#!/bin/sh

Usage() {
    cat <<EOF

Usage: scr [work patient directory]

EOF
    exit 1
}

# wildcard ver.
# File name definition; "MRI＝*T1" & "Smoothed and coregistered PET=sr*PET"

# <Run HD-BET>
echo "start time"
date
echo "HD-BET start"
hd-bet -i *T1.nii -o MRI_Betted.nii.gz -device cpu --disable_tta
echo "MRI BET done"

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

echo "end time"
date