brainiak / Brainiak
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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) 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
If you have Conda <conda.io>_::
conda install -c brainiak -c defaults -c conda-forge brainiak
Otherwise, or if you want to compile from source, install the requirements (see
docs/installation) and then install from PyPI::
python3 -m pip install brainiak
Note that to use the brainiak.matnormal package, you need to install
additional dependencies. As of October 2020, the required versions are not
available as Conda packages, so you should install from PyPI, even when using
Conda::
python3 -m pip install -U tensorflow tensorflow-probability
Note that we do not support Windows.
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 <https://gitter.im/brainiak/brainiak>_ or email our list at
[email protected]. If you find a problem with BrainIAK, you can also
open an issue on GitHub <https://github.com/brainiak/brainiak/issues>_.
Examples
We include BrainIAK usage examples in the examples directory of the code
repository, e.g., funcalign/srm_image_prediction_example.ipynb <https://github.com/brainiak/brainiak/blob/master/examples/funcalign/srm_image_prediction_example.ipynb>_.
To run the examples, download an archive of the latest BrainIAK release from GitHub <https://github.com/brainiak/brainiak/releases>_. 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.
.. _easy: https://github.com/brainiak/brainiak/issues?q=is%3Aissue+is%3Aopen+label%3Aeasy .. _CONTRIBUTING.rst: https://github.com/brainiak/brainiak/blob/master/CONTRIBUTING.rst
Citing
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://brainiak.org/docs/brainiak.funcalign.html>_.