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FreeSurfer Tutorial: Sample Data

A public distribution data set is available to run the tutorials. It contains 40+ subjects, and occupies about 11G of disk-space after download and decompression. There are two download methods: using a web browser, or using the wget application. The wget application is recommended, as some web browsers have difficulty downloading files greater than 4GB in size.There are also two tar files associated with the tutorial on the integration of FreeSurfer and FSL/FEAT.

Download using wget

Open a terminal, change to a directory where you know you have at least 12GB of space. The troubleshooting and group study analysis tutorials require the buckner_data-tutorial_subjs.tar.gz and buckner_data-tutorial_subjs-group_analysis_tutorial.tar.gz downloads, which are 6.5GB compressed (11GB decompressed). There is also FSL-FEAT tutorial data. To get these, 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/buckner_data-tutorial_subjs-group_analysis_tutorial.tar.gz &
wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fbert-feat.tar.gz &
wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/bert.recon.tar.gz &

The wget application will handle poor connections, and retry if it is having problems. Notice the commands have the ampersand, so you can run all four commands at once (although the wget output will be hard to decipher). Goto the Installation section below once the files are downloaded (this will likely take several hours).

Download using the web browser

Some web browsers seem to have difficulty downloading files greater than 4GB in size, but if you would like to attempt the download using your browser, then the one necessary file is listed next (click on the .tar.gz filename to download). If a popup window appears prompting for a username and password, use 'anonymous' as the username, and your email address as the password.

The troubleshooting and group study analysis tutorials require these downloads:

• buckner_data-tutorial_subjs.tar.gz

• buckner_data-tutorial_subjs-group_analysis_tutorial.tar.gz

The FSL-FEAT tutorial require these:

• fbert-feat.tar.gz

• bert.recon.tar.gz

Installation

Once the file is downloaded (via either ftp or web browser), move the file(s) to the $FREESURFER_HOME/subjects directory, and uncompress and install with the following commands:

tar xzvf buckner_data-tutorial_subjs.tar.gz
tar xzvf buckner_data-tutorial_subjs-group_analysis_tutorial.tar.gz

The downloaded .tar.gz files can then be deleted.

To setup the environment variable SUBJECTS_DIR to point to the tutorial data, type the following command or include in your .cshrc or .tcshrc file:

source $FREESURFER_HOME/subjects/buckner_data/tutorial_subjs/scripts/subjects.csh

Note: If you are within the NMR Center, because the default $FREESURFER_HOME is shared, you will not be able to copy your data to $FREESURFER_HOME/subjects. Instead, copy the subject data to a location where you have space, and set the SUBJECTS_DIR environment variable to point to that. You may have to make adjustments throughout the tutorial wherever it refers to $FREESURFER_HOME/subjects (which is equivalent to your $SUBJECTS_DIR).

The tutorial will also instruct you to set the SUBJECTS_DIR when appropriate.

Additional group study data

There is an additional data set available upon which further group study analysis could be conducted. It is composed of the 40 subjects from which the tutorial's group study component was created. The data set is the full Freesurfer reconstruction of the 40 subjects (conducted using stable v3.0.2). It is 10.5GB compressed, and 18GB decompressed. It is named buckner_data-group_study.tar.gz. Also, there is the file buckner_data-raw_dicoms.tar.gz, which, as indicated by the name, contains the original DICOM files for the subjects. Be sure to read these notes.

FSL-FEAT Tutorial Data

cd $SUBJECTS_DIR
tar xvfz bert.recon.tar.gz
cd /place/for/functional/data
tar xvfz fbert-feat.tar.gz