/
FS_binarization.sh
executable file
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/
FS_binarization.sh
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#!/bin/sh
OPTIND=1 #The variable OPTIND holds the number of options parsed by the last call to getopts. It is common practice to call the shift command at the end of your processing loop to remove options that have already been handled from $@.
LOBES_FLAG=0
HEMI_FLAG=0
BRAIN_FLAG=0
LOBES_USR=0
HEMI_USR=0
while getopts "lhba?" opt; do
case "$opt" in
\?) echo "Usage: $0 [-?] [-l | -h | -b ] subjID"
exit 0
;;
l)
echo "bash: lobes"
LOBES_FLAG=1
LOBES_USR=1
;;
h) echo "bash: hemi"
LOBES_FLAG=1
HEMI_FLAG=1
HEMI_USR=1
;;
b) echo "bash: brain"
LOBES_FLAG=1
HEMI_FLAG=1
BRAIN_FLAG=1
;;
esac
done
#echo "$#"
if [ "$#" -eq "1" ]
then
LOBES_FLAG=1
HEMI_FLAG=1
BRAIN_FLAG=1
fi
shift $((OPTIND-1))
if [ "$#" -lt "1" ]
then
echo
echo "Usage: $0 [-h] [-l | -h | -b] subjID"
echo
exit 1
fi
SUBJID=$1
echo "$SUBJID"
echo "LOBES_FLAG: $LOBES_FLAG"
echo "HEMI_FLAG: $HEMI_FLAG"
echo "BRAIN_FLAG: $BRAIN_FLAG"
echo "LOBES_USR: $LOBES_USR"
echo "HEMI_USR: $HEMI_USR"
if [ $LOBES_FLAG == 1 ] && [ $LOBES_USR == 0 ]
then
echo "lobes will be processed...but then deleted..."
elif [ $LOBES_FLAG == 1 ] && [ $LOBES_USR == 1 ]
then
echo "lobes will be processed..."
fi
if [ $HEMI_FLAG == 1 ] && [ $HEMI_USR == 0 ]
then
echo "hemispheres will be processed...but then deleted..."
elif [ $HEMI_FLAG == 1 ] && [ $HEMI_USR == 1 ]
then
echo "hemispheres will be processed..."
fi
if [ $BRAIN_FLAG == 1 ]
then
echo "brain will be processed..."
fi
MGZ=aparc+aseg.mgz
NII=aparc+aseg.nii.gz
IMG_PATH=${SUBJID}/mri
mri_convert ${IMG_PATH}/$MGZ ${IMG_PATH}/$NII
############################## LOBES ##############################
if [ $LOBES_FLAG == 1 ]
then
LOBES=(frontal parietal temporal occipital)
for i in ${LOBES[@]}
do
if [ $i == frontal ]
then
thr=(3 12 14 17 18 19 20 24 27 28 32)
elif [ $i == parietal ]
then
thr=(29 8 31 22 25)
elif [ $i == temporal ]
then
thr=(30 15 9 1 7 34 6 33 16)
else
thr=(11 13 5 21)
fi
LEFT_LOBE_GM=lh_${i}GM.nii.gz
RIGHT_LOBE_GM=rh_${i}GM.nii.gz
structures=(${LEFT_LOBE_GM} ${RIGHT_LOBE_GM})
fslmaths ${IMG_PATH}/$NII -sub ${IMG_PATH}/$NII ${IMG_PATH}/${LEFT_LOBE_GM}
fslmaths ${IMG_PATH}/$NII -sub ${IMG_PATH}/$NII ${IMG_PATH}/${RIGHT_LOBE_GM}
segbase=(1000 2000)
ind=0
for j in ${segbase[@]}
do
for k in ${thr[@]}
do
fslmaths ${IMG_PATH}/$NII -uthr $(( $j + $k )) -thr $(( $j + $k )) -bin -mul 255 ${IMG_PATH}/$(( $j + $k )).nii.gz
fslmaths ${IMG_PATH}/${structures[${ind}]} -add ${IMG_PATH}/$(( $j + $k )).nii.gz ${IMG_PATH}/${structures[${ind}]}
rm -rf ${IMG_PATH}/$(( $j + $k )).nii.gz
done
((ind=ind+1))
done
done
fi
############################## HEMISPHERES ##############################
if [ $HEMI_FLAG == 1 ]
then
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CEREBRAL GM ~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
NO_LOBES=(cingulate insula)
for i in ${NO_LOBES[@]}
do
if [ $i == cingulate ]
then
thr=(2 10 23 26)
else
thr=35
fi
LEFT_NO_LOBE_GM=lh_${i}GM.nii.gz
RIGHT_NO_LOBE_GM=rh_${i}GM.nii.gz
structures=(${LEFT_NO_LOBE_GM} ${RIGHT_NO_LOBE_GM})
fslmaths ${IMG_PATH}/$NII -sub ${IMG_PATH}/$NII ${IMG_PATH}/${LEFT_NO_LOBE_GM}
fslmaths ${IMG_PATH}/$NII -sub ${IMG_PATH}/$NII ${IMG_PATH}/${RIGHT_NO_LOBE_GM}
segbase=(1000 2000)
ind=0
for j in ${segbase[@]}
do
for k in ${thr[@]}
do
fslmaths ${IMG_PATH}/$NII -uthr $(( $j + $k )) -thr $(( $j + $k )) -bin -mul 255 ${IMG_PATH}/$(( $j + $k )).nii.gz
fslmaths ${IMG_PATH}/${structures[${ind}]} -add ${IMG_PATH}/$(( $j + $k )).nii.gz ${IMG_PATH}/${structures[${ind}]}
rm -rf ${IMG_PATH}/$(( $j + $k )).nii.gz
done
((ind=ind+1))
done
done
LEFT_CEREBRAL_GM=lh_cerebralGM.nii.gz
