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 easy_install or by downloading the source package and running the usual python setup.py install.

Installer and packages

The python package index

NiBabel is available via pypi. If you already have setuptools or distribute installed, you can run:

easy_install nibabel

to download nibabel and its dependencies. Alternatively go to the nibabel 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

NiBabel is available as a NeuroDebian package. Please follow the instructions on the NeuroDebian website on how 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

  • Python 2.5 or greater
  • NumPy 1.2 or greater
  • SciPy (for full SPM-ANALYZE support)
  • PyDICOM 0.9.5 or greater (for DICOM support)
  • nose 0.11 or greater (to run the tests)
  • sphinx (to build the documentation)

Get the sources

The latest release is always available from the SourceForge download page.

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 http://github.com/nipy/nibabel.git

(The first will 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 similar to this:

Python 2.5.5 (r255:77872, Apr 21 2010, 08:44:16)
[GCC 4.4.3] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import nibabel
>>>