Submitting Freesurfer batch jobs to the Cluster

Freesurfer 6.0 is the default version running on PBIC.

Once you have logged into the PBIC Cluster the following commands will need to be run to create your subject folder within you project folder:

cd /projects/buicxxx
mkdir subjects

Next you will need to set you subjects directory (equivalent to running export subjects_dir) by running the following script and entering the path to your subjects folder:

freesurfer_set_subdir /projects/buicxxx/subjects

You can now submit Freesurfer jobs to the cluster by using the following script (default Freesurfer Version 6) and entering the command and paramaters you would like to run:

freesurfer_sub  "command"

By default this will send jobs to the SGE freesurfer.q. This is the only queue that should be used for Freesurfer batch jobs.

The following is an example, multiple jobs can be run:

freesurfer_sub recon-all -i ./file_T1.nii.gz -s TEST_SUB_ID -cw256 -all

please make a note of the job-id given once it has been submitted.

You can check the status of submitted jobs by running the following command:

qstat

Once the job has completed you can check any errors or output in the files created ending in the jobid given earlier when submitting the jobs:

recon-all.e171827   (error file)
recon-all.o171827   (freesurfer output file)

 Using Freeviewer

Please run the following commands to use the Freesurfer Freeview utility:

freesurfer_setup_freeview
freeview

 

The following us a useful Freesurfer link:

https://www.youtube.com/channel/UCruQerP8aa-gYttXkAcyveA

 

Using Newer version of Freesurfer (v7.2.0)

Once you have logged into the PBIC Cluster the following commands will need to be run to create your subject folder within you project folder:

cd /projects/buicxxx
mkdir subjects

Next you will need to set you subjects directory (equivalent to running export subjects_dir) by running the following script and entering the path to your subjects folder:

freesurfer_set_subdir /projects/buicxxx/subjects

You can now submit Freesurfer jobs to the cluster by using the following script and entering the command and paramaters you would like to run:

freesurfer_sub_v7  "command"

By default this will send jobs to the SGE freesurfer.q. This is the only queue that should be used for Freesurfer batch jobs.

The following is an example, multiple jobs can be run:

freesurfer_sub_v7 recon-all -i ./file_T1.nii.gz -s TEST_SUB_ID -cw256 -all

please make a note of the job-id given once it has been submitted.

You can check the status of submitted jobs by running the following command:

qstat

Once the job has completed you can check any errors or output in the files created ending in the jobid given earlier when submitting the jobs:

recon-all.e171827   (error file)
recon-all.o171827   (freesurfer output file)

Using Freeviewer v7.2

Please run the following commands to use the Freesurfer Freeview utility:

freesurfer_setup_freeview_v7
freeview

 

Using Previous version of Freesurfer (v5.3.0)

 

You can now submit Freesurfer jobs to the cluster by using the following script and entering the command and paramaters you would like to run:

freesurfer_sub_v5  "command"

By default this will send jobs to the SGE freesurfer.q. This is the only queue that should be used for Freesurfer batch jobs.

The following is an example, multiple jobs can be run:

freesurfer_sub_v5 recon-all -i ./file_T1.nii.gz -s TEST_SUB_ID -cw256 -all

 

Using Previous version Freeviewer (V5.3.0)

Please run the following commands to use the Freesurfer Freeview utility:

freesurfer_setup_freeview_v5
freeview