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biac:freesurferguide [2014/08/04 16:03] (current)
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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:
 +  /​usr/​local/​packages/​qsub_templates/​RunFreeSurf.sh
 +
 +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/​RunFreeSurf.sh SubjID SeriesDir
 +
 +where:
 +  * 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:
 +     ​Analysis/​freesurfer/​SubjID
 +
 +**Example:​**\\
 +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/​RunFreeSurf.sh 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:
 +   ​Analysis/​freesurfer/​BS123
 +
 +**Notes:​**\\
 +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): [[biac:​cluster:​examples:​runfree|FreeSurfer template]]
 +
 +Obsolete: [[biac:​freesurfergolgi|Freesurfer on Golgi]]
  
biac/freesurferguide.txt · Last modified: 2014/08/04 16:03 (external edit)