation for Brain Images", Engineering with Computers, Volume 28, pages 305-318, 2012.

{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/MeshCompression

2018-08-07T14:08:26Z

Jbest: changed logo

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/CBC_3D_I2MConversion |CBC 3D I2MConversion]] 
Acknowledgments:
*This work was partially supported by NIH R44 OD018334-03A, grant CCF-1439079 and by the Richard T.Cheng Endowment.

Author: Fotis Drakopoulos 
Contributors: Joi Best (CRTC), Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andrey Fedorov (CRTC), Nikos Chrisochoides (CRTC) 
Contact: Nikos Chrisochoides: <email>npchris@gmail.com</email> , Joi Best: <email>jbest002@odu.edu</email> 
Website: https://crtc.cs.odu.edu 
License: BSD 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|Image:Crtc logo.png|Center for Real-time Computing
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
The Mesh Compression (MC) module deforms the input tetrahedral mesh towards the boundaries of the input labeled image. Two point sets are extracted for the mesh deformation. The first (source point set) consists of the surface vertices in the input mesh. The second (target point set) consists of the surface edge points in the input labeled image. After the extraction of the two point sets, the input mesh is deformed by registering the source to the target point set using a Physics-Based Non-Rigid Registration method. The current version of the module supports a single-tissue labeled image and mesh.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{|
|[[File:brain_before.jpg|thumb|300px|Brain BCC mesh before MC]]
|[[File:brain_after.jpg|thumb|300px|Brain BCC mesh after MC]]
|[[File:brain_after_section.jpg|thumb|300px|Brain BCC mesh after MC (cross-section)]]
|}

{|
|[[File:nidus_before.jpg|thumb|300px|Nidus BCC mesh before MC]]
|[[File:nidus_after.jpg|thumb|300px|Nidus BCC mesh after MC]] 
|[[File:nidus_after_section.jpg|thumb|300px|Nidus BCC mesh after MC (cross-section)]]
|}

{|
|[[File:ventricles_before.jpg|thumb|300px|Ventricles BCC mesh before MC]]
|[[File:ventricles_after.jpg|thumb|300px|Ventricles BCC mesh after MC]]
|[[File:ventricles_after_section.jpg|thumb|300px|Ventricles BCC mesh after MC (cross-section)]]
|}

{|
|[[File:target_points.jpg|thumb|960px|How the non-connectivity parameter influences the number of the extracted target points]]
|}


{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

{|
|
* '''Mesh Compression Parameters:'''
** '''Flexibility:''' Controls the trade-off between the regularization energy defined by the stress energy of a linear bio-mechanical elastic model, and the similarity energy. Value should be between [0.1,1] (default: 1).
** '''Number of Iterations:''' Controls the number of iterations for the compressor. The larger the value the closer the boundaries of the input mesh to the boundaries of the input image. A large number of iterations might cause distorted poor-quality elements. Value should be between [1,10] (default: 3).
** '''Non Connectivity:''' Controls the density of the extracted target points via a prohibited connectivity between adjacent blocks of voxels. The larger the value the denser the target point set. 0 is vertex non-connectivity (26 neighbors), 1 is edge non-connectivity (18 neighbors), 2 is face non-connectivity (6 neighbors) and 3 is no non-connectivity. Value should be 0 or 1 or 2 or 3. (default: 0).
* '''Input/Output:'''
** '''Input Labeled Image:''' The input labeled image.
** '''Input Mesh File:''' The input tetrahedral mesh in vtk file format.
** '''Output Mesh File:''' The output deformed mesh in vtk file format (optional) (default: deformedMesh.vtk).
** '''Output Source Points File:''' The extracted source points in vtk file format (optional). The source points are the surface vertices of the input mesh.
** '''Output Target Points File:''' The extracted target points in vtk file format (optional). The target points are the surface edge points of the input labeled image.
** '''Output Surface Triangles File:''' The extracted surface triangles of the input mesh in vtk file format (optional).
|[[Image:MCPanel.jpg|thumb|380px|User Interface]]
|}

'''Note: this module will only work if the input image has identity orientation!'''


