benzwick / mvox

MVox Mesh Voxelizer

MVox Mesh Voxelizer

MVox is a tool for generating structured finite element meshes from image data by converting image voxels to elements.

Build Status

Downloading

Clone the repository using Git:

git clone https://github.com/benzwick/mvox.git

Installing

MVox can be configured and installed using the CMake build system.

Dependencies

MVox depends on the MFEM and ITK libraries which must be installed first.

MFEM

For instructions on how to install MFEM see https://github.com/mfem/mfem/blob/master/INSTALL.

For use with MVox it is sufficient to configure MFEM with the default options. However, to use on-the-fly gzip compression of mesh and grid function files, the zlib library option is required (-DMFEM_USE_ZLIB=YES).

For example, configure and make MFEM 4.5 in the ../mfem-build build directory relative to the ./mfem-4.5.2 source directory:

wget https://github.com/mfem/mfem/archive/refs/tags/v4.5.2.tar.gz
tar -zxf v4.5.2.tar.gz
mkdir mfem-build
cd mfem-build
cmake -DCMAKE_INSTALL_PREFIX=/opt/mfem/mfem-4.5 -DMFEM_USE_ZLIB=YES ../mfem-4.5.2
make -j4
make install

ITK

For instructions on how to install ITK see https://itk.org/Wiki/ITK/Source#Linux_Package_Distributions.

For example, to install ITK on Debian or Ubuntu:

sudo apt-get install libinsighttoolkit4-dev

Building MVox from source

Configure and make MVox in the ../build build directory relative to the ./mvox source directory:

cd ..
mkdir build
cd build
cmake -DMFEM_DIR=/opt/mfem/mfem-4.5 ../mvox
make
make install

The MFEM_DIR variable is optional and can be used to specify the location of the MFEM library.

Running

MVox is a CLI program. For instructions on how to use MVox type mvox --help.

To create a mesh and symmetric tensors grid function:

mvox -imask brain_mask.nrrd -iattr label.nrrd -itensor dti.nrrd -omesh mesh.mesh -sym -otensor dti.gf.gz

To view a tensor components using GLVis:

glvis -m mesh.mesh -g dti.gf.gz -gc 0

Example scripts and input data files can be found in the examples directory.

Copying

MVox is free software: you can redistribute it and/or modify it under the terms of the BSD 3-Clause License. See file LICENSE for details.

Citing

If you use MVox for your research, please consider adding the following citation:

• Zwick, B.F. (2020) MVox Mesh Voxelizer. Available at: https://github.com/benzwick/mvox

BibTeX:

@Misc{zwick_2020_mvox,
  author =   {Benjamin F. Zwick},
  title =    {{MVox} {M}esh {V}oxelizer},
  howpublished = {\url{https://github.com/benzwick/mvox}},
  year = 2020
}