FreeSurfer Tutorial Data set

This page describes the setup process for running the freesurfer tutorials. These instructions apply to users who want to run the tutorials on their personal machine, users who are attending and upcoming freesurfer course, or as a guide for an administrator setting up a freesurfer course.

1. Install freesurfer

The first step is to install freesurfer on your personal machine. To install freesurfer, follow the instructions on the download and installation page. Important Note: The tutorials use the latest "development version" of freesurfer. So when it comes time so select the version for download do NOT select version 5.3, download the "development version" instead, which can be found on this page.

2. Download tutorial data

Before continuing, please ensure you have a functioning freesurfer installation by running the commands on the testing freesurfer installation page. It would be pointless to continue otherwise. If you are having issues running the commands, please follow the instructions on the Setup and Configuaration page.

Once you have a functioning freesurfer installation, it is time to download the freesurfer tutorial data set. When the download completes you will want to extract its contents. This can be done on most operating systems by simply double-clicking the file. Remember the location of this directory. It is used throughout all of the tutorials. The file should extract a directory called tutorial_data and its content should look as follows:

3. Configure your system

To begin doing the tutorials open a terminal window and source freesurfer. Then create an environment variable called TUTORIAL_DATA and set it to the location of the extracted file from above. If you ls $TUTORIAL_DATA you should see the directories extracted in step #2. The example below shows how you would perform these steps on a Mac OSX system. The only difference for your system would be the actual paths:

$> export FREESURFER_HOME=/Applications/freesurfer
$> source $FREESURFER_HOME/SetUpFreeSurfer.sh 
$> export TUTORIAL_DATA=/Users/localzeke/Downloads/tutorial_data
$> ls $TUTORIAL_DATA 
buckner_data                    fsfast-functional
diffusion_recons                fsfast-tutorial.subjects
diffusion_tutorial              long-tutorial

Here is an example of what the terminal window should look like:

Second

The data for the tutorials consists of several data sets:

• buckner_data-tutorial_subjs.tar.gz: the main 'recon-all' stream subject data processing (size: ~16GB uncompressed)Here is the md5sum.

• long-tutorial.tar.gz: the longitudinal tutorial (size: ~16GB uncompressed)

• fsfast-tutorial.subjects.tar.gz & fsfast-functional.tar.gz: the FS-FAST tutorial data set (size: ~5.6GB uncompressed & ~9.1GB uncompressed, respectively)

• diffusion_recons.tar.gz & diffusion_tutorial.tar.gz - the diffusion and Tracula tutorial data sets

• fbert-feat.tgz & bert.recon.tgz - tutorial on the integration of FreeSurfer and FSL/FEAT

If you only want to get started with the basics of FreeSurfer, you need only download the buckner_data set. This will allow you to do the following tutorials: