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FreeSurfer Tutorial Datasets

The full 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).

• 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

Also, 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:

• Intro to FreeSurfer Output

• Troubleshooting FreeSurfer Output

• Group Analysis via command-line

• Group Analysis via GUI

• ROI Analysis

• Multimodal Analysis

Download using wget

The wget application is recommended, as some web browsers have difficulty downloading files greater than 4GB in size. Mac OS NOTE: Use curl -O in place of wget.

Open a terminal, create a directory called tutorial_data where you know you have at least 100GB of space, and cd into that directory. To download, type:

wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.tar.gz &
wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/long-tutorial.tar.gz &
wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.tar.gz &
wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-tutorial.subjects.tar.gz &
wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fbert-feat.tgz &
wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/bert.recon.tgz &
wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/diffusion_recons.tar.gz &
wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/diffusion_tutorial.tar.gz &

This download will likely take several hours.

The wget application will handle poor connections, and retry if it is having problems. A failed download can be restarted by adding the -c flag to wget, which will cause it to continue from the point where a partial download stopped. Notice the commands have the ampersand, so you can run all these commands at once (although the wget output will be hard to decipher, so an alternative is to run each without the ampersand in a separate terminal). Go to the Installation section below once the files are downloaded.

Installation

Uncompress the files

Once the dataset(s) have been downloaded, uncompress and install with the following command run from a terminal window.

tar -xzvf <filename>.tar.gz

Replacing <filename> with the name of the file downloaded. The downloaded .tar.gz files can then be deleted.

Set variables to point FreeSurfer to data

To setup the environment variable TUTORIAL_DATA to point to the tutorial data, type the following commands every time you open a new terminal window. Alternatively, you can include the below commands in your .bashrc or .cshrc file so these variables are automatically set every time you open a new terminal window:

(bash)
export TUTORIAL_DATA=<absolute_path_to_tutorial_data_directory>

(csh)
setenv TUTORIAL_DATA <absolute_path_to_tutorial_data_directory>

Note: The tutorial references the TUTORIAL_DATA variable, which is the root directory containing the tutorial data (ie. the directories 'buckner_data', 'long-tutorial', 'fsfast-functional', etc.).

FreeSurfer Tutorial Datasets 5.1/5.3

• buckner_data-tutorial_subjs-5.3.tar.gz

• long-tutorial-5.3.tar.gz

• fsfast-tutorial.subjects-5.3.tar.gz & fsfast-functional-5.3.tar.gz

• diffusion_recons-5.3.tar.gz & diffusion_tutorial-5.3.tar.gz