brainview
Simple Python module to visualize morphometry data on 3D brain meshes. Based on matplotlib and Mayavi.
About
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.
Development stage
This is pre-alpha and not ready for usage yet. Come back another day.
Interface (WIP)
Command line
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 -iYou can run both programs with --help to get help, and find some examples in the documentation.
Documentation
A first draft of the Brainview documentation is now available:
Screenshots
Morphometry data
The smoothed mean curvature at each vertex of the brain mesh, for the white (left) and pial (right) surfaces of a human brain:
Annotations
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.
Obtaining suitable pre-processed sMRI input data for brainview
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.
Development and tests
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.
Related neuroimaging tools
- 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.
- 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.
