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biac:freesurferguide
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biac:freesurferguide [2014/08/04 16:03] |
biac:freesurferguide [2023/02/23 18:43] (current) |
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| + | ====== Freesurfer Guide ====== | ||
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| + | ===== 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 / | ||
| + | |||
| + | 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, | ||
| + | |||
| + | The job will create an output directory for this subject, within your MyExperiment directory | ||
| + | | ||
| + | |||
| + | **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, | ||
| + | qsub -v EXPERIMENT=BrainScan.02 / | ||
| + | |||
| + | The results will be found (about 20 hours later) in the following directory within the BrainScan.02 experiment directory: | ||
| + | | ||
| + | |||
| + | **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: | ||
| + | |||
| + | Obsolete: [[biac: | ||
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