From 4f4d79533d2bdd0c13d90cde6bbb67e5f313b638 Mon Sep 17 00:00:00 2001
From: Romulo Pinho <pinho@lyon.fnclcc.fr>
Date: Fri, 4 Nov 2011 09:32:30 +0100
Subject: [PATCH] corrections in mid-P scripts

- when checking clitk tools' return values
---
 scripts/create_midP-2.0.sh       | 3 ++-
 scripts/create_midP_masks-2.0.sh | 8 +++++---
 2 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/scripts/create_midP-2.0.sh b/scripts/create_midP-2.0.sh
index 0b3947b..239745f 100755
--- 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 6fadeec..bbf44f0 100755
--- 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
 }
 
-- 
2.47.1