Installation#

The developer version of InVesalius runs on Windows, macOS, and Linux operating systems. On this page, instructions to installing and running InVesalius on these systems can be found.

Windows#

These instructions are tested on Windows 10 64 bits. The packages required by InVesalius can be installed either through a Python system installation or the Anaconda package manager. In both cases, the following prerequisites apply:

Prerequisites#

Visual Studio (We are using the 2019 community edition).

It’s possible to install using chocolatey:

 choco install -y visualstudio2019buildtools
 choco install -y visualstudio2019-workload-vctools

Download InVesalius source code.

git clone --recurse-submodules https://github.com/invesalius/invesalius3

Python Installation#

Install the InVesalius either with Python system OR Anaconda.

Option 1: Python System Installation#

Download and install Python 3.8 from the Python website.
Install InVesalius main dependencies (WXPython, numpy, scipy, scikit-image, ImageIO, H5Py, Pillow, Pyserial, PSUtil, nibabel, configparser, PyPubsub, plaidml and Cython) using pip:

pip install -r requirements.txt

If you are going to use the neuronavigation features, install the wrappers to the tracking devices:

pip install pyclaron polhemusFT polhemus pypolaris pypolarisP4

Optional: To take advantage of the real-time tractography computation during neuronavigation, the package Trekker is required. The following command downloads and install the pre-generated wheel for Python 3.7:

pip install https://github.com/dmritrekker/trekker/raw/master/binaries/Trekker-0.9-cp38-cp38-win_amd64.whl

Option 2: Anaconda Installation#

Install Anaconda, preferably the 64-bit version.
In the Anaconda Powershell, navigate to the cloned InVesalius source code folder, for example:

cd C:\Users\%USERNAME%\repository\invesalius3\

Install the required packages with the following command:

conda env create -f environment.yml --name invesalius

This will create a virtual environment named invesalius. To activate it:

conda activate invesalius

Compiling InVesalius#

Some algorithms of InVesalius are written in Cython for performance. It’s needed to compile them. Open the command prompt of your Visual Studio and go to the InVesalius source code directory, then compile using this command:

python setup.py build_ext --inplace

Running InVesalius#

Inside InVesalius source code directory run:

python app.py

Warning: If using Anaconda, remember to always open the Anaconda Powershell and activate the environment before running the above command.

MacOS#

This guide is based on High Sierra.

Prerequisites#

The first step is the installation of homebrew. Access the homebrew site to know how to install it.

We recommend installing the python3 from brew, also install OpenMP (we use it):

brew install python3 libomp

If you are working with an Apple Silicon Mac, you also have to install the hdf5:

brew install hdf5

Clone InVesalius 3 using git:

git clone --recurse-submodules https://github.com/invesalius/invesalius3

Installation#

To run the following commands your shell must be inside the InVesalius folder:

cd invesalius3

Install InVesalius main dependencies wxpython, numpy, scipy, VTK, GDCM, imageio, scikit-image, Pillow, Pyserial, PSUtil, nibabel, configparser, H5py, PyPubsub and plaidml using pip:

If using Mac with Intel:

pip3 install -r requirements.txt

If using Mac with Apple Silicon:

pip3 install -r requirements_m1.txt

Compiling InVesalius#

If you are using Mac with Apple Silicon, you need to export some environment variable before the next step:

export CFLAGS="-I/opt/homebrew/opt/libomp/include"
export CPPFLAGS="-I/opt/homebrew/opt/libomp/include"
export LDFLAGS="-L/opt/homebrew/opt/libomp/lib"

Compile the cython packages used by InVesalius:

python3 setup.py build_ext --inplace

Running Invesalius#

Now your system is ready to run InVesalius directly from the source code. Just enter the InVesalius 3 source and run it.

python3 app.py

If you have this error:

This program needs access to the screen. Please run with a
Framework build of python, and only when you are logged in
on the main display of your Mac.

