#!/bin/sh

#   easythresh - quick method of getting stats outside of feat
#
#   Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
#
#   Copyright (C) 1999-2007 University of Oxford
#
#   Part of FSL - FMRIB's Software Library
#   http://www.fmrib.ox.ac.uk/fsl
#   fsl@fmrib.ox.ac.uk
#   
#   Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
#   Imaging of the Brain), Department of Clinical Neurology, Oxford
#   University, Oxford, UK
#   
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export LC_NUMERIC=C

Usage() {
    echo ""
    echo "Usage: easythresh <raw_zstat> <brain_mask> <cluster_z_thresh> <cluster_prob_thresh> <background_image> <output_root> [--mm]"
    echo "e.g.:  easythresh stats/zstat1 mask 2.3 0.01 example_func grot"
    echo ""
    echo "Or:    easythresh <stat> <stat_thresh> <background_image> <output_root>"
    echo "e.g.:  easythresh stats/zstat1 2.3 example_func grot"
    echo ""
    exit 1
}

if [ "$5" = "" ] ; then
    [ "$4" = "" ] && Usage
    MAX=`${FSLDIR}/bin/fslstats $1 -R | awk '{print $2}'`
    ${FSLDIR}/bin/overlay 1 0 $3 -a $1 $2 $MAX rendered_$4
    ${FSLDIR}/bin/slicer rendered_$4 -A 750 rendered_$4.png
    exit
fi

[ "$6" = "" ] && Usage

# estimate image smoothness
SM=`${FSLDIR}/bin/smoothest -z $1 -m $2`
DLH=`echo $SM | awk '{print $2}'`
VOLUME=`echo $SM | awk '{print $4}'`
RESELS=`echo $SM | awk '{print $6}'`
#echo "$DLH $VOLUME $RESELS"

# run clustering after fixing stats header for talspace
${FSLDIR}/bin/fslmaths $1 -mas $2 thresh_$6
${FSLDIR}/bin/fslcpgeom $5 thresh_$6
${FSLDIR}/bin/cluster -i thresh_$6 -t $3 -p $4 --volume=$VOLUME -d $DLH -o cluster_mask_$6 --othresh=thresh_$6 $7 > cluster_$6.txt

# colour rendering
MAX=`${FSLDIR}/bin/fslstats thresh_$6 -R | awk '{print $2}'`
${FSLDIR}/bin/overlay 1 0 $5 -a thresh_$6 $3 $MAX rendered_thresh_$6
${FSLDIR}/bin/slicer rendered_thresh_$6 -A 750 rendered_thresh_$6.png

