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| Perform the steps below | 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]]. |
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| 1. If you havent already done so, please download and install freesurfer. | 1. If you havent already done so, please download and install Freesurfer. |
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| 2. Source freesurfer. | 2. Source Freesurfer. |
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| ''if using bash'' | |
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| # if using bash | |
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| source $FREESURFER_HOME/SetUpFreeSuerfer.sh }}} |
source $FREESURFER_HOME/SetUpFreeSurfer.sh |
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| ''if using csh'' {{{ |
# if using csh |
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| source $FREESURFER_HOME/SetUpFreeSuerfer.csh | source $FREESURFER_HOME/SetUpFreeSurfer.csh |
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| ''if using bash'' | |
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| # if using bash | |
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# 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 |
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| ''if using csh'' | 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.)'' |
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| 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}/* $FREESURFER_HOME |
# if using bash export TUTORIAL_DATA=$FREESURFER_HOME/subjects/tutorial_data mkdir $TUTORIAL_DATA rsync -zrlv --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 -zrlv --progress "rsync://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data/*" $TUTORIAL_DATA |
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| 4. Download the tutorial data. This requires you set an environment variable {{{TUTORIAL_DATA}}}. The {{{TUTORIAL_DATA}}} environment variable is used throughtout the tutorials, so 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'' 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 }}} |
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. |
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.
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}/*" $FREESURFER_HOME4. Download the tutorial data. This requires you set an environment variable called TUTORIAL_DATA. The TUTORIAL_DATA environment variable is used throughout the tutorials. Set its value during the tutorials to the same value you set it here. (NOTE: this step involves downloading approximately 3Gigs of data, so it may take some time.)
# if using bash export TUTORIAL_DATA=$FREESURFER_HOME/subjects/tutorial_data mkdir $TUTORIAL_DATA rsync -zrlv --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 -zrlv --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 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.