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FreeSurfer: Difference between revisions
added info about hip/ brstem, batch, walltime, license.
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# Unload all modules: <code>module purge</code> | # Unload all modules: <code>module purge</code> | ||
# Install with Easybuild: <code>eb FreeSurfer-6.0.0-centos6_x86_64.eb</code> | # Install with Easybuild: <code>eb FreeSurfer-6.0.0-centos6_x86_64.eb</code> | ||
# register for the FreeSurfer license key [https://surfer.nmr.mgh.harvard.edu/registration.html] | |||
# Your user license will have to go in: <code>$HOME/.local/easybuild/software/2017/Core/freesurfer/6.0.0/.license</code> | # Your user license will have to go in: <code>$HOME/.local/easybuild/software/2017/Core/freesurfer/6.0.0/.license</code> | ||
<code> | |||
module load freesurfer/6.0.0 | |||
cd $FREESURFER_HOME | |||
nano .license</code> | |||
add the license text (example): | |||
<code> | |||
name.name@university.ca | |||
12345 | |||
*A1BCdEfGHiJK | |||
ABCd0EFgHijKl</code> | |||
type CTRL+x, y, enter | |||
To load the private module: <code>module load freesurfer/6.0.0</code> | To load the private module: <code>module load freesurfer/6.0.0</code> | ||
When this page was created, Compute Canada was supporting up to version 6.0.1. You can check for [https://github.com/ComputeCanada/easybuild-easyconfigs/tree/computecanada-master/easybuild/easyconfigs/f/FreeSurfer newer versions here]. | When this page was created, Compute Canada was supporting up to version 6.0.1. You can check for [https://github.com/ComputeCanada/easybuild-easyconfigs/tree/computecanada-master/easybuild/easyconfigs/f/FreeSurfer newer versions here]. | ||
==Hippocampus and brainstem processing== | |||
To perform processing of the hippocampus and brainstem, download and install matlab runtime 2012b from the freesurfer website: | |||
<code> | |||
module load freesurfer/6.0.0 | |||
cd $FREESURFER_HOME | |||
curl "http://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime? | |||
action=AttachFile&do=get&target=runtime2012bLinux.tar.gz" -o "matlab_runtime2012bLinux.tar.gz" | |||
tar xvf matlab_runtime2012bLinux.tar.gz | |||
</code> | |||
==Example of working batch script for freesurfer version >= 6.0.0== | |||
<code> | |||
#!/bin/sh | |||
#SBATCH --account=def-user | |||
#SBATCH --mail-type=FAIL | |||
#SBATCH --mem=16G | |||
#SBATCH --time=10:00:00 | |||
#SBATCH --output=outputfile | |||
module load freesurfer/6.0.0 | |||
export SUBJECTS_DIR=User_Defined_DIR | |||
export PATH=$PATH:$FREESURFER_HOME/mni/bin | |||
export PERL5LIB=$PERL5LIB:$FREESURFER_HOME/mni/lib/perl5/5.8.5 | |||
recon-all command</code> | |||
==Current average walltimes required with the upper batch== | |||
* recon-all -all : <code>#SBATCH --time=08:00:00</code> | |||
* recon-all -qcache : <code>#SBATCH --time=00:20:00</code> | |||
* recon-all -base -tp1 -tp2 : <code>#SBATCH --time=10:00:00</code> | |||
* recon-all -long subjid -base base : <code>#SBATCH --time=10:00:00</code> | |||
* recon-all -hippocampal-subfields-T1 : <code>#SBATCH --time=00:40:00</code> | |||
* recon-all -brainstem-structures: <code>#SBATCH --time=00:30:00</code> | |||
==Installation in a shared folder== | ==Installation in a shared folder== | ||