Download and Install

This page covers the necessary steps to install and run NIPY. Below is a list of required dependencies, along with additional software recommendations.

Dependencies for install

Must Have

• Python 2.5 or later
• NumPy 1.2 or later: Numpy is an array library for Python
• SciPy 0.7 or later: Scipy contains scientific computing libraries based on numpy
• Sympy 0.6.6 or later: Sympy is a symbolic mathematics library for Python. We use it for statistical formulae.

Strong Recommendations

• IPython: Interactive Python environment.
• Matplotlib: python plotting library.

Installing from binary packages

For Debian or Ubuntu

Please use the NeuroDebian repository, and install with:

sudo apt-get install python-nipy

This will install the dependencies for you.

For Fedora, CentOS

sudo yum install numpy scipy sympy python-setuptools
sudo yum install python-devel gcc
sudo easy_install nibabel
sudo easy_install nipy

For OSX

Install Python, Numpy, and Scipy via their respective dmg installers.

Install via distribute / setuptools and easy_install. See the distribute page for how to install easy_install and related tools. Then (from the command prompt):

easy_install nipy

For Windows

Option 1

You can make your life much easier by using Python (X, Y). This will install Python, Numpy, Scipy, IPython, Matplotlib, Sympy and many other useful things.

Then go to nipy pypi and download the .exe installer for nipy. Double click to install.

Option 2

• Download Python and install with the exe or msi installer
• Download and install the “Scipy stack” from Christophe Gohlke’s unofficial windows binaries.
• If the nipy version on the unofficial windows binaries page is current, use that, otherwise, go to nipy pypi, download and install the exe installer for nipy

Option 3

Consider one of the big Python bundles such as EPD free or Anaconda CE for the dependencies. Install nipy from the exe installer at nipy pypi.

Option 4

Do all the installs by hand:

• Download Python and install with the exe or msi installer. Make sure your python and the scripts directory (say, c:\Python27\Scripts) are on your windows path.

• Download Numpy and Scipy exe installers for your Python version from their respective Numpy and Scipy download sites.

• Install distribute to give you easy_install.

• Install pip using easy_install from a windows cmd shell:

  easy_install pip

• Install sympy and nibabel using pip from a window cmd shell:

  pip install sympy
  pip install nibabel

• On 32-bit Windows, install nipy using easy_install:

  easy_install nipy

  This will pick up and use the exe installer. For 64-bits install use the installer at the unofficial windows binaries site.

Otherwise

I’m afraid you might need to build from source...

Building from source code

Dependencies for build

• A C compiler: NIPY does contain a few C extensions for optimized routines. Therefore, you must have a compiler to build from source. XCode (OSX) and MinGW (Windows) both include a C compiler. On Linux, try sudo apt-get build-essential on Debian / Ubuntu, sudo yum install gcc on Fedora and related distributions.

Recommended for build

• Cython 0.12.1 or later: Cython is a language that is a fusion of Python and C. It allows us to write fast code using Python and C syntax, so that it easier to read and maintain. You don’t need it to build a release, unless you modify the Cython *.pyx files in the nipy distribution.

Procedure

Developers should look through the development quickstart documentation. There you will find information on building NIPY, the required software packages and our developer guidelines.

If you are primarily interested in using NIPY, download the source tarball from nipy pypi and follow these instructions for building. The installation process is similar to other Python packages so it will be familiar if you have Python experience.

Unpack the source tarball and change into the source directory. Once in the source directory, you can build the neuroimaging package using:

python setup.py build

To install, simply do:

sudo python setup.py install

Note

As with any Python installation, this will install the modules in your system Python site-packages directory (which is why you need sudo). Many of us prefer to install development packages in a local directory so as to leave the system python alone. This is merely a preference, nothing will go wrong if you install using the sudo method.

If you have Python 2.6 or later, you might want to do a user install

python setup.py install –user

To install nipy in some other local directory, use the –prefix option. For example, if you created a local directory in your home directory, you would install nipy like this:

python setup.py install --prefix=$HOME/local

Installing useful data files

See Optional data packages for some instructions on installing data packages.