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FreeSurfer Tutorial: Sample Data

A [http://surfer.nmr.mgh.harvard.edu/pub/dist/buckner_public_distribution.README.txt 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 ftp application. The ftp 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 the FTP application

At your terminal, type ftp surfer.nmr.mgh.harvard.edu. Login as anonymous and use your email address as the password.

Example login:

$ ftp surfer.nmr.mgh.harvard.edu
Connected to surfer.nmr.mgh.harvard.edu (132.183.202.158).
220 surfer.nmr.mgh.harvard.edu FTP server (Version wu-2.6.2-15.7x.legacy) ready.
Name (surfer.nmr.mgh.harvard.edu:fsurfer): anonymous
331 Guest login ok, send your complete e-mail address as password.
Password:
230 Guest login ok, access restrictions apply.
Remote system type is UNIX.
Using binary mode to transfer files.
ftp>

The tutorial datasets are found in the pub/dist directory:

ftp> cd pub/dist

The troubleshooting and group study analysis tutorials require the buckner_data-tutorial_subjs.tar.gz download, which is 6.5GB compressed (11GB decompressed):

ftp> get buckner_data-tutorial_subjs.tar.gz

To get the FSL-FEAT tutorial data

ftp> get fbert.feat.tar.gz
ftp> get bert.recon.tar.gz

Now exit the ftp application:

ftp> quit

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).

The troubleshooting and group study analysis tutorials require this download:

The FSL-FEAT tutorial require this download:

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 command:

tar xzvf buckner_data-tutorial_subjs.tar.gz

The downloaded .tar.gz file 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

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 [http://surfer.nmr.mgh.harvard.edu/pub/dist/buckner_public_distribution.README.txt read these notes.]

FSL-FEAT Tutorial Data

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