NiBabel is a pure Python package, and it should be easy to get NiBabel running on any system. For the most popular platforms and operating systems there should be packages in the respective native packaging format (DEB, RPM or installers). On other systems you can install NiBabel using pip.
Installer and packages¶
pip and the Python package index¶
Then open a terminal (
Terminal.app on OSX,
Windows), and type:
pip install nibabel
This will download and install NiBabel.
If you really like doing stuff manually, you can install NiBabel by downloading the source from NiBabel pypi . Go to the pypi page and select the source distribution you want. Download the distribution, unpack it, and then, from the unpacked directory, run:
pip install .
If you get permission errors, this may be because
pip is trying to install
to the system directories. You can solve this error by using
sudo, but we
strongly suggest you either do an install into your “user” directories, like
pip install --user .
or you work inside a virtualenv.
Our friends at NeuroDebian have packaged NiBabel at NiBabel NeuroDebian. Please follow the instructions on the NeuroDebian website on how to access their repositories. Once this is done, installing NiBabel is:
apt-get update apt-get install python-nibabel
Install a development version¶
If you want to test the latest development version of nibabel, or you’d like to help by contributing bug-fixes or new features (excellent!), then this section is for you.
Python 3.8 or greater
NumPy 1.19 or greater
Packaging 17.0 or greater
importlib-resources 1.3 or greater (or Python 3.9+)
SciPy (optional, for full SPM-ANALYZE support)
h5py (optional, for MINC2 support)
PyDICOM 1.0.0 or greater (optional, for DICOM support)
Python Imaging Library (optional, for PNG conversion in DICOMFS)
pytest (optional, to run the tests)
sphinx (optional, to build the documentation)
Get the development sources¶
You can download a tarball of the latest development snapshot (i.e. the current state of the master branch of the NiBabel source code repository) from the NiBabel github page.
If you want to have access to the full NiBabel history and the latest development code, do a full clone (AKA checkout) of the NiBabel repository:
git clone https://github.com/nipy/nibabel.git
Just install the modules by invoking:
pip install .
See pip and the Python package index for advice on what to do for permission errors.
Validating your install¶
For a basic test of your installation, fire up Python and try importing the module to see if everything is fine. It should look something like this:
Python 3.8.5 (default, Sep 4 2020, 07:30:14) [GCC 7.3.0] :: Anaconda, Inc. on linux Type "help", "copyright", "credits" or "license" for more information. >>> import nibabel >>>
To run the nibabel test suite, from the terminal run
pytest --pyargs nibabel or
python -c "import nibabel; nibabel.test().
To run an extended test suite that validates
nibabel for long-running and
resource-intensive cases, please see Advanced Testing.