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Download and install

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

Dependencies

Must Have

Python 2.5 -2.7

Matplotlib 1.0
Plotting library
NetworkX 1.0 - 1.4
Python package for working with complex networks.

NumPy 1.3 - 1.5

SciPy 0.7 - 0.9
Numpy and Scipy are high-level, optimized scientific computing libraries.
simplejson
json is included in Python 2.6, but if you are using Python 2.5 you will need to install simplejson.

Enthought Traits 4.0.0

Note

Full distributions such as pythonxy or EPD provide the above packages.

Nibabel

Strong Recommendations

IPython 0.10.2 or 0.11
Interactive python environment. This is necessary for some parallel components of the pipeline engine.
Sphinx
Required for building the documentation
Graphviz
Required for building the documentation

Interface Dependencies

These are the software packages that nipype.interfaces wraps:

FSL
4.1.0 or later
matlab
2008a or later
SPM
SPM5/8
FreeSurfer
FreeSurfer version 4 and higher
AFNI
2009_12_31_1431 or later
Slicer
3.6 or later
Nipy
0.1.2+20110404 or later (required for doc building)
Nitime
(optional; required for doc building)

Camino

Camino2Trackvis

ConnectomeViewer

Download

Download the latest release from our github page.

To check out the latest development version:

git clone git://github.com/nipy/nipype.git

Install

The installation process is similar to other Python packages so it will be familiar if you have Python experience. Nipype is also hosted on the PyPi repository so you can do:

easy_install nipype

or:

pip install nipype

Debian and Ubuntu

Add the NeuroDebian repository and install the python-nipype package using apt-get or your favourite package manager.

Max OS X

The easiest way to get nipype running on MacOSX is to install EPD and then add nibabel and nipype by executing:

easy_install nibabel
easy_install nipype

If you are running a 64 bit version of EPD, you will need to compile ETS. Instructions for a 64-bit boot mode are available: https://gist.github.com/845545

From source

If you downloaded the source distribution named something like nipype-x.y.tar.gz, then unpack the tarball, change into the nipype-x.y directory and install nipype using:

python setup.py install

Note: Depending on permissions you may need to use sudo.

Testing the install

The best way to test the install is to run the test suite. If you have nose installed, then do the following:

python -c "import nipype; nipype.test()"

you can also test with nosetests:

nosetests --with-doctest /software/nipy-repo/masternipype/nipype
--exclude=external --exclude=testing

All tests should pass (unless you’re missing a dependency). If any tests fail, please report them on our bug tracker.

On Debian systems, set the following environment variable before running tests:

export MATLABCMD=$pathtomatlabdir/bin/$platform/MATLAB

where, $pathtomatlabdir is the path to your matlab installation and $platform is the directory referring to x86 or x64 installations (typically glnxa64 on 64-bit installations).