Software Setup

We rely on a number of different software packages to analyze MRI and MEG data. Here is a growing tally of what we use and where to get it. Most of these tools reside on github and you should definitely use git to clone the repositories rather than download a snapshot of the code. e.g.

git clone https://github.com/yeatmanlab/mritools.git

Yeatman Lab Tools

https://github.com/yeatmanlab/mritools

Vistasoft

MATLAB based toolbox, from Brian Wandell's lab at Stanford, that contains many functions we rely on for analyzing diffusion MRI and functional MRI data

https://github.com/vistalab/vistasoft

Automated Fiber Quantification

https://github.com/jyeatman/AFQ

nibabel

Python based toolbox for dealing with nifti images. While nibabel is on github we suggest installing using apt-get:

apt-get update
apt-get install python-nibabel

or pip

pip install nibabel