Home

This vmtk fork adds additional scripts to vmtk designed to facilitate cardiac mesh generation and the creation of custom pipelines in this context.

Additional information can be found in this paper:

Fedele, M, Quarteroni, A. Polygonal surface processing and mesh generation tools for the numerical simulation of the cardiac function. Int J Numer Meth Biomed Engng. 2021;e3435. https://doi.org/10.1002/cnm.3435

How to install this vmtk fork on Linux

This instruction should work on debian-based distributions, tested on Ubuntu 20.04 and Debian 10.

Linux packages

Make sure you have installed the following packages:

sudo apt install gcc cmake cmake-curses-gui git libgsl-dev libeigen3-dev libxt-dev libgl1-mesa-glx libgl1-mesa-dev libglapi-mesa libosmesa-dev build-essential libtbb2 libtbb-dev

Anaconda

Download and install anaconda for Linux from this link.

vmtk

Make sure you have a GitHub account configured with SSH key.

Create a conda environment where to build and use vmtk:

VMTK_CONDA_ENV=vmtk
conda install anaconda-client
conda update conda anaconda-client
conda config --set restore_free_channel true
conda create -n ${VMTK_CONDA_ENV} python=3.6 numpy joblib

Save this bash script as install_vmtk.sh and, optionally editing the first lines, run it with the command:

source install_vmtk.sh

After installing vmtk, this script will also add the alias loadvmtk (if VMTK_CONDA_ENV=vmtk, otherwise loadYOUR_CONDA_ENV_NAME) to your .bashrc file that configures your shell to use vmtk. Each time you want to use vmtk on a new shell it is sufficient to run the command loadvmtk and all the vmtk scripts will be available from any locations.

Update this vmtk fork

1. go to your source directory and run the command git pull origin master
2. go to your build directory and run the command loadvmtk && make VMTK