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--- biac:cluster:examples:runfree [2011/09/07 13:53]
petty [submitting runFREE.sh]
+++ biac:cluster:examples:runfree [2023/02/23 18:43]
@@ Line 1: / Line 1: @@
-====== runFREE.sh Example Script ======
-The example script below will run freesurfer segmentation (using recon-all) on a hi-resolution anatomical series.
-**NOTE**:  Please be considerate when running freesurfer scripts on the cluster.  Since Freesurfer can take over a day to complete, please do not submit too many jobs as other users will have to wait for these processes to complete before theirs will start.
-===== submitting runFREE.sh =====
-Example usage:
-<code>
-[user@head ~]$ qsub -v EXPERIMENT=Dummy.01 runFREE.sh 20071031_12345 300
-</code>
-<code bash RunFree.sh>
-#!/bin/sh
-# This is a BIAC template script for running FreeSurfer reconstruction on the cluster
-# You can use this script with no modification by entering the following command on
-# the cluster head-node:
-#
-# >  qsub -v EXPERIMENT=MyExperiment RunFree.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
-#
-# Note: The QSUB command will automatically insert your email address to notify you of job
-# status.
-#
-# If you want to modify this template script, there are 2 USER sections:
-#  1. USER DIRECTIVE: If you want mail notifications when
-#     your job is completed or fails you need to set the
-#     correct email address.
-#
-#  2. USER SCRIPT: Add the user script in this section.
-#     Within this section you can access your experiment
-#     folder using $EXPERIMENT. All paths are relative to this variable
-#     eg: $EXPERIMENT/Data $EXPERIMENT/Analysis
-#     By default all terminal output is routed to the " Analysis "
-#     folder under the Experiment directory i.e. $EXPERIMENT/Analysis
-#     To change this path, set the OUTDIR variable in this section
-#     to another location under your experiment folder
-#     eg: OUTDIR=$EXPERIMENT/Analysis/GridOut
-#     By default on successful completion the job will return 0
-#     If you need to set another return code, set the RETURNCODE
-#     variable in this section. To avoid conflict with system return
-#     codes, set a RETURNCODE higher than 100.
-#     eg: RETURNCODE=110
-#     Arguments to the USER SCRIPT are accessible in the usual fashion
-#     eg:  $1 $2 $3
-# The remaining sections are setup related and don't require
-# modifications for most scripts. They are critical for access
-# to your data
-# --- BEGIN GLOBAL DIRECTIVE --
-#$ -S /bin/sh
-#$ -o $HOME/$JOB_NAME.$JOB_ID.out
-#$ -e $HOME/$JOB_NAME.$JOB_ID.out
-#$ -m ea
-# -- END GLOBAL DIRECTIVE --
-# -- BEGIN PRE-USER --
-#Name of experiment whose data you want to access
-EXPERIMENT=${EXPERIMENT:?"Experiment not provided"}
-EXPERIMENT=`findexp $EXPERIMENT`
-EXPERIMENT=${EXPERIMENT:?"Returned NULL Experiment"}
-if [ $EXPERIMENT = "ERROR" ]
-then
-        exit 32
-else
-#Timestamp
-echo "----JOB [$JOB_NAME.$JOB_ID] START [`date`] on HOST [$HOSTNAME]----"
-# -- END PRE-USER --
-# **********************************************************
-# -- BEGIN USER DIRECTIVE --
-# Send notifications to the following address
-#$ -M user@somewhere.edu
-# -- END USER DIRECTIVE --
-# -- BEGIN USER SCRIPT --
-SUBJ=$1
-SERIESDIR=$2
-RAWDIR=${EXPERIMENT}/${SERIESDIR}
-FREEOUT=${EXPERIMENT}/Analysis/freesurfer
-#if out directory doesn't exist, then make it
-if [ ! -d "$FREEOUT" ]; then
-        mkdir -p $FREEOUT
-fi
-#if the fsaverage subject doesn't exist there, then copy it
-for freedirs in fsaverage lh.EC_average rh.EC_average; do
-        if [ ! -d "${FREEOUT}/${freedirs}" ]; then
-                cp -R $FREESURFER_HOME/subjects/${freedirs} $FREEOUT/
-        fi
-done
-export SUBJECTS_DIR=$FREEOUT
-cd $SUBJECTS_DIR
-recon-all -i $RAWDIR/*_00001.dcm -s $SUBJ
-recon-all -autorecon-all -s $SUBJ
-# -- END USER SCRIPT -- #
-# **********************************************************
-# -- BEGIN POST-USER --
-echo "----JOB [$JOB_NAME.$JOB_ID] STOP [`date`]----"
-OUTDIR=${OUTDIR:-$EXPERIMENT/Analysis}
-mv $HOME/$JOB_NAME.$JOB_ID.out $OUTDIR/$JOB_NAME.$JOB_ID.out
-RETURNCODE=${RETURNCODE:-0}
-exit $RETURNCODE
-fi
-# -- END POST USER--
-</code>

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