basil_var.in

#!/bin/sh

# basil_var
# Variance calculator for BASIL
# Calculates variance for all parameters in all the steps using fabber_var
# M Chappell 1/11/2007 and M Webster
# Analysis Group, FMRIB, University of Oxford

#HISTORY
#13-12-2007 Update to work with new fabber_var (requries mask)

#deal with options
#   Copyright (C) 2007-2012 University of Oxford

#   SHCOPYRIGHT

# Make script use local copies of helper scripts/programs in the same
# directory, if present. This allows for multiple versions of the scripts
# to be used, possibly with bundled dependencies
PATH=`dirname $0`:${FSLDIR}/bin:${PATH}

if [ -z $1 ]; then
    echo "Variance calculator for BASIL @GIT_SHA1@ (@GIT_DATE@)"
    echo ""
    echo "Usage:"
    echo "-d     : BASIL results directory"
    echo "-m     : mask"
    echo ""
    break
else

fabber_var=fabber_var

until [ -z $1 ]; do
    case $1 in
	-d) dirflag=1 datdir=$2;;
	-m) maskflag=1 mask=$2;;
	-c) trashflag=1;;
     esac
    shift
done
echo "BASIL variance calcualtor '@GIT_SHA1@' '@GIT_DATE@'"
echo "Working in $datdir"

steps=`ls -d $datdir/step[0-9]`

if [ ! -z $trashflag ]; then
    # Remove extra NLLS outputs
    echo "Delting model fit and residual images from NLLS to save space"
    rm $datdir/step?/residuals.nii.gz
    rm $datdir/step?/modelfit.nii.gz
fi

for step in $steps; do
    echo "Calculating variances in $step"
    $fabber_var -d $step -m $mask
    if [ ! -z $trashflag ]; then
	#echo "Deleting z-stat images to save space"
	#rm $step/zstat_*
	echo "Compacting logfile"
	zip $step/logfile $step/logfile
	rm $step/logfile
    fi
done
fi

echo "Done."