Run InVesalius using this command:

pythonw app.py

Linux#

Packages Debian and Ubuntu#

InVesalius is already packaged and is in the main repos from Debian and Ubuntu. Install it using this command:

sudo apt install invesalius

If you want the most updated packages, there is also a PPA to Ubuntu:

sudo add-apt-repository ppa:tfmoraes/invesalius
sudo apt-get update
sudo apt install invesalius

After the installation, InVesalius appears in your system menu. You can also run it from the command line:

invesalius3

Other Distros#

InVesalius is packaged as Flatpak. First, you need to add the Flathub repo:

flatpak remote-add --if-not-exists flathub https://flathub.org/repo/flathub.flatpakrepo

Then install InVesalius:

flatpak install flathub br.gov.cti.invesalius

After the installation, InVesalius appears in your system menu. You can also run it from the command line:

flatpak run br.gov.cti.invesalius

Source Code#

Use this command to get InVesalius source code from GitHub:

git clone --recurse-submodules https://github.com/invesalius/invesalius3

Installing Dependencies#

Using PIP Packages (recommended)#

First, you have to install some system packages to compile wxPython and H5py:

Fedora (tested on Fedora 34)

sudo dnf -y install \
    gcc-c++ \
    python3-devel \
    freeglut-devel \
    gstreamer1-devel \
    gstreamer1-plugins-base-devel \
    gtk3-devel \
    libjpeg-turbo-devel \
    libnotify-devel \
    libpng-devel \
    libSM-devel \
    libtiff-devel \
    libXtst-devel \
    SDL-devel \
    webkit2gtk3-devel \
    which \
    hdf5-devel

Ubuntu (tested on Ubuntu 20.10 and 21.04)

sudo apt install -y \
    freeglut3 \
    freeglut3-dev \
    libgl1-mesa-dev \
    libglu1-mesa-dev \
    libgstreamer-plugins-base1.0-dev \
    libgtk-3-dev \
    libjpeg-dev \
    libnotify-dev \
    libsdl2-dev \
    libsm-dev \
    libtiff-dev \
    libwebkit2gtk-4.0-dev \
    libxtst-dev \
    python3-dev \
    libhdf5-dev \
    build-essential \
    python3-venv

Arch

sudo pacman -syu \
    wxgtk3 \
    glu \
    mesa \
    webkit2gtk

It’s recommended to create a virtualenv:

# Go to InVesalius folder
cd invesalius3
# Create my_env environment
python3 -m venv my_env
# Activate it every time you want to run InVesalius
source my_env/bin/activate
pip install -r requirements.txt

Using System Packages#

Debian and Ubuntu (Tested in Ubuntu 20.04)#

sudo apt install python3-wxgtk4.0 python3-numpy python3-scipy python3-pil python3-matplotlib python3-skimage python3-nibabel python3-serial python3-psutil python3-vtk7 python3-vtkgdcm python3-gdcm cython3 python3-h5py python3-imageio python3-keras python3-pubsub

Ubuntu don’t have PlaidML in their repositories, so install it using pip:

pip3 install --user plaidml-keras

Fedora (Tested in Fedora 32)#

sudo dnf install gcc gcc-g++ python3-wxpython4 python3-numpy python3-scipy python3-matplotlib python3-scikit-image python3-nibabel python3-pyserial python3-psutil python3-vtk python3-gdcm python3-Cython python3-h5py python3-pypubsub

Unfortunately, Fedora doesn’t have python3-imageio package. But it’s possible to install it using pip:

pip3 install --user imageio

Fedora don’t have PlaidML in their repositories, so install it using pip:

pip3 install --user plaidml-keras

Arch Linux#

sudo pacman -S cython python-pip python-numpy python-scipy python-scikit-learn python-wxpython python-pyserial python-psutil python-h5py python-pypubsub python-mpi4py python-matplotlib vtk clinfo opencl-headers gdal glew hdf5 jsoncpp netcdf pdal pugixml proj

You have to install some packages from AUR, I’m using Pikaur to install them:

pikaur -S --noconfirm gdcm python-nibabel python-scikit-image python-imageio python-plaidml python-plaidml-keras

Building the Cython Modules#

Enter on invesalius3 folder and execute: python3 setup.py build_ext --inplace

Running InVesalius#

To run InVesalius, enter the InVesalius folder and run the command:

python3 app.py

You can pass a DICOM folder as parameter to make InVesalius starts with the DICOM loaded.

python3 app.py -i /dicom/folder

It’s possible to make InVesalius load a DICOM folder, create a surface (mesh) with the given threshold and export the surface to an STL file without loading any GUI:

python3 app.py --no-gui -i /media/thiago/Documentos/dcm/0051 -t 200,3033 -e /tmp/0051.stl