====== FSL False Discovery Rate Example Script ======
The example script below will run FSL's FDR calculation on a 3rd level cope image.  The output will be a p-map (activation map of P-values) masked by the FDR threshold calculated (based on the degrees-of-freedom in the 3rd level analysis), as well as text output file that will list the various thresholds that were calculated.  This script is based on information taken from the [[http://www.fmrib.ox.ac.uk/fsl/randomise/fdr.html|FDR User Guide]].

===== fsl_fdr_allcopes.sh =====
This script will loop through all copes sending each one to a different computing node for speed.  
<code bash>
#!/bin/bash

FDRRATE=0.05

for i in 1 2 3 4 5 6 7 8 9
do
  qsub -v EXPERIMENT=Dummy.01 qsub_fsl_fdr.sh $i $FDRRATE
done
</code>


===== qsub_fsl_fdr.sh =====
Example usage:
<code>
[user@head ~]$ qsub -v EXPERIMENT=Dummy.01 qsub_fsl_fdr.sh 1 0.05
</code>

Copy and edit script below:
<code bash>
#!/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 yourname@somewhere.edu

# -- END USER DIRECTIVE --

# -- BEGIN USER SCRIPT --
# User script goes here

COPE=$1
FDRRATE=$2

STATSDIR=$EXPERIMENT/Analysis/FSL/3rdLevel/GroupTrialtypeA.gfeat/cope1.feat/stats
OUTDIR=$STATSDIR

# Convert T-values to P-values using the cope and variance cope images
cd $STATSDIR
ttologp -logpout logp${COPE} varcope${COPE} cope${COPE} `cat dof`

# Caclulate the p-value image
fslmaths logp${COPE} -exp p${COPE}

# Calculate the FDR from the p-value image
fdr -i p${COPE} -m ../mask -q $FDRRATE > fdr${COPE}

# Get the FDR threshold
echo "FDR (rate) is" $FDRRATE
FDRTHRESH=`awk 'NR==2' fdr${COPE}`
echo "FDR threshold is" $FDRTHRESH
FDRTHRESH=`awk -v a=$FDRTHRESH -v b="1" 'BEGIN{print (b - a)}'`
echo "1 minus FDR threshold is" $FDRTHRESH

# Calculate a p-value image using the FDR threshold 
fslmaths p${COPE} -mul -1 -add 1 -thr $FDRTHRESH -mas ../mask thresh_fdr_1_minus_p${COPE}

# Clean up unneccesary files
rm -f logp${COPE}.nii.gz p${COPE}.nii.gz fdr${COPE}

# -- 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.cope${COPE}.$JOB_ID.out	 
RETURNCODE=${RETURNCODE:-0}
exit $RETURNCODE
fi
# -- END POST USER-- 


</code>