Using the Grid/Freesurfer

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

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

myhost=`hostname -f`
echo "Running on $myhost"
if [ ! -e $HOME/subjects ]; then
	mkdir -p $HOME/subjects
cp -r $SUBJECTS_DIR/bert $HOME/subjects
export SUBJECTS_DIR=$HOME/subjects
recon-all -s bert -autorecon1


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