Installing and Getting Started

Installing PySurfer is quite simple with pip:

pip install pysurfer

If you already have PySurfer installed, you can also use pip to update it:

pip install -U pysurfer

If you would like to save movies of time course data, also include the optional dependency imageio with:

pip install -U pysurfer[save_movie]

If you’d like to install the development version, you have two options. You can use pip:

pip install git+git://github.com/nipy/pysurfer.git#egg=pysurfer

Or you can clone the git repository and install from the source directory:

python setup.py install

If you don’t have pip, you can also install PySurfer with easy_install, or use easy_install to get pip.

Dependencies

PySurfer requires Python 2.7, and it does not work on Python 3.

To use PySurfer, you will need to have the following Python packages:

Some functions also make use of the Python Imaging Library (PIL), although it’s not mandatory.

An easy option to set up this environment is the Anaconda distribution, which is free and ships with many of the required packages. If you use Anaconda, you’ll need to install Mayavi separately. This can be done using the conda command:

conda install mayavi

You’ll also need to install nibabel, which can be done using pip as above.

Another option for getting set up is the Enthough Canopy environment, which is similar to Anaconda and free for academic use.

Getting started

PySurfer generally works out of the box on Linux systems. Getting started on OSX can be a bit more difficult. We have had success using the Anaconda distribution with the additional step of setting the environment variable QT_API to pyqt:

export QT_API=pyqt

If you’re using Canopy, you need to do something similar with the ETS_TOOLKIT variable:

export ETS_TOOLKIT=qt4

If you want to use PySurfer interactively, you should do so in ipython. After starting ipython (either in the terminal, qtconsole, or notebook), you have to activate the correct GUI backend, which is probably qt:

%gui qt

This will allow you to have an open PySurfer window while still being able to execute code in the console/notebook.

If you are having trouble getting started using PySurfer, please describe the problem on the nipy mailing list.