fabber_var

#!/bin/sh

# fabber_var
# Calculate variances from fabber results (using zstat and mean images)
# M Chappell 1/11/2007
# Analysis Group, FMRIB, University of Oxford

# HISTORY
# 13-12-2007 Update to use mvntool to get varainces directly from the saved mvn (rather than from the z-stat)
# 26-11-2008 Add option to only extract varaince of a specified parameter
# 29-8-2013 Add anchors to grep expression to find exact match for a parameter name

#deal with options
#   Copyright (C) 2007-2012 University of Oxford
#
#   SHCOPYRIGHT
until [ -z $1 ]; do
    case $1 in
	-d) dirflag=1 datdir=$2;;
	-m) maskflag=1 mask=$2;;
	-p) paramflag=1 params=$2;; #parameter name, or comma separated list
     esac
    shift
done
echo "Fabber variance calculator"
echo "Working in $datdir"

if [ -z $paramflag ]; then
    params=`cat $datdir/paramnames.txt`
else
    params=`echo $params | sed 's:,: :g'`
fi

#index=1
for param in $params; do
    index=`grep -n ^$param$ $datdir/paramnames.txt | sed -n 's/^\([0-9]*\)[:].*/\1/p'`
    if [ -z $index ];then
	echo "Parameter $param not found - skipping"
    else
	echo "Calculating variance for: $param"
	mvntool --input=$datdir/finalMVN --mask=$mask --output=$datdir/var_$param --param=$index --var
    fi
	
    #index=`echo "$index +1" | bc`
done

echo "Done."