PySurfer: Neuroimaging visualization in Python
PySurfer is a Python package for interacting with a cortical surface representations of neuroimaging data. It extends Mayavi's powerful visualization engine with a high-level interface for working with MRI and MEG data.
PySurfer offers both a command-line interface designed to broadly the Freesurfer Tksurfer program and a Python library for writing scripts to efficiently explore complex datasets and prepare publication-ready figures.
To goal of the project is to facilitate the production of figures that are both beautiful and scientifically informative.
Important Links
- Official source code repository: https://github.com/nipy/PySurfer
- Online documentation (stable): http://pysurfer.github.com/
- NITRC page: http://www.nitrc.org/projects/pysurfer
- Freesurfer: http://surfer.nmr.mgh.harvard.edu/
- Mailing list: https://mail.python.org/mailman/listinfo/neuroimaging
Install
This packages uses setuptools. To install it for all users, run:
python setup.py build
sudo python setup.py install
If you do not have sudo privileges, you can install locally:
python setup.py install --home
For information about dependencies, please see the online documentation
License
Available under the Revised BSD (3-clause) license.
Testing
You can launch the test suite by running nosetests from the source folder.
Another way to test is to build the documentation, which will run the example scripts and automatically generate static image output. From the source directory:
cd doc/
make clean
make html
The resulting documentation will live at _build/html/index.html, which can be compared to the online docs.
Either method will work only if you have Freesurfer installed on your machine with a valid SUBJECTS_DIR folder.