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FreeSurfer Tutorial Datasets

The data for the tutorials consists of several data sets:

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:

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, change to a directory where you know you have at least 100GB of space. 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.

Optional Verification Step

If you want to verify the files transferred correctly using md5sum, the md5sum for each of these downloads can found in files named *.md5sum.txt in this directory or get them this way:

wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.md5sum.txt &
wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/long-tutorial.md5sum.txt &
wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.md5sum.txt &
wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-tutorial.subjects.md5sum.txt &
wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fbert-feat.md5sum.txt &
wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/bert.recon.md5sum.txt &
wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/diffusion_recons.md5sum.txt &
wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/diffusion_tutorial.md5sum.txt &

You will want to ensure that these md5sum's match what you find when you run md5sum on your own local downloads. If they do not match, the file transfer may have been faulty or there may have been a disk error. Mac OS NOTE: Use md5 -r to get the same results as md5sum. More on md5sum can be found here.

Installation

Uncompress the files

Once the datasets have been downloaded, move them to the $FREESURFER_HOME/subjects directory, and uncompress and install with the following command run from a terminal window. You'll have to cd $FREESURFER_HOME/subjects first if you haven't already:

tar xzvf <filename>.tar.gz

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

Set variables to point FreeSurfer to data

To setup the environment variable SUBJECTS_DIR 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 .cshrc or .tcshrc file so these variables are automatically set every time you open a new terminal window:

setenv TUTORIAL_DATA $FREESURFER_HOME/subjects
setenv SUBJECTS_DIR $TUTORIAL_DATA/buckner_data/tutorial_subjs/

Note for Martinos Center employees: Because the default $FREESURFER_HOME is shared, you will not be able to copy your data to $FREESURFER_HOME/subjects when doing so on a Martinos Center workstation. Instead, copy the subject data to a location where you have space, and set the TUTORIAL_DATA and SUBJECTS_DIR environment variables to point to that location. 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. 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.).

FSL-FEAT Tutorial Data

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

FsTutorial/Data (last edited 2014-06-21 22:33:11 by AllisonStevens)