{{documentation/{{documentation/version}}/module-section|Similar Modules}}
*[[Documentation/Nightly/Modules/BodyCentricCubicMesh]]


{{documentation/{{documentation/version}}/module-section|References}}
* Yixun Liu, Panagiotis Foteinos, Andrey Chernikov and Nikos Chrisochoides, "Mesh Deformation-based Multi-tissue Mesh Generation for Brain Images", Engineering with Computers, Volume 28, pages 305-318, 2012.

{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Extensions/CBC 3D I2MConversion

2018-08-07T14:07:54Z

Jbest: changed logo

Documentation/Nightly/Extensions/CBC 3D I2MConversion

2018-08-07T13:58:31Z

Jbest:

Documentation/Nightly/Modules/MeshCompression

2018-08-07T13:57:55Z

Jbest:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/CBC_3D_I2MConversion |CBC 3D I2MConversion]] 
Acknowledgments:
*This work was partially supported by NIH R44 OD018334-03A, grant CCF-1439079 and by the Richard T.Cheng Endowment.

Author: Fotis Drakopoulos 
Contributors: Joi Best (CRTC), Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andrey Fedorov (CRTC), Nikos Chrisochoides (CRTC) 
Contact: Nikos Chrisochoides: <email>npchris@gmail.com</email> , Joi Best: <email>jbest002@odu.edu</email> 
Website: https://crtc.cs.odu.edu 
License: BSD 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|Image:CRTC_logo.jpg|Center for Real-time Computing
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
The Mesh Compression (MC) module deforms the input tetrahedral mesh towards the boundaries of the input labeled image. Two point sets are extracted for the mesh deformation. The first (source point set) consists of the surface vertices in the input mesh. The second (target point set) consists of the surface edge points in the input labeled image. After the extraction of the two point sets, the input mesh is deformed by registering the source to the target point set using a Physics-Based Non-Rigid Registration method. The current version of the module supports a single-tissue labeled image and mesh.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{|
|[[File:brain_before.jpg|thumb|300px|Brain BCC mesh before MC]]
|[[File:brain_after.jpg|thumb|300px|Brain BCC mesh after MC]]
|[[File:brain_after_section.jpg|thumb|300px|Brain BCC mesh after MC (cross-section)]]
|}

{|
|[[File:nidus_before.jpg|thumb|300px|Nidus BCC mesh before MC]]
|[[File:nidus_after.jpg|thumb|300px|Nidus BCC mesh after MC]] 
|[[File:nidus_after_section.jpg|thumb|300px|Nidus BCC mesh after MC (cross-section)]]
|}

{|
|[[File:ventricles_before.jpg|thumb|300px|Ventricles BCC mesh before MC]]
|[[File:ventricles_after.jpg|thumb|300px|Ventricles BCC mesh after MC]]
|[[File:ventricles_after_section.jpg|thumb|300px|Ventricles BCC mesh after MC (cross-section)]]
|}

{|
|[[File:target_points.jpg|thumb|960px|How the non-connectivity parameter influences the number of the extracted target points]]
|}


{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

{|
|
* '''Mesh Compression Parameters:'''
** '''Flexibility:''' Controls the trade-off between the regularization energy defined by the stress energy of a linear bio-mechanical elastic model, and the similarity energy. Value should be between [0.1,1] (default: 1).
** '''Number of Iterations:''' Controls the number of iterations for the compressor. The larger the value the closer the boundaries of the input mesh to the boundaries of the input image. A large number of iterations might cause distorted poor-quality elements. Value should be between [1,10] (default: 3).
** '''Non Connectivity:''' Controls the density of the extracted target points via a prohibited connectivity between adjacent blocks of voxels. The larger the value the denser the target point set. 0 is vertex non-connectivity (26 neighbors), 1 is edge non-connectivity (18 neighbors), 2 is face non-connectivity (6 neighbors) and 3 is no non-connectivity. Value should be 0 or 1 or 2 or 3. (default: 0).
* '''Input/Output:'''
** '''Input Labeled Image:''' The input labeled image.
** '''Input Mesh File:''' The input tetrahedral mesh in vtk file format.
** '''Output Mesh File:''' The output deformed mesh in vtk file format (optional) (default: deformedMesh.vtk).
** '''Output Source Points File:''' The extracted source points in vtk file format (optional). The source points are the surface vertices of the input mesh.
** '''Output Target Points File:''' The extracted target points in vtk file format (optional). The target points are the surface edge points of the input labeled image.
** '''Output Surface Triangles File:''' The extracted surface triangles of the input mesh in vtk file format (optional).
|[[Image:MCPanel.jpg|thumb|380px|User Interface]]
|}

