Difference between revisions of "Software Setup"

Revision as of 23:47, 21 March 2016

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.

Setting up a user account

sudo adduser userid

Yeatman Lab Tools

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

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

git clone https://github.com/vistalab/vistasoft.git

Automated Fiber Quantification

git clone https://github.com/jyeatman/AFQ.git

Anaconda

Each user should have anaconda set up to manage their Python packages. See instructions here:

https://www.continuum.io/downloads

nibabel and DIPY

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

pip install nibabel
pip install dipy

Neurodebian repo

The neurodebian project is an incredible resource making it easy to install most of the widely used nueroimaging software packages.

wget -O- http://neuro.debian.net/lists/trusty.us-nh.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list
sudo apt-key adv --recv-keys --keyserver hkp://pgp.mit.edu:80 0xA5D32F012649A5A9
sudo apt-get update

FSL, ANTS and other Neurodebian packages

Once you have added the neurodebian repos you can easily install fsl and other packages

sudo apt-get install fsl-5.0-complete
sudo apt-get install fsl-5.0-eddy-nonfree
sudo apt-get install ants