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. It was developed at the Martinos Center for Biological Imaging at Harvard.

• Freesurfer website

• Module Name: freesurfer (see the modules page for more information). The freesurfer initialization scripts need to be run in addition to loading the module.

  module load freesurfer ; source $FREESURFER_HOME/SetUpFreeSurfer.sh
  

• FreeSurfer is not a parallel program. The advantage of running on Biowulf is that you can run many simultaneous freesurfer runs.
• The GUI-based FreeSurfer programs should be run by allocating an interactive node (as described below).
• tksurfer is deprecated, so command-line saving to a tiff file is not directly possible.
• Freesurfer uses temporary files for some calculations. By default, these will go to /scratch (i.e. the top level of the shared scratch directory) which is low-performance (i.e. reading and writing to /scratch is slowing down your jobs). Instead, you should allocate local disk (/lscratch) and set the environment variable tmpdir=/lscratch/$SLURM_JOBID to speed up your jobs. See the examples below.

Allocate an interactive session with 5 GB of local disk and run the program. Sample session below::

[user@biowulf]$ sinteractive --gres=lscratch:5
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load freesurfer
[+] Loading Freesurfer 6.0.0 ...
[+] Bash users should now type: source $FREESURFER_HOME/SetUpFreeSurfer.sh
[+] Csh users should now type: source $FREESURFER_HOME/SetUpFreeSurfer.csh

[user@cn3144 ~]$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/apps/freesurfer/6.0.0
FSFAST_HOME       /usr/local/apps/freesurfer/6.0.0/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /usr/local/apps/freesurfer/6.0.0/subjects
MNI_DIR           /usr/local/apps/freesurfer/6.0.0/mni

[user@cn3144 ~]$ export tmpdir=/lscratch/$SLURM_JOBID

[user@cn3144 ~]$ tkmedit bert orig.mgz
Setting subject to bert
Reading 0 control points...
Reading 0 control points...
Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl
Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl
Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl
Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl



[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. freesurfer.sh). For example:

#!/bin/bash
set -e
module load freesurfer
source $FREESURFER_HOME//SetUpFreeSurfer.sh
# set the environment variable tmpdir to local scratch for better performance
export tmpdir=/lscratch/$SLURM_JOBID

cd /data/user/mydir
recon-all -subject hv1 -all

Submit this job using the Slurm sbatch command.

sbatch  [--mem=#] --gres=lscratch:5 freesurfer.sh

For swarm jobs, it might be simplest to have the line

module load freesurfer/5.3.0 > /dev/null 2>&1 ; source $FREESURFER_HOME/SetUpFreeSurfer.sh

Create a swarmfile (e.g. freesurfer.swarm). For example:

export tmpdir=/lscratch/$SLURM_JOBID; cd /data/$USER/mydir/; recon-all -subject hv1 -all
export tmpdir=/lscratch/$SLURM_JOBID; cd /data/$USER/mydir/; recon-all -subject hv2 -all
export tmpdir=/lscratch/$SLURM_JOBID; cd /data/$USER/mydir/; recon-all -subject hv3 -all

Submit this job using the swarm command.

swarm -f freesurfer.swarm [-t #] --gres=lscratch:1