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.

If you need to submit an IT ticket, do so at http://help.ilabs.uw.edu/otrs/customer.pl. For help getting an account on this site, contact Cary Dubinksy.

To add a new user with sudo privileges (userid should be maintained across all systems).

 sudo useradd -m -G bde,sudo -s /bin/bash userid

To set user password.

 sudo passwd userid

Have new user enter desired password.

All git directories should be maintained together.

 mkdir ~/git

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

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

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

 cd ~/git
 git clone https://github.com/yeatmanlab/AFQ.git

AFQ requires Matlab r2014a, SPM8, Vistasoft, and AFQ. If you wish to use a different version of Matlab for your core coding, you can set aliases in your ~/.bashrc file

 alias matlabr2016="/usr/local/MATLAB/R2016a/bin/matlab"

For Matlab to see all of the necessary code create a file named startup.m and place it in your home directory. The startup file gets executed automatically when Matlab starts up. To add folders of code to your Matlab search path (making it visible to Matlab):

 addpath(genpath('~/Documents/MATLAB/spm8/'))
 addpath(genpath('~/git/AFQ/'))
 addpath(genpath('~/git/BrainTools/'))
 addpath(genpath('~/git/vistasoft/'))

Each user should have anaconda set up to manage their Python packages. All code for REDCap was written using Python3. Do this before installing nibabel and dipy. Anaconda will manage versions and dependencies for each user separately. Each install will be specific to the user that installs it. Do not install as root, as you will deny yourself privileges to your own directory. You must restart your terminal session after install before using Python or the conda command. See instructions here: https://www.continuum.io/downloads

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

 pip install nibabel
 pip install dipy

While we are still in the processing of developing a full implementation of AFQ in Python, some of these files are required for running DKI.

 cd ~/git
 git clone https://github.com/yeatmanlab/pyAFQ
 cd pyAFQ
 python setup.py develop
 pip install boto3

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

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

FSL requires an edit to the .bashrc file

 gedit ~/.bashrc

Copy the following into the file that open

 # FSL setup
 . /etc/fsl/5.0/fsl.sh

The steps and download is here, instructions are repeated below. Download the Linux CentOS 6 x86_64 install file.

 cd ~/Downloads
 sudo tar -C /usr/local -xzvf freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz

You'll need to register here. The registration e-mail will tell you which text to copy into a new file, which you can create/edit by

 sudo gedit /usr/local/freesurfer/license.txt

We'll be creating a directory for processed subject files on the scratch drive.

 mkdir -p /mnt/scratch/projects/freesurfer

We need to resolve an issue with a jpeg library by creating a symbolic link.

 cd /usr/lib/x86_64-linux-gnu
 sudo ln -s libjpeg.so.8 libjpeg.so.62

Finally, you'll need to edit your bashrc file.

 gedit ~/.bashrc

Copy the following text

 export FREESURFER_HOME=/usr/local/freesurfer
 source $FREESURFER_HOME/SetUpFreeSurfer.sh > /dev/null
 export SUBJECTS_DIR=/mnt/scratch/projects/freesurfer

Fill out the form located here in order, making sure to select SPM8. Run this script from the terminal to install.

 unzip ~/Downloads/spm8.zip -d ~/Documents/MATLAB/

Requires Neurodebian repo to install.

 sudo apt-get install matlab-psychtoolbox-3

In order to launch Matlab with Psychtoolbox, use terminal command

 ptb3-matlab