Slicer-CleaverExtension

This extension packages Cleaver, a multimaterial tetrahedral meshing library.

Cleaver is a C++ library for generating guaranteed-quality, tetrahedral meshes of multimaterial volumetric data. It is based on the 'Lattice Cleaving' algor- ithm:

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)

The method is theoretically guaranteed to produce valid meshes with bounded dihedral angles, while still conforming to multimaterial surfaces. Empirically these bounds have been shown to be significant.

Acknowledgement: Cleaver is an Open Source software project that is principally funded through the SCI Institute's NIH/NIGMS CIBC Center. Please use the following acknowledg- ment 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 grants from the National Center for Research Resources (5P41RR012553-15) and the National Institute of General Medical Sciences (8 P41 GM103545-15) from the National Institutes of Health.

Dependencies

1. Git (www.git-scm.com)
2. Cmake (www.cmake.org)
3. Slicer (www.slicer.org)

Building

Once the dependencies are obtained, you can build the module.

cd Slicer-CleaverExtension
mkdir build
cd build
cmake ..
make .. 

**NOTES** * You can set Slicer_DIR to the directory where you have build Slicer3D. * You can set Testing to OFF is desired. * You can set BUILD_STANDALONE to ON if building outside of Slicer.

Running and Using

Inside of Slicer, you can edit the program properties:

1. Edit->Application Settings->Modules
2. In "Additional module paths", add the directory where the Cleaver Module was built (../Slicer-CleaverExtension/build/CleaverCLI)
3. Click OK and restart Slicer.
4. Search for "Cleaver" in the Modules. The module should appear.
5. Load NRRD data and choose desired volumes.
6. In Output Model 1-10, create as many models as you desire. The program will automatically load the geometry for each model you specify. If more are generated than specified, the program will notify you (in the terminal) where the extra models are saved. If there is no terminal for your running Slicer, be sure to set "Output Directory".
7. Set additional settings and click "Apply" at the bottom.
8. When the program is done, you can manually load the extra models into the Slicer Scenewith the ones automatically loaded. A MRML scene is also created with model colors already provided. You can close the current scene and load this one (location noted in the terminal).