Documentation/4.3/Extensions/CleaverExtension - Revision history

Lasso at 02:20, 4 November 2014

2014-11-04T02:20:08Z

Lasso at 01:30, 4 November 2014

2014-11-04T01:30:01Z

Brigb123 at 17:30, 20 June 2014

2014-06-20T17:30:08Z

Brigb123: Wiki page complete.

2014-06-17T20:07:02Z

Wiki page complete.

Brigb123 at 18:44, 17 June 2014

2014-06-17T18:44:28Z

Brigb123: Initial page creation using module template.

2014-06-17T18:41:20Z

Initial page creation using module template.

New page

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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
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Extension: [[Documentation/{{documentation/version}}/Extensions/CleaverExtension|CleaverExtension]] 
Cleaver - A MultiMaterial Tetrahedral Meshing Library and Application 

Acknowledgments: 
Cleaver is an Open Source software project that is principally funded through the SCI Institute's NIH/NIGMS CIBC Center. Please use the following acknowledgment and send us references to any publications, presentations, or successful funding applications that make use of NIH/NIGMS CIBC software or data sets. 
"This project was supported by the National Institute of General Medical Sciences of the National Institutes of Health under grant number P41GM103545." 

Developed at the [http://sci.utah.edu SCI Institute], [http://www.utah.edu University of Utah]. 
[http://www.sci.utah.edu/cibc-software/cleaver-cibc.html Project Webpage] 

Author: Jonathan Bronson 
Contributor1: Josh Levine (Co-Author) 
Contributor2: Ross Whitaker (Co-Author) 
Contributor3: Brig Bagley (Developer) 
Contact1: Jonathan Bronson, <email>bronson@sci.utah.edu</email> 
Contact2: Brig Bagley, <email>brig@sci.utah.edu</email> 

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CleaverExtension is a Slicer CLI Module that takes a set of NRRD Volumes and creates a set of tetrahedral meshes
to import into the Slicer MRML. 

Based on the "Lattice Cleaving" algorithm (see References), this method is theoretically guaranteed to produce valid meshes with bounded dihedral angles, while still conforming to multimaterial material surfaces. Empirically these bounds have been shown to be significant.


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|[[Image:SkullStripperInput-3-6.png|thumb|340px|Input T1 Image]]
|[[Image:SkullStripperOutput-3-6.png|thumb|340px|Brain mask as contour]]
|[[Image:SkullStripperSurface-3-6.png|thumb|375px|Brain surface]]
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{{documentation/{{documentation/version}}/module-section|References}}
* Bronson J., Levine, J., Whitaker R., "Lattice Cleaving: Conforming Tetrahedral Meshes of Multimaterial Domains with Bounded Quality". Proceedings of the 21st International Meshing Roundtable (San Jose, CA, Oct 7-10, 2012).


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For technical questions or problems, please use contacts in the introduction. 
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@@ Line 97: / Line 97: @@
 |}<br>
-Sample data:
+Sample data: [[Media:CleaverSampleData.zip]]
-* Option 1 - Use  MRHead-label.nrrd + MRHeader-label-inverse.nrrd.
+* Option 1 - Use  Cleaver-MRHead-label.nrrd + Cleaver-MRHeader-label-inverse.nrrd.
-* Option 2a - Use MRHead-label-shifted.nrrd and let Cleaver infer the inverse.
+* Option 2a - Use Cleaver-MRHead-label-shifted.nrrd and let Cleaver infer the inverse.
-* Option 2b - Use Gaussian_MRHead-label-shifted.nrrd and let Cleaver infer the inverse. This is a Gaussian smoothed version of option 2a to show how a smooth function can prevent stair-stepping artefacts.
+* Option 2b - Use Cleaver-MRHead-label-shifted-Gaussian.nrrd and let Cleaver infer the inverse. This is a Gaussian smoothed version of option 2a to show how a smooth function can prevent stair-stepping artefacts.
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 *Apply : Runs the CLI with the above options within Slicer. See output in the console.
 *Cancel : Stop the current process.
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 |[[Image:Screenshot4.jpeg|thumb|700px|Example1]]
 |}<br>
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 {|
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-|[[Image:SlicerGui.png|thumb|280px|Module UI]]
+|[[Image:SlicerGui.png|thumb|300px|Module UI]]
 |}
 *Input Volume 1-8 : Import up to 8 different volumes (NRRD) of the same dimension for Cleaver to mesh.
 *Output Model1-10 : Create up to 10 new models for Cleaver to write mesh data to. If none or too few are specified for the output, the console will provide the locations of the VTK mesh files and MRML scene file to load.
 *Use Padding : Often a good option to allow if material transitions exist at the volume boundaries.
 *Alpha Short : The minimum distance on an edge cut after which Cleaver does not warp a vertex.
 *Alpha Long : The maximum distance on an edge cut after which Cleaver will create a sub-tetrahedron (Cleave the current tet).

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 Extension: [[Documentation/{{documentation/version}}/Extensions/CleaverExtension|CleaverExtension]]<br><br>
-Cleaver - A MultiMaterial Tetrahedral Meshing Library and Application<br><br>
+Cleaver - A MultiMaterial Tetrahedral Meshing Library and Application<br>

@@ Line 28: / Line 28: @@
 Contact2: Brig Bagley, <email>brig@sci.utah.edu</email><br>
-{{documentation/{{documentation/version}}/module-introduction-row}}
+{|
+|[[Image:Sci.png|thumb|340px|SCI Institute]]
-{{documentation/{{documentation/version}}/module-introduction-logo-gallery
+|[[Image:CleaverCIBC.png|thumb|340px|Cleaver - CIBC]]
-|{{collaborator|logo|ge}}|{{collaborator|longname|ge}}
+|[[Image:uofu.jpg|thumb|340px|University of Utah]]
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+|}
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 {|
-|[[Image:SkullStripperInput-3-6.png|thumb|340px|Input T1 Image]]
+|[[Image:FrogSlices.jpeg|thumb|540px|Input Frog image slices]]
-|[[Image:SkullStripperOutput-3-6.png|thumb|340px|Brain mask as contour]]
+|[[Image:SlicerFrogOutput.png|thumb|375px|Frog Surface]]
 |}
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 {|
+|
-|[[Image:SkullStripper-3-6.png|thumb|280px|Module UI]]
+|[[Image:SlicerGui.png|thumb|280px|Module UI]]
 |}
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-{{documentation/{{documentation/version}}/module-section|Similar Modules}}
+{{documentation/{{documentation/version}}/module-section|Tutorials}}
+*Both volumes and models are provided and created, respectively. When running in VTKtet output mode, the tet models are automatically loaded into Slicer.<br>
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 {{documentation/{{documentation/version}}/module-section|References}}
-* Bronson J., Levine, J., Whitaker R., "Lattice Cleaving: Conforming Tetrahedral Meshes of Multimaterial Domains with Bounded Quality". Proceedings of the 21st International Meshing Roundtable (San Jose, CA, Oct 7-10, 2012).
+* Bronson J., Levine, J., Whitaker R., "Lattice Cleaving: Conforming Tetrahedral Meshes of Multimaterial Domains with Bounded Quality". Proceedings of the 21st International Meshing Roundtable (San Jose, CA, Oct 7-10, 2012).<br>
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 {{documentation/{{documentation/version}}/module-section|Information for Developers}}
-For technical questions or problems, please use contacts in the introduction. <br><br>
+For technical questions or problems, please use contacts in the introduction. <br>
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