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Freesurfer Guide

Running Freesurfer on the BIAC cluster

An easy way to run FreeSurfer is to submit a cluster batch job using the QSUB command with a standard FreeSurfer batch processing script. To do so, you need just 2 things:

  • a high resolution whole-brain T1-weighted anatomical DICOM image data set within a BIAC experiment directory
  • a name you want to assign for the FreeSurfer reconstruction of this subject

The standard FreeSurfer batch processing script is located on the cluster head node at:


You can use this script with no modification by entering the following command on the cluster head-node (not on a qinteract node):

qsub -v EXPERIMENT=MyExperiment /usr/local/packages/qsub_templates/ SubjID SeriesDir


  • MyExperiment is your BIAC experiment name (eg. Expt.02)
  • SubjID is the name you want to assign for this subject reconstruction (eg. 1234 or subj21)
  • SeriesDir is the directory path to get to your anatomical DICOM images for the subject you want to reconstruct, within your MyExperiment directory (eg. Data/Anat/20110101_12345/series300 )

The job will create an output directory for this subject, within your MyExperiment directory at:


To perform a full FreeSurfer reconstruction of anatomical series 300 of scanner exam 10123 acquired on Feb 1, 2011 under BIAC experiment BrainScan.02, and store the results as subject BS123, enter the command:

qsub -v EXPERIMENT=BrainScan.02 /usr/local/packages/qsub_templates/ BS123 Data/Anat/20110201_10123/series300

The results will be found (about 20 hours later) in the following directory within the BrainScan.02 experiment directory:


The QSUB command will automatically insert your email address to notify you of job status.

It takes about 20 hours for a full FreeSurfer reconstruction to run on the cluster.

See Also:
Another sample template script (requires some editting): FreeSurfer template

Obsolete: Freesurfer on Golgi

biac/freesurferguide.txt · Last modified: 2014/08/04 16:03 (external edit)