Simple Python module to visualize morphometry data on 3D brain meshes. Based on matplotlib and Mayavi. This is a prototype and not ready for production.

After playing with it for a while I have come to the conclusion that I don't really like Mayavi. For now, this project is on halt.

I suggest to have a look at pycortex or PySurfer for brain visulization in Python.

brainview is designed to visualize arbitrary data in 3D on brain surface meshes (see the screenshots below for an example). The typical usage is to plot brain morphometry data loaded with brainload, nibabel or similar tools during interactive data analysis.

Note that brainload plots data, not colors, i.e., the colors are usually derived from a separate colormap.

IMPORTANT: Brainload only provides basic visualization functions intended for quick (and usually interactive) live inspection of your data. If you are interesting in a full-featured brain visualization solution that can provide output in publication quality, I suggest you have a look at PySurfer instead. Brainview is in no way intended to be a replacement for tools like PySurfer.

A first alpha release exists since Jan 2019. Feel free to try it, but it's very early. ALso see the note above regarding project status.

The package comes with an example client: after installation, you can use the brainviewer and atlasviewer commands from your shell.

If you have FreeSurfer installed and want to interactively inspect the curvature for bert, a Freesurfer example subject, try:

brainviewer bert -d "$FREESURFER_HOME" -m curv -i

You can run both programs with --help to get help, and find some examples in the documentation.

A first draft of the Brainview documentation is now available:

Brainview documentation

The smoothed mean curvature at each vertex of the brain mesh, for the white (left) and pial (right) surfaces of a human brain:

Two examples for visualization of annotations based on cortical parcellations using different atlases: the Desikan-Killiany Atlas on the white surface (left), and the Destrieux Atlas on the pial surface (right) of the same subject.

pip install --user brainview

You can also install into a virtual environment (python2: virtualenv, python3: venv) of course, omit the --user part in that case.

Both source and wheel packages are also available here in the brainview releases section at GitHub, but you should not need them.

System dependencies:

Brainview itself does not have system-level dependencies, but it is based on other packages which have them. When using pip, you may need to install system dependencies using your OS package system.

This is only needed if you do not have the packages already. In that case, you will get errors like these when loading brainview:

• ModuleNotFoundError: No module named 'PyQt5.QtSvg'

To install the dependencies under deb-based Distros (Debian, Ubuntu, ...):

sudo apt-get install python3-pyqt5 python3-pyqt5.qtsvg

I started building conda packages for different operating systems, check https://anaconda.org/dfspspirit/brainview to see whether one is available for yours. In case it is:

conda install -c dfspspirit brainview

If it is not, you can use the recipe in this repo to build it yourself, see README_DEVELOPMENT.

The brainview module is designed to plot arbitrary per-vertex data onto brain meshes. Usually, this is morphometry data based on measures derived from Magnetic Resonance Imaging (MRI) data that has been pre-processed with the popular FreeSurfer software suite or any other tool. You could also plot properties of the mesh itself (like its curvature at each point) or other data, e.g., spatial gene expression data, of course.

If you do not have your MRI data / FreeSurfer output at hand but still want to try brainview, you could use the bert example subject that comes with FreeSurfer. You can load the data using brainload or nibabel.

Tests and test data are not shipped in the releases, see the README_DEVELOPMENT file in this repository for instructions on installing the development version and running the tests.

• If you want a full brain visualization package for Python that allows you to plot morphometry data in various ways and in publication quality, you should definitely have a look at PySurfer. PySurfer also offers different views of the brain in a single overview image and supports time data. Another interesting tool for Python is pycortex.
• If you have to use Matlab instead of Python, I can recommend SurfStat. It can do way more than visualization: it also features terms which allow you do conveniently formulate GLMs and it has support for different methods to detect spatial clusters of significant group differences, correct for multiple comparisons and more.
• If you like GNU R, you should have a look at my fsbrain package. It provides a high-level API for the visualization of brain surface data and is way more advanced than brainview.

MIT