== FreeSurfer Tutorial Datasets ==

Below are instruction of how to update your freesurfer installation so that you can run the [[http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial|Freesurfer tutorials]].

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

https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall

2. Source Freesurfer.

{{{
# if using bash
export FREESURFER_HOME=<absolute_path_to_freesurfer>
source $FREESURFER_HOME/SetUpFreeSurfer.sh

# 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 $FREESURFER_HOME/build-stamp.txt`
rsync -zbrlv --progress --suffix=.bak_`date +%s` rsync://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/${build}/* $FREESURFER_HOME

# if using csh
set build=`cat $FREESURFER_HOME/build-stamp.txt`
rsync -zbrlv --progress --suffix=.bak_`date +%s` "rsync://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/${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
mkdir $TUTORIAL_DATA
rsync -ztrlv --progress rsync://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data/* $TUTORIAL_DATA

# if using csh
setenv TUTORIAL_DATA $FREESURFER_HOME/subjects/tutorial_data
mkdir $TUTORIAL_DATA
rsync -ztrlv --progress "rsync://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data/*" $TUTORIAL_DATA
}}}

5. You are now all set up for doing the Freesurfer tutorials. Go to the [[http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial|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.