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.

Quickstart

You can install BrainIAK wheels from PyPI on Linux, macOS, and Windows, e.g. using pip:

python3 -m pip install brainiak

If you need MPI, see the installation requirements in docs/installation.

If you have Conda, you can also use our Conda packages (not available for Windows). Installing BrainIAK will also install MPI:

conda install -c brainiak -c conda-forge brainiak

Docker

You can also test BrainIAK without installing it using Docker:

docker pull brainiak/brainiak
docker run -it -p 8899:8899 brainiak/brainiak

Jupyter Notebook will start automatically; visit the URL shown in the Docker command output to access it. You can then run the BrainIAK examples or create new notebooks. You can also try a sample example.

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 Matrix via 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 http://brainiak.org/docs.

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.