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
.
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.
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"
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
In the future, the Brain Imaging Analysis Kit will be available on PyPI. For the moment, it must be installed from a Git repository.
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
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 .
Assuming you're already in the brainiak
folder, do:
cd docs make
This will generate HTML documentation in the _build/html
folder within the
docs
folder. _build/html/index.html
is the starting page.
We welcome contributions. Please read the guide in CONTRIBUTING.rst.