Brain Imaging Analysis Kit
==========================
.. image:: https://travis-ci.org/brainiak/brainiak.svg?branch=master
:target: https://travis-ci.org/brainiak/brainiak
.. image:: https://codecov.io/gh/brainiak/brainiak/branch/master/graph/badge.svg
:target: https://codecov.io/gh/brainiak/brainiak
.. image:: https://badges.gitter.im/brainiak/brainiak.svg
:alt: Join the chat at https://gitter.im/brainiak/brainiak
:target: https://gitter.im/brainiak/brainiak?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge
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
brainiak@googlegroups.com. 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>`_.
Raw data
{
"_id": null,
"home_page": "http://brainiak.org",
"name": "brainiak",
"maintainer": "",
"docs_url": null,
"requires_python": ">=3.5",
"maintainer_email": "",
"keywords": "neuroscience,algorithm,fMRI,distributed,scalable",
"author": "Princeton Neuroscience Institute and Intel Corporation",
"author_email": "mihai.capota@intel.com",
"download_url": "https://files.pythonhosted.org/packages/59/9a/c60a06af9d04270b94e6440855a230efda66fab6fe9ae203402b90639b68/brainiak-0.11.tar.gz",
"platform": "",
"description": "Brain Imaging Analysis Kit\n==========================\n\n.. image:: https://travis-ci.org/brainiak/brainiak.svg?branch=master\n :target: https://travis-ci.org/brainiak/brainiak\n\n.. image:: https://codecov.io/gh/brainiak/brainiak/branch/master/graph/badge.svg\n :target: https://codecov.io/gh/brainiak/brainiak\n\n.. image:: https://badges.gitter.im/brainiak/brainiak.svg\n :alt: Join the chat at https://gitter.im/brainiak/brainiak\n :target: https://gitter.im/brainiak/brainiak?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge\n\nThe Brain Imaging Analysis Kit is a package of Python modules useful for\nneuroscience, primarily focused on functional Magnetic Resonance Imaging (fMRI)\nanalysis.\n\nThe package was originally created by a collaboration between Intel and the\nPrinceton Neuroscience Institute (PNI).\n\nTo reduce verbosity, we may refer to the Brain Imaging Analysis Kit using the\n``BrainIAK`` abbreviation. Whenever lowercase spelling is used (e.g., Python\npackage name), we use ``brainiak``.\n\n\nQuickstart\n==========\n\nIf you have `Conda <conda.io>`_::\n\n conda install -c brainiak -c defaults -c conda-forge brainiak\n\nOtherwise, or if you want to compile from source, install the requirements (see\n`docs/installation`) and then install from PyPI::\n\n python3 -m pip install brainiak\n\nNote that to use the ``brainiak.matnormal`` package, you need to install\nadditional dependencies. As of October 2020, the required versions are not\navailable as Conda packages, so you should install from PyPI, even when using\nConda::\n\n python3 -m pip install -U tensorflow tensorflow-probability\n\nNote that we do not support Windows.\n\n\nDocker\n======\n\nYou can also test BrainIAK without installing it using Docker::\n\n docker pull brainiak/brainiak\n docker run -it -p 8888:8888 -v brainiak:/mnt --name demo brainiak/brainiak\n\nTo run Jupyter notebooks in the running container, try::\n\n python3 -m notebook --allow-root --no-browser --ip=0.0.0.0\n\nThen visit http://localhost:8888 in your browser and enter the token. Protip:\nrun ``screen`` before running the notebook command.\n\nNote that we do not support MPI execution using Docker containers and that performance will not be optimal.\n\n\nSupport\n=======\n\nIf you have a question or feedback, chat with us on `Gitter\n<https://gitter.im/brainiak/brainiak>`_ or email our list at\nbrainiak@googlegroups.com. If you find a problem with BrainIAK, you can also\n`open an issue on GitHub <https://github.com/brainiak/brainiak/issues>`_.\n\n\nExamples\n========\n\nWe include BrainIAK usage examples in the examples directory of the code\nrepository, e.g., `funcalign/srm_image_prediction_example.ipynb\n<https://github.com/brainiak/brainiak/blob/master/examples/funcalign/srm_image_prediction_example.ipynb>`_.\n\nTo run the examples, download an archive of the `latest BrainIAK release from\nGitHub <https://github.com/brainiak/brainiak/releases>`_. Note that we only\nsupport the latest release at this moment, so make sure to upgrade your\nBrainIAK installation.\n\n\nDocumentation\n=============\n\nThe documentation is available at http://brainiak.org/docs.\n\n\nContributing\n============\n\nWe welcome contributions. Have a look at the issues labeled \"`easy`_\" for\nstarting contribution ideas. Please read the guide in `CONTRIBUTING.rst`_\nfirst.\n\n.. _easy:\n https://github.com/brainiak/brainiak/issues?q=is%3Aissue+is%3Aopen+label%3Aeasy\n.. _CONTRIBUTING.rst:\n https://github.com/brainiak/brainiak/blob/master/CONTRIBUTING.rst\n\n\nCiting\n======\n\nPlease cite BrainIAK in your publications as: \"Brain Imaging Analysis Kit,\nhttp://brainiak.org.\" Additionally, if you use `RRIDs\n<https://scicrunch.org/resolver>`_ to identify resources, please mention\nBrainIAK as \"Brain Imaging Analysis Kit, RRID:SCR_014824\". Finally, please cite\nthe publications referenced in the documentation of the BrainIAK modules you\nuse, e.g., `SRM <http://brainiak.org/docs/brainiak.funcalign.html>`_.",
"bugtrack_url": null,
"license": "Apache 2",
"summary": "Brain Imaging Analysis Kit",
"version": "0.11",
"project_urls": {
"Homepage": "http://brainiak.org"
},
"split_keywords": [
"neuroscience",
"algorithm",
"fmri",
"distributed",
"scalable"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "599ac60a06af9d04270b94e6440855a230efda66fab6fe9ae203402b90639b68",
"md5": "a5ded8e22eb6201cef392af083c07fcf",
"sha256": "0d5ce0d9f2eeced5638b74cbbc97df62bce40ca6098cd71b40f75fa4407cd947"
},
"downloads": -1,
"filename": "brainiak-0.11.tar.gz",
"has_sig": false,
"md5_digest": "a5ded8e22eb6201cef392af083c07fcf",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.5",
"size": 6839886,
"upload_time": "2020-10-15T20:45:08",
"upload_time_iso_8601": "2020-10-15T20:45:08.451571Z",
"url": "https://files.pythonhosted.org/packages/59/9a/c60a06af9d04270b94e6440855a230efda66fab6fe9ae203402b90639b68/brainiak-0.11.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2020-10-15 20:45:08",
"github": false,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"lcname": "brainiak"
}
JSON