brainiak 0.6

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.

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

python3 -m pip install --user -U pip

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

xcode-select --install

brew doctor

brew install llvm cmake mpich python3

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

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"

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.

Docker

You can also test BrainIAK without installing it using Docker:

docker pull brainiak/brainiak
docker run -it -p 8888:8888 -v brainiak:/mnt --name demo brainiak/brainiak

To run Jupyter notebooks in the running container, try:

python3 -m notebook --allow-root --no-browser --ip=0.0.0.0

Then visit http://localhost:8888 in your browser and enter the token. Protip: run screen before running the notebook command.

Note that we do not support MPI execution using Docker containers and that performance will not be optimal.

Support

If you have a question or feedback, chat with us on Gitter or email our list at brainiak@googlegroups.com. If you find a problem with BrainIAK, you can also open 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.