Using the Grid/Freesurfer

Freesurfer

FreeSurfer is a set of automated tools for reconstruction of the brain’s cortical surface from structural MRI data, and overlay of functional MRI data onto the reconstructed surface <ref>http://surfer.nmr.mgh.harvard.edu/</ref>

Freesurfer is installed as LSGRID VO software. When you are a member of the LSGRID VO Freesurfer is available; upon request it can be made available to other VO's as well.

This page shortly demonstrates how to use Freesurfer.

To find out where Freesurfer is installed, please type:

lcg-info --vo lsgrid --list-ce --query Tag=VO-lsgrid-freesurfer-4.5

Test File

A jdl file looks like this test_freesurfer.jdl:

Executable = "test_freesurfer.sh";
Stdoutput = "stdout";
StdError = "stderror";
InputSandbox = {"test_freesurfer.sh"};
OutputSandbox = {"stdout","stderror"};
Requirements = Member("VO-lsgrid-freesurfer-4.5", other.GlueHostApplicationSoftwareRunTimeEnvironment);
RetryCount = 0;

This JDL makes use of the following the test_freesurfer.sh bash script with the following contents:

#!/bin/bash
myhost=`hostname -f`
echo "Running on $myhost"
export FREESURFER_HOME=$VO_LSGRID_SW_DIR/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
if [ ! -e $HOME/subjects ]; then
	mkdir -p $HOME/subjects
fi
cp -r $SUBJECTS_DIR/bert $HOME/subjects
export SUBJECTS_DIR=$HOME/subjects
recon-all -s bert -autorecon1

<references/>