'''Note: this module will only work if the input image has identity orientation!'''


{{documentation/{{documentation/version}}/module-section|Similar Modules}}
*[[Documentation/Nightly/Modules/BodyCentricCubicMesh]]


{{documentation/{{documentation/version}}/module-section|References}}
* Yixun Liu, Panagiotis Foteinos, Andrey Chernikov and Nikos Chrisochoides, "Mesh Deformation-based Multi-tissue Mesh Generation for Brain Images", Engineering with Computers, Volume 28, pages 305-318, 2012.

{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/BodyCentricCubicMesh

2018-08-07T13:57:04Z

Jbest:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/CBC_3D_I2MConversion |CBC 3D I2MConversion]] 
Acknowledgments:
*This work was partially supported by NIH R44 OD018334-03A, grant CCF-1439079 and by the Richard T.Cheng Endowment.

Author: Fotis Drakopoulos 
Contributors: Joi Best (CRTC), Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andrey Fedorov (CRTC), Nikos Chrisochoides (CRTC) 
Contact: Nikos Chrisochoides: <email>npchris@gmail.com</email> , Joi Best: <email>jbest002@odu.edu</email> 
Website: https://crtc.cs.odu.edu
 
License: BSD 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|Image:CRTC_logo.jpg|Center for Real-time Computing
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
The module generates a Body Centric Cubic (BCC) mesh from a labeled image. Initially the generated mesh is homogeneous, that means does not distinguish different tissues. Later the module specifies which tissue each tetrahedron belongs to. Each tissue is capable of automatically adjusting its resolution based on its geometric complexity and the predefined subdivision criterion. The current version of the module supports a single-tissue input labeled image.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{|
|[[File:brain.jpg|thumb|280px|Brain BCC mesh]]
|[[File:nidus.jpg|thumb|280px|Nidus BCC mesh]]
|[[File:ventricles.jpg|thumb|280px|Ventricles BCC mesh]]
|}
{|
|[[File:brain_section.jpg|thumb|280px|Brain BCC mesh cross-section]]
|[[File:nidus_section.jpg|thumb|280px|Nidus BCC mesh cross-section]]
|[[File:ventricles_section.jpg|thumb|280px|Ventricles BCC mesh cross-section]]
|}

{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

{|
|
* '''Mesh Generation Parameters:'''
** '''Size:''' Controls the size of the mesh. The smaller the value the larger the mesh. Value should be between [1,20] (default: 8).
** '''Fidelity:''' Controls the subdivision of the elements that belong to more than one image labels. The larger the value the better the conformity of the mesh on the image label boundaries. Value should be between [0.1,1] (default: 0.8).
** '''Resample Resolution:''' Controls the image resampling. Suggested value is 0 (no-resampling) for large tissues and 1 or 2 for smaller tissues. Value should be 0 or 1 or 2 (default: 0).
* '''Input/Output:'''
** '''Input Labeled Image:''' The input labeled image.
** '''Output Mesh File:''' The output tetrahedral mesh in vtk file format. (default: outputMesh.vtk)
|[[Image:BCCPanel.jpg|thumb|320px|User Interface]]
|}

'''Note: this module will only work if the input image has identity orientation!'''


