NiBabel

Access a cacophony of neuro-imaging file formats

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NiBabel Manual

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Getting Started

Reggie -- the one

Installation

NiBabel is a pure Python package at the moment, 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 or by downloading the source package and running the usual python setup.py install.

Installer and packages

pip and the Python package index

If you are not using a Linux package manager, then best way to install NiBabel is via pip. If you don’t have pip already, follow the pip install instructions.

Then open a terminal (Terminal.app on OSX, cmd or Powershell on Windows), and type:

pip install nibabel

This will download and install NiBabel.

If you really like doing stuff manually, you can install NiBabel by downoading 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:

python setup.py install

or (if you need root permission to install on a unix system):

sudo python setup.py install

Debian/Ubuntu

Our friendas 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 from source

If no installer or package is provided for your platfom, you can install NiBabel from source.

Requirements

Get the sources

The latest release is always available from NiBabel pypi.

Alternatively, 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 git://github.com/nipy/nibabel.git

or:

git clone https://github.com/nipy/nibabel.git

(The first may be faster, the second more likely to work behind a firewall).

Installation

Just install the modules by invoking:

sudo python setup.py install

If sudo is not configured (or even installed) you might have to use su instead.

Now fire up Python and try importing the module to see if everything is fine. It should look something like this:

Python 2.7.8 (v2.7.8:ee879c0ffa11, Jun 29 2014, 21:07:35)
[GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import nibabel
>>>