Software to install for the class

  • A text editor to edit python code - see Choosing an editor
  • Python and the Python scientific libraries installed - see below.

If you already have some large Python packaging system installed, such as the Enthought Python Distribution, you can stick with that, it should provide the dependencies you need. To make sure, see Check your installation. If you don’t have something like that (most of you won’t), please read on...

If you are using Windows

Please install Python (X, Y) :

You want the file Python(x,y)- - not the updates, but the full release.

Choose the default installation options for now.

If you are using OSX

We have an exciting new installer for the course. If you do not have python 2.7, installed, or you aren’t sure if you have it installed, please start by running the installer at

Next, please try the fancy installer I built for this course, called Reginald. Download reginald.dmg with right-click and Save link as from the course web directory. Double click to mount the installer, then open the mounted disk image and look at the ReadMe.txt file, and then double click the installer.

Remember to Check your installation

If you are using Linux

If you are using Ubuntu or Debian, please set up NeuroDebian using the instructions on the NeuroDebian website. Then:

sudo apt-get install python-nipy
sudo apt-get install ipython-notebook
sudo apt-get install python-matplotlib python-nose

On Fedora or related distros, it’s a little more complicated:

sudo yum install numpy scipy sympy python-setuptools
sudo yum install python-matplotlib python-nose
sudo yum install python-ipython-notebook
sudo easy_install nibabel
sudo easy_install nipy

Check your installation

To check you have a working installation, please download this checklist script from Fernando Perez’ website, and run it. To download, please Right click on the link and Save link as to save to your hard disk. The instructions on what to do are at the top of the file. If you have problems, please come to office hours and we’ll try and help you.