{{documentation/{{documentation/version}}/module-section|Similar Modules}}
*[[Documentation/Nightly/Modules/MeshCompression]]


{{documentation/{{documentation/version}}/module-section|References}}
* Fedorov A., Chrisochoides N., Kikinis R., Warfield S, "Tetrahedral mesh generation for medical imaging", The Insight Journal-2005 MICCAI Open-Source Workshop, 2005
* Yixun Liu, Panagiotis Foteinos, Andrey Chernikov and Nikos Chrisochoides, "Mesh Deformation-based Multi-tissue Mesh Generation for Brain Images", Engineering with Computers, Volume 28, pages 305-318, 2012.

{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Extensions/CBC 3D I2MConversion

2018-07-16T19:32:27Z

Jbest:

Documentation/Nightly/Modules/BodyCentricCubicMesh

2018-07-16T19:32:02Z

Jbest:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/CBC_3D_I2MConversion |CBC 3D I2MConversion]] 
Acknowledgments:
*This work was partially supported by NIH R44 OD018334-03A, grant CCF-1139864 and by the Richard T.Cheng Endowment.

Author: Fotis Drakopoulos 
Contributors: Joi Best (CRTC), Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andrey Fedorov (CRTC), Nikos Chrisochoides (CRTC) 
Contact: Nikos Chrisochoides: <email>npchris@gmail.com</email> , Joi Best: <email>jbest002@odu.edu</email> 
Website: https://crtc.cs.odu.edu
 
License: BSD 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|Image:CRTC_logo.jpg|Center for Real-time Computing
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
The module generates a Body Centric Cubic (BCC) mesh from a labeled image. Initially the generated mesh is homogeneous, that means does not distinguish different tissues. Later the module specifies which tissue each tetrahedron belongs to. Each tissue is capable of automatically adjusting its resolution based on its geometric complexity and the predefined subdivision criterion. The current version of the module supports a single-tissue input labeled image.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{|
|[[File:brain.jpg|thumb|280px|Brain BCC mesh]]
|[[File:nidus.jpg|thumb|280px|Nidus BCC mesh]]
|[[File:ventricles.jpg|thumb|280px|Ventricles BCC mesh]]
|}
{|
|[[File:brain_section.jpg|thumb|280px|Brain BCC mesh cross-section]]
|[[File:nidus_section.jpg|thumb|280px|Nidus BCC mesh cross-section]]
|[[File:ventricles_section.jpg|thumb|280px|Ventricles BCC mesh cross-section]]
|}

{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

{|
|
* '''Mesh Generation Parameters:'''
** '''Size:''' Controls the size of the mesh. The smaller the value the larger the mesh. Value should be between [1,20] (default: 8).
** '''Fidelity:''' Controls the subdivision of the elements that belong to more than one image labels. The larger the value the better the conformity of the mesh on the image label boundaries. Value should be between [0.1,1] (default: 0.8).
** '''Resample Resolution:''' Controls the image resampling. Suggested value is 0 (no-resampling) for large tissues and 1 or 2 for smaller tissues. Value should be 0 or 1 or 2 (default: 0).
* '''Input/Output:'''
** '''Input Labeled Image:''' The input labeled image.
** '''Output Mesh File:''' The output tetrahedral mesh in vtk file format. (default: outputMesh.vtk)
|[[Image:BCCPanel.jpg|thumb|320px|User Interface]]
|}

'''Note: this module will only work if the input image has identity orientation!'''


{{documentation/{{documentation/version}}/module-section|Similar Modules}}
*[[Documentation/Nightly/Modules/MeshCompression]]


{{documentation/{{documentation/version}}/module-section|References}}
* Fedorov A., Chrisochoides N., Kikinis R., Warfield S, "Tetrahedral mesh generation for medical imaging", The Insight Journal-2005 MICCAI Open-Source Workshop, 2005
* Yixun Liu, Panagiotis Foteinos, Andrey Chernikov and Nikos Chrisochoides, "Mesh Deformation-based Multi-tissue Mesh Generation for Brain Images", Engineering with Computers, Volume 28, pages 305-318, 2012.

{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/MeshCompression

2018-07-16T19:31:36Z

Jbest:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/CBC_3D_I2MConversion |CBC 3D I2MConversion]] 
Acknowledgments:
*This work was partially supported by NIH R44 OD018334-03A, grant CCF-1139864 and by the Richard T.Cheng Endowment.

