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Index

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

Once the download is complete you may uncompress the tar files. In order to do the tutorials, users must define an environment variable called TUTORIAL_DATA which is set to the location of the extracted data. For example:

export TUTORIAL_DATA=/home/username/Downloads/tutorial_data
ls $TUTORIAL_DATA
buckner_data                    fsfast-functional
diffusion_recons                fsfast-tutorial.subjects
diffusion_tutorial              long-tutorial

You are now ready to start the Freesurfer tutorials.

(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