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Brain Imaging Analysis Kit

Project description

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.

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 14.04 is used for the examples):

apt install build-essential cmake libgomp1 mpich python3-pip

Install updated version of the following Python packages:

pip3 install --user -U pip virtualenv

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 clang-omp cmake mpich python3

You must instruct programs to use clang-omp. 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=clang-omp
export CXX=clang-omp++

Install updated versions of the following Python packages:

pip3 install -U pip virtualenv

Install

In the future, the Brain Imaging Analysis Kit will be available on PyPI. For the moment, it must be installed from a Git repository.

Install directly from GitHub

To install directly from GitHub, do:

pip3 install git+https://github.com/intelpni/brainiak.git

Or, if you have ssh keys installed, you can do:

pip3 install git+ssh://github.com/intelpni/brainiak.git

Install from local clone

If you prefer to install from a local clone of the repository, follow these steps:

git clone https://github.com/intelpni/brainiak
cd brainiak
pip install .

Documentation

The documentation is available at:

https://pythonhosted.org/brainiak

Contribute

We welcome contributions. Please read the guide in CONTRIBUTING.rst.

Project details


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