#!/bin/sh

#   lesions.....this doesn't work!!
#
#   Stephen Smith, FMRIB Image Analysis Group
#
#   Copyright (C) 1999-2004 University of Oxford
#
#   SHCOPYRIGHT



#### process options ###################################################################

if [ _$2 = _ ] ; then
    echo "Usage:  lesions <t1_root> <t2_root> [-f] [-lt <thr>]"
    echo "-f        :  second image is FLAIR not T2"
    echo "-lt <thr> :  set lesion threshold (default 0.5)"
    exit 1
fi

A=$1
B=$2
shift 2

lesion_thr=0.5
nclasses=2
t2segopts="-t2 -a"
t2lesions=${B}_brain_pve_0

for opts in $@ ; do

    if [ $opts = -f ] ; then
	echo "processing second input as FLAIR image"
	nclasses=4
	t2segopts=""
	t2lesions=${B}_brain_pve_3
	shift
    fi

    if [ $opts = -lt ] ; then
	lesion_thr=$2
	shift 2
    fi

done

echo "working" > ${A}_lesions.txt

#### T1 ################################################################################

# brain-extract t1 and run segmentation; pve_0 should be CSF only
${FSLDIR}/bin/bet $A ${A}_brain -m
${FSLDIR}/bin/fast1 -e -ov ${A}_brain

# register t1 to standard space and invert transform
${FSLDIR}/bin/flirt -ref ${FSLDIR}/etc/standard/avg152T1_brain -in ${A}_brain -omat ${A}_brain_2_std.mat
${FSLDIR}/bin/convert_xfm -inverse -omat std_2_${A}_brain.mat ${A}_brain_2_std.mat

# dilate (6mm) standard space ventricles+deep-grey, bring into t1 space and re-binarise to make "CENTRAL MASK"
${FSLDIR}/bin/fslmaths ${FSLDIR}/etc/standard/avg152T1_strucseg -thr 3.5 -bin -dilM -dilM -dilM strucseg_2_${A}_brain
${FSLDIR}/bin/flirt -in strucseg_2_${A}_brain -ref ${A}_brain -out strucseg_2_${A}_brain -applyxfm -init std_2_${A}_brain.mat
${FSLDIR}/bin/fslmaths strucseg_2_${A}_brain -bin strucseg_2_${A}_brain

# produce t1-derived CSF mask and also dilate in-plane: 5 voxels outside CENTRAL MASK, 1 voxel inside mask
${FSLDIR}/bin/fslmaths ${A}_brain_pve_0 -thr 0.3 -bin ${A}_csf
${FSLDIR}/bin/fslmaths ${A}_csf -kernel 2D -dilM -dilM -dilM -dilM -dilM -sub strucseg_2_${A}_brain -thr 0.5 -bin ${A}_grot
${FSLDIR}/bin/fslmaths ${A}_csf -kernel 2D -dilM -mul strucseg_2_${A}_brain -add ${A}_grot -bin ${A}_csf_dil



#### T2 or FLAIR #######################################################################

# register t2 to t1 and invert transform
${FSLDIR}/bin/flirt -in $B -ref $A -omat ${B}_to_${A}.mat
${FSLDIR}/bin/convert_xfm -inverse -omat ${A}_to_${B}.mat ${B}_to_${A}.mat

# transform t1 brain mask into t2 space and apply to t2 to get t2_brain
${FSLDIR}/bin/flirt -in ${A}_brain_mask -out ${B}_brain_mask -ref $B -applyxfm -init ${A}_to_${B}.mat
${FSLDIR}/bin/fslmaths $B -mas ${B}_brain_mask ${B}_brain

# run segmentation on t2; $t2lesions should be CSF+lesions; transform into t1 space, remask with t1 brain mask
${FSLDIR}/bin/fast1 $t2segopts -c $nclasses -e -ov ${B}_brain
${FSLDIR}/bin/flirt -in $t2lesions -ref $A -out ${A}_lesion+CSF -applyxfm -init ${B}_to_${A}.mat
${FSLDIR}/bin/fslmaths ${A}_lesion+CSF -mas ${A}_brain_mask ${A}_lesion+CSF



#### combine to remove CSF from CSF+lesions ############################################

# combine masks and use to mask out CSF from t2-derived lesion+CSF probability; output lesion volume
${FSLDIR}/bin/fslmaths ${A}_csf_dil -mul -1 -add 1 -mul ${A}_lesion+CSF ${A}_lesions -odt float
${FSLDIR}/bin/fslmaths ${A}_lesions -thr $lesion_thr ${A}_lesions_thr -odt float
echo `${FSLDIR}/bin/fslstats ${A}_lesions_thr -m -v | awk '{print "2 k " $1 " " $3 " * 1000 / p" }' | dc -` > ${A}_lesions.txt
echo "$A	`cat ${A}_lesions.txt`"

# create display output
                                                                                                  ${FSLDIR}/bin/slicer $A                                   -A 400 $A.png
                                                                                                  ${FSLDIR}/bin/slicer ${A}_brain_seg strucseg_2_${A}_brain -A 400 ${A}_brain_seg.png
${FSLDIR}/bin/flirt -in $B             -ref $A -out ${B}_grot -applyxfm -init ${B}_to_${A}.mat ;  ${FSLDIR}/bin/slicer ${B}_grot                            -A 400 $B.png 
${FSLDIR}/bin/flirt -in ${B}_brain_seg -ref $A -out ${B}_grot -applyxfm -init ${B}_to_${A}.mat ;  ${FSLDIR}/bin/slicer ${B}_grot -i 0 $nclasses             -A 400 ${B}_brain_seg.png
${FSLDIR}/bin/overlay 0 1 $A -a ${A}_lesions $lesion_thr 1 ${A}_lesions_render ;                  ${FSLDIR}/bin/slicer ${A}_lesions_render                  -A 400 ${A}_lesions_render.png
${FSLDIR}/bin/pngappend ${A}.png ${A}_brain_seg.png ${B}.png ${B}_brain_seg.png ${A}_lesions_render.png ${A}_lesions.png



#### clean up #########################################################################

/bin/rm -f ${A}.png ${B}.png ${A} ${B} ${A}_brain_seg.png ${B}_brain_seg.png ${A}_lesions_render* ${A}_brain_delesioned_seg.png ${A}_grot* ${B}_grot*