RIGHT_CEREBRAL_GM=rh_cerebralGM.nii.gz
fslmaths ${IMG_PATH}/lh_frontalGM.nii.gz -add ${IMG_PATH}/lh_parietalGM.nii.gz -add ${IMG_PATH}/lh_temporalGM.nii.gz -add ${IMG_PATH}/lh_occipitalGM.nii.gz -add ${IMG_PATH}/lh_cingulateGM.nii.gz -add ${IMG_PATH}/lh_insulaGM.nii.gz -bin -mul 255 ${IMG_PATH}/$LEFT_CEREBRAL_GM
fslmaths ${IMG_PATH}/rh_frontalGM.nii.gz -add ${IMG_PATH}/rh_parietalGM.nii.gz -add ${IMG_PATH}/rh_temporalGM.nii.gz -add ${IMG_PATH}/rh_occipitalGM.nii.gz -add ${IMG_PATH}/rh_cingulateGM.nii.gz -add ${IMG_PATH}/rh_insulaGM.nii.gz -bin -mul 255 ${IMG_PATH}/$RIGHT_CEREBRAL_GM
for i in ${NO_LOBES[@]}
do
LEFT_NO_LOBE_GM=lh_${i}GM.nii.gz
RIGHT_NO_LOBE_GM=rh_${i}GM.nii.gz
rm -rf ${IMG_PATH}/$LEFT_NO_LOBE_GM
rm -rf ${IMG_PATH}/$RIGHT_NO_LOBE_GM
done
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CEREBRAL WM ~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
LEFT_CEREBRAL_WM=lh_cerebralWM.nii.gz
RIGHT_CEREBRAL_WM=rh_cerebralWM.nii.gz
fslmaths ${IMG_PATH}/$NII -uthr 2 -thr 2 -bin -mul 255 ${IMG_PATH}/$LEFT_CEREBRAL_WM
fslmaths ${IMG_PATH}/$NII -uthr 41 -thr 41 -bin -mul 255 ${IMG_PATH}/$RIGHT_CEREBRAL_WM
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CEREBELLAR GM ~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
LEFT_CEREBELLAR_GM=lh_cerebellarGM.nii.gz
RIGHT_CEREBELLAR_GM=rh_cerebellarGM.nii.gz
fslmaths ${IMG_PATH}/$NII -uthr 8 -thr 8 -bin -mul 255 ${IMG_PATH}/$LEFT_CEREBELLAR_GM
fslmaths ${IMG_PATH}/$NII -uthr 47 -thr 47 -bin -mul 255 ${IMG_PATH}/$RIGHT_CEREBELLAR_GM
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CEREBELLAR WM ~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
LEFT_CEREBELLAR_WM=lh_cerebellarWM.nii.gz
RIGHT_CEREBELLAR_WM=rh_cerebellarWM.nii.gz
fslmaths ${IMG_PATH}/$NII -uthr 7 -thr 7 -bin -mul 255 ${IMG_PATH}/$LEFT_CEREBELLAR_WM
fslmaths ${IMG_PATH}/$NII -uthr 46 -thr 46 -bin -mul 255 ${IMG_PATH}/$RIGHT_CEREBELLAR_WM
fi
###################################################################
############################## BRAIN ##############################
if [ $BRAIN_FLAG == 1 ]
then
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CEREBRAL GM ~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
fslmaths ${IMG_PATH}/$LEFT_CEREBRAL_GM -add ${IMG_PATH}/$RIGHT_CEREBRAL_GM ${IMG_PATH}/cerebralGM.nii.gz
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CEREBRAL WM ~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
fslmaths ${IMG_PATH}/$LEFT_CEREBRAL_WM -add ${IMG_PATH}/$RIGHT_CEREBRAL_WM ${IMG_PATH}/cerebralWM.nii.gz
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CEREBELLAR GM ~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
fslmaths ${IMG_PATH}/$LEFT_CEREBELLAR_GM -add ${IMG_PATH}/$RIGHT_CEREBELLAR_GM ${IMG_PATH}/cerebellarGM.nii.gz
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CEREBELLAR WM ~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
fslmaths ${IMG_PATH}/$LEFT_CEREBELLAR_WM -add ${IMG_PATH}/$RIGHT_CEREBELLAR_WM ${IMG_PATH}/cerebellarWM.nii.gz
fi
if [ $LOBES_USR == 0 ] && [ $LOBES_FLAG == 1 ]
then
echo "lobes deleting..."
LOBES=(frontal parietal temporal occipital)
for k in ${LOBES[@]}
do
LEFT_LOBE_GM=lh_${k}GM.nii.gz
RIGHT_LOBE_GM=rh_${k}GM.nii.gz
rm -rf ${IMG_PATH}/$LEFT_LOBE_GM
rm -rf ${IMG_PATH}/$RIGHT_LOBE_GM
done
fi
if [ $HEMI_USR == 0 ] && [ $HEMI_FLAG == 1 ]
then
echo "hemispheres deleting..."
rm -rf ${IMG_PATH}/$LEFT_CEREBRAL_GM
rm -rf ${IMG_PATH}/$RIGHT_CEREBRAL_GM
rm -rf ${IMG_PATH}/$LEFT_CEREBRAL_WM
rm -rf ${IMG_PATH}/$RIGHT_CEREBRAL_WM
rm -rf ${IMG_PATH}/$LEFT_CEREBELLAR_GM
rm -rf ${IMG_PATH}/$RIGHT_CEREBELLAR_GM
rm -rf ${IMG_PATH}/$LEFT_CEREBELLAR_WM
rm -rf ${IMG_PATH}/$RIGHT_CEREBELLAR_WM
fi
rm -rf ${IMG_PATH}/$NII