Author: Fotis Drakopoulos 
Contributors: Joi Best (CRTC), Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andrey Fedorov (CRTC), Nikos Chrisochoides (CRTC) 
Contact: Nikos Chrisochoides: <email>npchris@gmail.com</email> , Joi Best: <email>jbest002@odu.edu</email> 
Website: https://crtc.cs.odu.edu 
License: BSD 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|Image:CRTC_logo.jpg|Center for Real-time Computing
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
The Mesh Compression (MC) module deforms the input tetrahedral mesh towards the boundaries of the input labeled image. Two point sets are extracted for the mesh deformation. The first (source point set) consists of the surface vertices in the input mesh. The second (target point set) consists of the surface edge points in the input labeled image. After the extraction of the two point sets, the input mesh is deformed by registering the source to the target point set using a Physics-Based Non-Rigid Registration method. The current version of the module supports a single-tissue labeled image and mesh.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{|
|[[File:brain_before.jpg|thumb|300px|Brain BCC mesh before MC]]
|[[File:brain_after.jpg|thumb|300px|Brain BCC mesh after MC]]
|[[File:brain_after_section.jpg|thumb|300px|Brain BCC mesh after MC (cross-section)]]
|}

{|
|[[File:nidus_before.jpg|thumb|300px|Nidus BCC mesh before MC]]
|[[File:nidus_after.jpg|thumb|300px|Nidus BCC mesh after MC]] 
|[[File:nidus_after_section.jpg|thumb|300px|Nidus BCC mesh after MC (cross-section)]]
|}

{|
|[[File:ventricles_before.jpg|thumb|300px|Ventricles BCC mesh before MC]]
|[[File:ventricles_after.jpg|thumb|300px|Ventricles BCC mesh after MC]]
|[[File:ventricles_after_section.jpg|thumb|300px|Ventricles BCC mesh after MC (cross-section)]]
|}

{|
|[[File:target_points.jpg|thumb|960px|How the non-connectivity parameter influences the number of the extracted target points]]
|}


{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

{|
|
* '''Mesh Compression Parameters:'''
** '''Flexibility:''' Controls the trade-off between the regularization energy defined by the stress energy of a linear bio-mechanical elastic model, and the similarity energy. Value should be between [0.1,1] (default: 1).
** '''Number of Iterations:''' Controls the number of iterations for the compressor. The larger the value the closer the boundaries of the input mesh to the boundaries of the input image. A large number of iterations might cause distorted poor-quality elements. Value should be between [1,10] (default: 3).
** '''Non Connectivity:''' Controls the density of the extracted target points via a prohibited connectivity between adjacent blocks of voxels. The larger the value the denser the target point set. 0 is vertex non-connectivity (26 neighbors), 1 is edge non-connectivity (18 neighbors), 2 is face non-connectivity (6 neighbors) and 3 is no non-connectivity. Value should be 0 or 1 or 2 or 3. (default: 0).
* '''Input/Output:'''
** '''Input Labeled Image:''' The input labeled image.
** '''Input Mesh File:''' The input tetrahedral mesh in vtk file format.
** '''Output Mesh File:''' The output deformed mesh in vtk file format (optional) (default: deformedMesh.vtk).
** '''Output Source Points File:''' The extracted source points in vtk file format (optional). The source points are the surface vertices of the input mesh.
** '''Output Target Points File:''' The extracted target points in vtk file format (optional). The target points are the surface edge points of the input labeled image.
** '''Output Surface Triangles File:''' The extracted surface triangles of the input mesh in vtk file format (optional).
|[[Image:MCPanel.jpg|thumb|380px|User Interface]]
|}

'''Note: this module will only work if the input image has identity orientation!'''


{{documentation/{{documentation/version}}/module-section|Similar Modules}}
*[[Documentation/Nightly/Modules/BodyCentricCubicMesh]]


{{documentation/{{documentation/version}}/module-section|References}}
* Yixun Liu, Panagiotis Foteinos, Andrey Chernikov and Nikos Chrisochoides, "Mesh Deformation-based Multi-tissue Mesh Generation for Brain Images", Engineering with Computers, Volume 28, pages 305-318, 2012.

