Brain Imaging Analysis Kit
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The Brain Imaging Analysis Kit is a package of Python modules useful for
neuroscience, primarily focused on functional Magnetic Resonance Imaging (fMRI)
The package was originally created by a collaboration between Intel and the
Princeton Neuroscience Institute (PNI).
To reduce verbosity, we may refer to the Brain Imaging Analysis Kit using the
``BrainIAK`` abbreviation. Whenever lowercase spelling is used (e.g., Python
package name), we use ``brainiak``.
We support Linux and MacOS with Python version 3.4 or higher. Most of the
dependencies will be installed automatically. However, a few need to be
Install the following packages (Ubuntu 14.04 is used in these instructions)::
apt install build-essential libgomp1 libmpich-dev mpich python3-dev \
Install updated version of the following Python packages::
python3 -m pip install --user -U pip virtualenv
Note the ``--user`` flag, which instructs Pip to not overwrite system
files. You must add ``$HOME/.local/bin`` to your ``$PATH`` to be able to run
the updated Pip, e.g., by adding the following line to ``$HOME/.profile``
and launching a new login shell (e.g., logout or execute ``bash -l``)::
Install the Xcode Command Line Tools::
Install ``brew`` from https://brew.sh. If you already have ``brew``, examine
the output of the following command to make sure it is working::
Then install the following::
brew install llvm cmake mpich python3
You must instruct programs to use this ``clang`` version at ``/usr/local/opt/llvm/bin``.
One way to do this, which
works for most programs, is setting the ``CC`` environment variable. You can
add the following lines to ``$HOME/.profile`` (or ``$HOME/.bash_profile``, if
you have one). For them to take effect, you must logout or launch a new login
shell, e.g., ``bash -l``::
In addition, you also need to specify the directories that the newly installed `clang`
will seek for compiling and linking::
export LDFLAGS="-L/usr/local/opt/llvm/lib "\
export CPPFLAGS="-I/usr/local/opt/llvm/include $CPPFLAGS"
Install updated versions of the following Python packages::
python3 -m pip install -U pip virtualenv
The Brain Imaging Analysis Kit is available on PyPI::
python3 -m pip install -U brainiak
Note that you may see a ``Failed building wheel for brainiak`` message (`issue
#61`_). Installation will proceed despite this failure. You can safely ignore it
as long as you see ``Successfully installed`` at the end.
.. _issue #61:
The documentation is available at `pythonhosted.org/brainiak`_.
We welcome contributions. Please read the guide in `CONTRIBUTING.rst`_.
Please cite BrainIAK in your publications as: "Brain Imaging Analysis Kit,
http://brainiak.org." Additionally, if you use `RRIDs
<https://scicrunch.org/resolver>`_ to identify resources, please mention
BrainIAK as "Brain Imaging Analysis Kit, RRID:SCR_014824". Finally, please cite
the publications referenced in the documentation of the BrainIAK modules you
use, e.g., `SRM <http://pythonhosted.org/brainiak/brainiak.funcalign.html>`_.
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.