#!/bin/sh

Usage() {
    cat <<EOF

Usage: scr [work patient directory]

EOF
    exit 1
}

# wildcard ver.
# File name definition; "TPMgray＝c1*.nii" "TPMWhite＝c2*.nii" "Smoothed and coregistered PET=sr*PET"

# <Run FSL-merge>
echo "start time"
date
echo "FSL-merge start"
fslmaths c1*.nii -add  c2*.nii MRI_Betted.nii.gz
echo "FSL-merge done"

# <PET BET>
echo "PET BET start"
fslmaths sr*.nii -mas MRI_Betted.nii.gz PET_Betted.nii.gz
echo "PET BET done"

# <Generate Top20%Map>
echo "Top 20% map generating"
fslmaths sr*.nii -mas MRI_Betted.nii.gz -thrP 80 PET_Top20.nii.gz
fslmaths PET_Top20.nii.gz -bin PET_Top20_bin.nii.gz
echo "Top 20% map done"

# <Generate GM/WM mask>
fslmaths c1*.nii -thr 0.5 c1mask.nii.gz
fslmaths c2*.nii -thr 0.5 c2mask.nii.gz

# <Generate image for GWratio>
fslmaths PET_Top20_bin.nii.gz -mas c1mask.nii.gz PET_Top20_GM.nii.gz
fslmaths PET_Top20_bin.nii.gz -mas c2mask.nii.gz PET_Top20_WM.nii.gz

echo "end time"
date
