====== QA Cluster Example Script ======
The script below is an example script that will run Syam's fMRI QA program, which performs a variety of metrics to assess data quality (SNR, SFNR, center of mass, standard deviations, etc). Naturally, this syntax is courtesy of Syam.
===== my_qsub_qa_script =====
Example usage:
[user@head ~]$ qsub -v EXPERIMENT=MyExperiment.01 my_qsub_qa_script SUBJNUM
Copy and edit code below:
#!/bin/sh
# This is a BIAC template script for jobs on the cluster
# You have to provide the Experiment on command line
# when you submit the job the cluster.
#
# > qsub -v EXPERIMENT=Dummy.01 script.sh args
#
# 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 --
# User script goes here
# For fmriqa_generate.pl to run you need to either navigate to your subject's directory or
# list the file location in the command line below
# Note that this example lists all required variables in the text below (other than the standard
# EXPERIMENT=MyExperiment.01), but these could easily be incorporated as arguments
#
# Example:
# qsub -v EXPERIMENT=MyExperiment.01 my_qsub_qa_script
#
# MyExperiment.01 is your experiment (e.g., TestSuite.01)
# my_qsub_qa_script is your script's full name.
#Perform QA
SUBJECT=$1
#SUBJECT="20080505_12345"
MAINFUNCDIR=${EXPERIMENT}/Data/Func
cd ${MAINFUNCDIR}/${SUBJECT}
fmriqa_generate.pl run*/run*.bxh QA
# run*/run*.bxh is the input (this looks for all folders beginning with run, and all the files that match run*.bxh # within those folders)
# QA is the output directory (this will create a QA folder in ${EXPERIMENT}/Data/Func)
# -- END USER SCRIPT -- #
# **********************************************************
# -- BEGIN POST-USER --
echo "----JOB [$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--