Warning

Iceberg reaches end-of-life on 30th November 2020. If you are running jobs on Iceberg then you need to take urgent action to ensure that your jobs/scripts will run on ShARC or Bessemer. If you have never used ShARC or Bessemer then now is the time to test your scripts. Not all software on Iceberg is available on ShARC/Bessemer.

Freesurfer¶

An open source software suite for processing and analyzing (human) brain MRI images.

Interactive Usage¶

After connecting to iceberg (see Establishing a SSH connection), start an interactive graphical session with the qsh command.

The latest version of Freesurfer is made available with the command

module load apps/binapps/freesurfer

Alternatively, you can load a specific version with

module load apps/binapps/freesurfer/5.3.0

Important note¶

Freesurfer is known to produce differing results when used across platforms. See http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0038234 for details. We recommend that you run all of your analyses for any given study on the same operating system/hardware combination and record details of these as part of your results.

Testing¶

No formal test suite was found. A set of commands to try were suggested at https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer (Accessed November 6th 2015)

The following were tried

freeview -v $SUBJECTS_DIR/bert/mri/brainmask.mgz -v $SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f $SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red -f $SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red

tkmedit bert orig.mgz

tkmedit bert norm.mgz -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt

tksurfer bert rh pial

qdec

Installation notes¶

These are primarily for administrators of the system. The github issue for the original install request is at https://github.com/rcgsheffield/sheffield_hpc/issues/164

Freesurfer was installed as follows

wget -c ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz
tar -xvzf ./freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz
mv freesurfer 5.3.0
mkdir -p /usr/local/packages6/apps/binapps/freesurfer
mv ./5.3.0/ /usr/local/packages6/apps/binapps/freesurfer/

The license file was obtained from the vendor and placed in /usr/local/packages6/apps/binapps/freesurfer/license.txt. The vendors were asked if it was OK to use this license on a central system. The answer is ‘yes’ - details at http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg43872.html

To find the information necessary to create the module file

env >base.env
source /usr/local/packages6/apps/binapps/freesurfer/5.3.0/SetUpFreeSurfer.sh
env > after.env
diff base.env after.env

The script SetUpFreeSurfer.sh additionally creates a MATLAB startup.m file in the user’s home directory if it does not already exist. This is for MATLAB support only, has not been replicated in the module file and is currently not supported in this install.

The module file is at /usr/local/modulefiles/apps/binapps/freesurfer/5.3.0

#%Module10.2#####################################################################

## Module file logging
source /usr/local/etc/module_logging.tcl
##

# Freesurfer version (not in the user's environment)
set ver 5.3.0

proc ModulesHelp { } {
      global ver

      puts stderr "Makes Freesurfer $ver available to the system."
}

module-whatis "Sets the necessary Freesurfer $ver paths"

prepend-path PATH /usr/local/packages6/apps/binapps/freesurfer/$ver/bin
prepend-path FREESURFER_HOME /usr/local/packages6/apps/binapps/freesurfer/$ver

# The following emulates the results of 'source $FREESURFER_HOME/SetUpFreeSurfer.csh'
setenv FS_OVERRIDE 0
setenv PERL5LIB /usr/local/packages6/apps/binapps/freesurfer/5.3.0/mni/lib/perl5/5.8.5
setenv OS Linux
setenv LOCAL_DIR /usr/local/packages6/apps/binapps/freesurfer/5.3.0/local
setenv FSFAST_HOME /usr/local/packages6/apps/binapps/freesurfer/5.3.0/fsfast
setenv MNI_PERL5LIB /usr/local/packages6/apps/binapps/freesurfer/5.3.0/mni/lib/perl5/5.8.5
setenv FMRI_ANALYSIS_DIR /usr/local/packages6/apps/binapps/freesurfer/5.3.0/fsfast
setenv FSF_OUTPUT_FORMAT nii.gz
setenv MINC_BIN_DIR /usr/local/packages6/apps/binapps/freesurfer/5.3.0/mni/bin
setenv SUBJECTS_DIR /usr/local/packages6/apps/binapps/freesurfer/5.3.0/subjects

prepend-path PATH /usr/local/packages6/apps/binapps/freesurfer/5.3.0/fsfast/bin:/usr/local/packages6/apps/binapps/freesurfer/5.3.0/tktools:/usr/local/packages6/apps/binapps/freesurfer/5.3.0/mni/bin

setenv FUNCTIONALS_DIR /usr/local/packages6/apps/binapps/freesurfer/5.3.0/sessions
setenv MINC_LIB_DIR /usr/local/packages6/apps/binapps/freesurfer/5.3.0/mni/lib
setenv MNI_DIR /usr/local/packages6/apps/binapps/freesurfer/5.3.0/mni
#setenv FIX_VERTEX_AREA #How do you set this to the empty string? This was done in the original script.
setenv MNI_DATAPATH /usr/local/packages6/apps/binapps/freesurfer/5.3.0/mni/data