FreeSurfer Tutorial Data set
This page describes the setup process for running the freesurfer tutorials. These instructions are for users who want to run the tutorials on their personal machine, or users who are attending and upcoming freesurfer course and wish to use their own laptop, or as a guide for an administrator setting up a freesurfer course. These instruction are valid on Mac OSX and Linux platforms (freesurfer is not available on Windows platform).
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 require users to have the "development version" of freesurfer installed. 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 test commands on the testing freesurfer installation page. It would be pointless to continue otherwise. If you are having issues running the test 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 tutorial_data.tar.gz. 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
Configuring your freesurfer installation for the tutorials requires one simple step, creating the TUTORIAL_DATA environment variable and setting it to the location of the extracted file from above. Continuing with the example from above, the steps below show the commands to type AFTER sourcing freesurfer. If you type the ls $TUTORIAL_DATA command and see the directories extracted in step #2, you are ready to begin the freesurfer tutorials.
$> export TUTORIAL_DATA=/Users/localzeke/Downloads/tutorial_data $> ls $TUTORIAL_DATA buckner_data fsfast-functional diffusion_recons fsfast-tutorial.subjects diffusion_tutorial long-tutorial
