extract_lungs()
{
echo "$phase_file -> Extracting lungs..."
- clitkExtractLung -i $phase_file -o $mask_dir_tmp/lungs_$phase_nb.mhd -a $afdb_file --noAutoCrop --doNotSeparateLungs
+ clitkExtractLung -i $phase_file -o $mask_dir_tmp/lungs_$phase_nb.mhd -a $afdb_file --noAutoCrop --doNotSeparateLungs --type 1
}
{
echo "$phase_file -> Resampling..."
clitkResampleImage -i $mask_dir_tmp/patient_$phase_nb.mhd -o $mask_dir_tmp/patient_$phase_nb.mhd --spacing $resample_spacing --interp $resample_algo
+ clitkResampleImage -i $mask_dir_tmp/patient_mask_$phase_nb.mhd -o $mask_dir_tmp/patient_mask_$phase_nb.mhd --spacing $resample_spacing --interp $resample_algo
clitkResampleImage -i $mask_dir_tmp/lungs_$phase_nb.mhd -o $mask_dir_tmp/lungs_$phase_nb.mhd --like $mask_dir_tmp/patient_$phase_nb.mhd
}
motion_mask()
{
#set cmd line variables
- mhd4d=$1
+ mhd4d=`basename $1`
if [ $# -eq 3 ] ; then
resample_spacing=$2
resample_algo=$3