Create volumetric mesh from segmentation using Cleaver2 or TetGen
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README.md

Segment Mesher extension

This is a 3D Slicer extension for creating volumetric meshes from segmentation using Cleaver2 or TetGen.

Cleaver2 mesher is freely usable, without any restrictions. TetGen mesher is only free for private, research, and educational use (see license for details).

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Installation

  • Download and install a recent nightly version of 3D Slicer (https://download.slicer.org).
  • Start 3D Slicer application, open the Extension Manager (menu: View / Extension manager)
  • Install SegmentMesher extension.

Tutorial

  • Start 3D Slicer
  • Load a volume (for example: switch to SampleData module and load MRBrainTumor1 imaage)
  • Switch to Mesh Segmenter module (in Segmentation category)
  • Select "Create new Model" for Output model (this will contain the generated volumetric mesh)
  • Click Apply button and wait a about a minute

Visualize and save results

  • Open "Display" section to enable clipping with slices.
  • Go to "Segmentations" module to hide current segmentation.
  • Switch to "Models" module to adjust visualization parameters.
  • To save Output model select in menu: File / Save.

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Mesh generation parameters

Cleaver parameters are described at https://sciinstitute.github.io/cleaver.pages/manual.html. Increase --scale parameter value to genereate a finer resolution mesh.

TetGen parameters are described at http://wias-berlin.de/software/tetgen/1.5/doc/manual/manual005.html#sec%3Acmdline

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 references to any publications, presentations, or successful funding applications that make use of NIH/NIGMS CIBC software or data sets to SCI: "This project was supported by the National Institute of General Medical Sciences of the National Institutes of Health under grant number P41 GM103545-18."

TetGen citation: Si, Hang (2015). "TetGen, a Delaunay-based Tetrahedral Mesh Generator". ACM Transactions on Mathematical Software. 41 (2): 11:1-11:36. doi:10.1145/2629697