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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, 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.

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 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. 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:

Screen Shot 2015-08-24 at 2.55.20 PM.png

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. The TUTORIAL_DATA environment variable is required for all tutorials. The example below shows 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

Screen Shot 2015-08-24 at 4.56.51 PM.png

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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. The '''TUTORIAL_DATA''' environment variable is required for all tutorials. The example below shows the commands to type AFTER sourcing freesurfer. If you {{{ls $TUTORIAL_DATA}}} you should see the directories extracted in step #2 and you may now begin the [[FsTutorial\|freesurfer tutorials]].	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. The '''TUTORIAL_DATA''' environment variable is required for all tutorials. The example below shows 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 [[FsTutorial\|freesurfer tutorials]].