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FreeSurfer: Difference between revisions
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</pre> | </pre> | ||
==Installation in a shared folder== | ==Installation in a shared folder== | ||
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* Move the data to the desired location in the project space | * Move the data to the desired location in the project space | ||
* Copy the module file to a shared location, and edit all paths in the module file. | * Copy the module file to a shared location, and edit all paths in the module file. | ||
rrrrrr | |||
==Example of working batch script for freesurfer version >= 6.0.0== | |||
{{File | |||
|name=mysub.sh | |||
|lang="bash" | |||
|contents= | |||
#!/bin/bash | |||
#SBATCH --account=def-someuser | |||
#SBATCH --mem=16G | |||
#SBATCH --time=10:00:00 | |||
# Load the module: | |||
module load freesurfer/6.0.0 | |||
# set the variables: | |||
export SUBJECTS_DIR=<User_Defined_DIR> | |||
source $EBROOTFREESURFER/FreeSurferEnv.sh | |||
echo "Starting run at: `date`" | |||
recon-all command | |||
echo "Program finished with exit code $? at: `date`" | |||
}} | |||
==Examples of required walltimes== | |||
* 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> | |||