Installation and setup

Python installation

This package requires Python >= 3.6. Assuming you have the correct version of Python installed, you can install netneurotools by opening a terminal and running the following:

git clone https://github.com/netneurolab/netneurotools.git
cd netneurotools
pip install .

Alternatively, you can install netneurotools directly from PyPi with:

pip install netneurotools

Optional installation for surface plotting

Pyvista

This is the new plotting library used in the package. This will allow you to use functions like

You will need a working pyvista installation. Generally, we recommend using a clean conda environment, and install Pyvista using the following commands:

 conda create -n plotting python=3.12
 conda activate plotting
 conda install -c conda-forge pyvista
 # if you are using Jupyter notebooks
conda install -c conda-forge jupyterlab trame trame-vtk trame-vuetify trame-jupyter-extension

If you meet any issues, please refer to the detailed installation guide.

Pysurfer (deprecated)

This is the old plotting library used in the package. It is now deprecated in favor of Pyvista. This will allow you to use functions like

You will need a working vtk/mayavi/pysurfer installation. These can generally be installed with the following command:

pip install vtk mayavi pysurfer

However, we include instructions below for installing the bleeding-edge version of the dependencies. Note: if you already have a working mayavi/pysurfer installation, there is generally no need to follow these instructions!

  • Install Qt

    • Installing Jupyterlab using conda (conda install jupyterlab) should automatically install the required qt/pyqt packages.

    • If otherwise, using pip install PyQt5 should also work as suggested by here and here

    • If not working, search for the error prompts like this.

  • Install VTK

    • Official wheels for the latest VTK9 are available for download here.

    • For Python>=3.9, official wheel is not available at the moment. Following here and here, it’s possible to build the wheel. See the example code below.

git clone https://github.com/Kitware/VTK
cd VTK

mkdir build
cd build
PYBIN=<PATH TO YOUR PYTHON EXECUTABLE>
cmake -GNinja -DVTK_BUILD_TESTING=OFF -DVTK_WHEEL_BUILD=ON -DVTK_PYTHON_VERSION=3 -DVTK_WRAP_PYTHON=ON -DPython3_EXECUTABLE=$PYBIN ../

# optionally, apt install ninja
ninja
$PYBIN setup.py bdist_wheel

# to install
pip install dist/vtk-*.whl

  • Install mayavi

    • Install from source pip install git+https://github.com/enthought/mayavi.git

  • Install pysurfer

    • Install from source pip install git+https://github.com/nipy/PySurfer.git

  • Install netneurotools

    • Install from source pip install git+https://github.com/netneurolab/netneurotools.git

Here are some common issues and their solutions:

  • Error related to from tvtk.vtk_module import VTK_MAJOR_VERSION

    • Currently not fixed

    • Temporary workaround: adding VTK_MAJOR_VERSION = 9 to mayavi/tvtk/vtk_module.py

  • Error related to GLX

    • Try glxgears or glxinfo

    • Check display driver compatibility