FreeSurfer: Difference between revisions

FreeSurfer (view source)

60 bytes added , 4 years ago

cc_staff

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 ==Example of working batch script for freesurfer version >= 6.0.0==
-<code>
-     #!/bin/sh
-     #SBATCH --account=def-user
+{{File
-     #SBATCH --mail-type=FAIL
+|name=mysub.sh
-     #SBATCH --mem=16G
+|lang="bash"
-     #SBATCH --time=10:00:00
+|contents=
-     #SBATCH --output=outputfile
+#!/bin/sh
-     module load freesurfer/6.0.0
+#SBATCH --account=def-someuser
-     export SUBJECTS_DIR=User_Defined_DIR
+#SBATCH --mem=16G
-     source $EBROOTFREESURFER/FreeSurferEnv.sh
+#SBATCH --time=10:00:00
-     recon-all command</code>
+# Load the module:
+module load freesurfer/6.0.0
+# set the variables:
+export SUBJECTS_DIR=<User_Defined_DIR>
+source $EBROOTFREESURFER/FreeSurferEnv.sh
+echo "Starting run at: `date`"
+recon-all command
+echo "Program finished with exit code $? at: `date`"
+}}
 ==Examples of required walltimes==