Download and install

This page covers the necessary steps to install Nipype.

1. Install Nipype

Getting Nipype to run on your system is rather straightforward. And there are multiple ways to do the installation:

Using docker

  • You can pull the nipype/nipype image from Docker hub:

      docker pull nipype/nipype

  • You may also build custom docker containers with specific versions of software using Neurodocker (see the Neurodocker Tutorial).

Using conda

If you have conda, miniconda or anaconda on your system, than installing Nipype can be done with just the following command:

conda install --channel conda-forge nipype

It is possible to list all of the versions of nipype available on your platform with:

conda search nipype --channel conda-forge

For more information, please see https://github.com/conda-forge/nipype-feedstock.

Using Pypi

The installation process is similar to other Python packages.

If you already have a Python environment set up, you can do:

pip install nipype

If you want to install all the optional features of nipype, use the following command:

pip install nipype[all]

While all installs everything, one can also install select components as listed below:

'doc': ['Sphinx>=1.4', 'matplotlib', 'pydotplus', 'pydot>=1.2.3'],
'tests': ['pytest-cov', 'codecov'],
'nipy': ['nitime', 'nilearn', 'dipy', 'nipy', 'matplotlib'],
'profiler': ['psutil'],
'duecredit': ['duecredit'],
'xvfbwrapper': ['xvfbwrapper'],

Debian and Ubuntu

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

apt-get install python-nipype

Using Github

To make sure that you really have the newest version of Nipype on your system, you can run the pip command with a flag that points to the github repo:

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

Mac OS X

The easiest way to get nipype running on Mac OS X is to install Miniconda and follow the instructions above. If you have a non-conda environment you can install nipype by typing:

pip install nipype

Note that the above procedure may require the availability of gcc on your system path to compile the traits package.

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:

      pip install .

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

Installation for developers

Developers should start here.

Developers can also use this docker container:

docker pull nipype/nipype:master

2. Interface Dependencies

Nipype provides wrappers around many neuroimaging tools and contains some algorithms. These tools will need to be installed for Nipype to run. You can create containers with different versions of these tools installed using Neurodocker (see the Neurodocker Tutorial).

3. Testing the install

The best way to test the install is checking nipype's version and then running the tests:

python -c "import nipype; print(nipype.__version__)"
python -c "import nipype; nipype.test(doctests=False)"

The test will create a lot of output, but if all goes well you will see at the end something like this:

----------------------------------------------------------------------
 2091 passed, 68 skipped, 7 xfailed, 1 warnings in 236.94 seconds

The number of tests and time will vary depending on which interfaces you have installed on your system.

Don’t worry if some modules are being skipped or marked as xfailed. As long as no main modules cause any problems, you’re fine. The number of tests and time will vary depending on which interfaces you have installed on your system. But if you receive an OK, errors=0 and failures=0 then everything is ready.

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