motion masks with and without bands

[clitk.git] / scripts / create_midP_masks-2.0.sh

diff --git a/scripts/create_midP_masks-2.0.sh b/scripts/create_midP_masks-2.0.sh
index 2d9ab8ec2f14f222fca3f74283148654e148622a..5bd0c9fa0c554798eef7e6998420886deb1d8fbc 100755 (executable)
--- a/scripts/create_midP_masks-2.0.sh
+++ b/scripts/create_midP_masks-2.0.sh
@@ -43,7 +43,7 @@ extract_bones()
 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
 }
 
 
@@ -52,6 +52,7 @@ resample()
 {
   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
 }
 
@@ -118,10 +119,12 @@ create_registration_masks()
   # 
   echo "$phase_file -> Creating registration masks..."
   # inside
-  create_banded_mask $mask_dir_tmp/inside_$phase_nb.mhd $mask_dir_tmp/mm_$phase_nb.mhd $mask_dir_tmp/banded_inside_$phase_nb.mhd $mask_dir_tmp/mask_inside_$phase_nb.mhd 4
+  clitkMorphoMath -i $mask_dir_tmp/mm_$phase_nb.mhd -o $mask_dir_tmp/mask_inside_$phase_nb.mhd --type 1 --radius 8
+  create_banded_mask $mask_dir_tmp/inside_$phase_nb.mhd $mask_dir_tmp/mm_$phase_nb.mhd $mask_dir_tmp/banded_inside_$phase_nb.mhd $mask_dir_tmp/banded_mask_inside_$phase_nb.mhd 4
   # outside 
   clitkExtractPatient -i $mask_dir_tmp/outside_$phase_nb.mhd -o $mask_dir_tmp/mm_outside_$phase_nb.mhd --noAutoCrop
-  create_banded_mask $mask_dir_tmp/outside_$phase_nb.mhd $mask_dir_tmp/mm_outside_$phase_nb.mhd $mask_dir_tmp/banded_outside_$phase_nb.mhd $mask_dir_tmp/mask_outside_$phase_nb.mhd 4
+  clitkMorphoMath -i $mask_dir_tmp/mm_outside_$phase_nb.mhd -o $mask_dir_tmp/mask_outside_$phase_nb.mhd --type 1 --radius 8
+  create_banded_mask $mask_dir_tmp/outside_$phase_nb.mhd $mask_dir_tmp/mm_outside_$phase_nb.mhd $mask_dir_tmp/banded_outside_$phase_nb.mhd $mask_dir_tmp/banded_mask_outside_$phase_nb.mhd 4
 }
 
 mm_preprocessing()
@@ -145,7 +148,7 @@ mm_postprocessing()
 motion_mask()
 {
   #set cmd line variables
-  mhd4d=$1
+  mhd4d=`basename $1`
   if [ $# -eq 3 ] ; then
     resample_spacing=$2
     resample_algo=$3