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
In order to use surface plotting functionality like
netneurotools.plotting.plot_fsaverage()
, you will need a working
vtk
/mayavi
/pysurfer
installation. These can generally be installed
with the following command:
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
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
Troubleshooting
Error related to
from tvtk.vtk_module import VTK_MAJOR_VERSION
Temporary workaround: adding
VTK_MAJOR_VERSION = 9
tomayavi/tvtk/vtk_module.py
Error related to GLX
Try
glxgears
orglxinfo
Check display driver compatibility