Diff for "FsTutorial/Data_lite"

Differences between revisions 1 and 2

FreeSurfer Tutorial Datasets

Perform the steps below

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/SetUpFreeSuerfer.sh

if using csh

setenv FREESURFER_HOME <absolute_path_to_freesurfer>
source $FREESURFER_HOME/SetUpFreeSuerfer.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 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

Deletions are marked like this.	Additions are marked like this.
Line 3:	Line 3:
This page provides instruction on how to update your freesurfer installation so that you can run the freesurfer tutorials.	Perform the steps below 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/SetUpFreeSuerfer.sh }}} ''if using csh'' {{{ setenv FREESURFER_HOME <absolute_path_to_freesurfer> source $FREESURFER_HOME/SetUpFreeSuerfer.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 {{{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 }}}