corrections in mid-P scripts

- when checking clitk tools' return values

diff --git a/scripts/create_midP-2.0.sh b/scripts/create_midP-2.0.sh
index 0b3947be5ddb94d1a16d0a7540db3cd0e67f2c80..239745f5348c9daade6feefb3108ace546fea60a 100755 (executable)
--- a/scripts/create_midP-2.0.sh
+++ b/scripts/create_midP-2.0.sh
@@ -1,4 +1,4 @@
-#!/bin/sh 
+#!/bin/sh -x
 
 ###############################################################################
 #
@@ -85,6 +85,7 @@ registration()
       clitkZeroVF -i $vf_in -o vf_zero.mhd
       abort_on_error registration $? clean_up_registration
 
+      patient_mask=$mask_dir/patient_mask_$phase_nb.mhd
       clitkCombineImage -i $vf_result -j vf_zero.mhd -m $patient_mask -o $vf_result
       abort_on_error registration $? clean_up_registration
 

diff --git a/scripts/create_midP_masks-2.0.sh b/scripts/create_midP_masks-2.0.sh
index 6fadeec15d28f2b612982e95857ca8dc48e28915..bbf44f0fa9a857da69581133681ddb046f715905 100755 (executable)
--- a/scripts/create_midP_masks-2.0.sh
+++ b/scripts/create_midP_masks-2.0.sh
@@ -42,10 +42,12 @@ extract_bones()
 
 extract_lungs()
 {
-  echo "$phase_file -> Extracting lungs..."
-  clitkExtractLung -i $phase_file -o $mask_dir_tmp/lungs_$phase_nb.mhd -a $afdb_file --noAutoCrop
+  echo "$phase_file -> Extracting lungs..."  
+  clitkExtractLung -i $phase_file -o $mask_dir_tmp/lungs_$phase_nb.mhd -a $afdb_file --noAutoCrop --doNotSeparateLungs
 }
 
+
+
 resample()
 {
   echo "$phase_file -> Resampling..."
@@ -62,7 +64,7 @@ compute_motion_mask()
     FillingLevel=94
   fi
 
-  clitkMotionMask -i $mask_dir_tmp/patient_$phase_nb.mh -o $mask_dir_tmp/mm_$phase_nb.mhd --featureLungs $mask_dir_tmp/lungs_$phase_nb.mhd --upperThresholdLungs -400 --fillingLevel $FillingLevel --offsetDetect $MotionMaskOffsetDetect --pad --writeFeature=$mask_dir_tmp/feature_$phase_nb.mhd $MotionMaskExtra 
+  clitkMotionMask -i $mask_dir_tmp/patient_$phase_nb.mhd -o $mask_dir_tmp/mm_$phase_nb.mhd --featureLungs $mask_dir_tmp/lungs_$phase_nb.mhd --upperThresholdLungs -400 --fillingLevel $FillingLevel --offsetDetect $MotionMaskOffsetDetect --pad --writeFeature=$mask_dir_tmp/feature_$phase_nb.mhd $MotionMaskExtra 
   #--monitor=$mask_dir_tmp/monitor_$phase_nb.mhd
 }