FreeSurfer Tutorial Datasets

Below are instruction of how to update your freesurfer installation so that you can run the Freesurfer tutorials.

1. If you havent already done so, please download and install Freesurfer.

2. Source Freesurfer.

# if using bash
export FREESURFER_HOME=<absolute_path_to_freesurfer>

# if using csh
setenv FREESURFER_HOME <absolute_path_to_freesurfer>
source $FREESURFER_HOME/SetUpFreeSurfer.csh

3. Run the commands below to apply updates to your freesurfer installation.

# if using bash
build=`cat $FREESURFER_HOME/build-stamp.txt`
rsync -zbrlv --progress --suffix=.bak_`date +%s` rsync://${build}/* $FREESURFER_HOME

# if using csh
set build=`cat $FREESURFER_HOME/build-stamp.txt`
rsync -zbrlv --progress --suffix=.bak_`date +%s` "rsync://${build}/*" $FREESURFER_HOME

4. Download the tutorial data. This requires you set an environment variable called TUTORIAL_DATA. The TUTORIAL_DATA environment variable is used throughout the tutorials. Set its value during the tutorials to the same value you set it here. (NOTE: this step involves downloading approximately 3Gigs of data, so it may take some time.)

# if using bash
export TUTORIAL_DATA=$FREESURFER_HOME/subjects/tutorial_data
rsync -ztrlv --progress rsync://* $TUTORIAL_DATA

# if using csh
setenv TUTORIAL_DATA $FREESURFER_HOME/subjects/tutorial_data
rsync -ztrlv --progress "rsync://*" $TUTORIAL_DATA

5. You are now all set up for doing the Freesurfer tutorials. Go to the Freesurfer tutorials page for links to the individual talks tutorials. Remember your TUTORIAL_DATA environment variable you set above. You will need to have this value set correctly while doing the tutorials.

FsTutorial/Data_lite (last edited 2015-04-27 14:27:02 by ZekeKaufman)