dpys/brainiak

Brain Imaging Analysis Kit

Brain Imaging Analysis Kit

The Brain Imaging Analysis Kit is a package of Python modules useful for neuroscience, primarily focused on functional Magnetic Resonance Imaging (fMRI) analysis.

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.

Requirements

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 installed manually.

Linux

Install the following packages (Ubuntu 16.04 is used in these instructions):

apt install build-essential libgomp1 libmpich-dev mpich python3-dev \
    python3-pip python3-venv

Install updated version of the following Python packages:

python3 -m pip install --user -U pip

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):

PATH="$HOME/.local/bin:$PATH"

MacOS

Install the Xcode Command Line Tools:

xcode-select --install

Install brew from https://brew.sh. If you already have brew, examine the output of the following command to make sure it is working:

brew doctor

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:

export CC=/usr/local/opt/llvm/bin/clang
export CXX=/usr/local/opt/llvm/bin/clang++

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 "\
"-Wl,-rpath,/usr/local/opt/llvm/lib $LDFLAGS"
export CPPFLAGS="-I/usr/local/opt/llvm/include $CPPFLAGS"

Install updated versions of the following Python packages:

python3 -m pip install -U pip

Installing and upgrading

The Brain Imaging Analysis Kit is available on PyPI. You can install it (or upgrade to the latest version) using the following command:

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.

Until we reach version 1.0, we will only support the latest released version. Therefore, if you have a problem with an older version, please upgrade to the latest version before creating an issue on GitHub.

Examples

We include BrainIAK usage examples in the examples directory of the code repository, e.g., funcalign/srm_image_prediction_example.ipynb.

To run the examples, download an archive of the latest BrainIAK release from GitHub. Note that we only support the latest release at this moment, so make sure to upgrade your BrainIAK installation.

Documentation

The documentation is available at pythonhosted.org/brainiak.

Contributing

We welcome contributions. Have a look at the issues labeled "easy" for starting contribution ideas. Please read the guide in CONTRIBUTING.rst first.

Citing

Please cite BrainIAK in your publications as: "Brain Imaging Analysis Kit, http://brainiak.org." Additionally, if you use RRIDs 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.