{{documentation/{{documentation/version}}/module-section|Information for Developers}}
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Documentation/Nightly/Extensions/CBC 3D I2MConversion

2018-07-16T19:29:55Z

Jbest:

Documentation/Nightly/Modules/BodyCentricCubicMesh

2018-07-16T19:29:30Z

Jbest:

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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
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Extension: [[Documentation/{{documentation/version}}/Extensions/CBC_3D_I2MConversion |CBC 3D I2MConversion]] 
Acknowledgments:
*This work was partially supported by NIH R44 OD018334-03A, grant CCF-1139864 and by the Richard T.Cheng Endowment.

Author: Fotis Drakopoulos 
Contributors: Joi Best (CRTC), Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andrey Fedorov (CRTC), Nikos Chrisochoides (CRTC) 
Contact: Nikos Chrisochoides, <email>npchris@gmail.com</email> , Joi Best, <email>jbest002@odu.edu</email> 
Website: https://crtc.cs.odu.edu
 
License: BSD 
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|Image:CRTC_logo.jpg|Center for Real-time Computing
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{{documentation/{{documentation/version}}/module-section|Module Description}}
The module generates a Body Centric Cubic (BCC) mesh from a labeled image. Initially the generated mesh is homogeneous, that means does not distinguish different tissues. Later the module specifies which tissue each tetrahedron belongs to. Each tissue is capable of automatically adjusting its resolution based on its geometric complexity and the predefined subdivision criterion. The current version of the module supports a single-tissue input labeled image.


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{|
|[[File:brain.jpg|thumb|280px|Brain BCC mesh]]
|[[File:nidus.jpg|thumb|280px|Nidus BCC mesh]]
|[[File:ventricles.jpg|thumb|280px|Ventricles BCC mesh]]
|}
{|
|[[File:brain_section.jpg|thumb|280px|Brain BCC mesh cross-section]]
|[[File:nidus_section.jpg|thumb|280px|Nidus BCC mesh cross-section]]
|[[File:ventricles_section.jpg|thumb|280px|Ventricles BCC mesh cross-section]]
|}

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N/A


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{|
|
* '''Mesh Generation Parameters:'''
** '''Size:''' Controls the size of the mesh. The smaller the value the larger the mesh. Value should be between [1,20] (default: 8).
** '''Fidelity:''' Controls the subdivision of the elements that belong to more than one image labels. The larger the value the better the conformity of the mesh on the image label boundaries. Value should be between [0.1,1] (default: 0.8).
** '''Resample Resolution:''' Controls the image resampling. Suggested value is 0 (no-resampling) for large tissues and 1 or 2 for smaller tissues. Value should be 0 or 1 or 2 (default: 0).
* '''Input/Output:'''
** '''Input Labeled Image:''' The input labeled image.
** '''Output Mesh File:''' The output tetrahedral mesh in vtk file format. (default: outputMesh.vtk)
|[[Image:BCCPanel.jpg|thumb|320px|User Interface]]
|}

'''Note: this module will only work if the input image has identity orientation!'''


{{documentation/{{documentation/version}}/module-section|Similar Modules}}
*[[Documentation/Nightly/Modules/MeshCompression]]


{{documentation/{{documentation/version}}/module-section|References}}
* Fedorov A., Chrisochoides N., Kikinis R., Warfield S, "Tetrahedral mesh generation for medical imaging", The Insight Journal-2005 MICCAI Open-Source Workshop, 2005
* Yixun Liu, Panagiotis Foteinos, Andrey Chernikov and Nikos Chrisochoides, "Mesh Deformation-based Multi-tissue Mesh Generation for Brain Images", Engineering with Computers, Volume 28, pages 305-318, 2012.

{{documentation/{{documentation/version}}/module-section|Information for Developers}}
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Documentation/Nightly/Extensions/CBC 3D I2MConversion

2018-07-16T19:26:49Z

Jbest: