From c134c94d6663e0678a41f801a96c81501f632887 Mon Sep 17 00:00:00 2001
From: Romulo Pinho <romulo.pinho@lyon.unicancer.fr>
Date: Wed, 16 Nov 2011 10:22:37 +0100
Subject: [PATCH] change in midP script to create 4D warped image

---
 scripts/create_midP-2.0.sh | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/scripts/create_midP-2.0.sh b/scripts/create_midP-2.0.sh
index 239745f..a422e4f 100755
--- a/scripts/create_midP-2.0.sh
+++ b/scripts/create_midP-2.0.sh
@@ -76,8 +76,14 @@ registration()
         registration_elastix $reference_out $target_out $mask_ref_out $mask_targ_out $vf_out $result_out $params $log_out
       fi
 
-      # combine in and out vf
       motion_mask=$mask_dir/mm_$phase_nb.mhd
+
+      # combine in and out results
+      out_result=$output_dir/result_${ref_phase_nb}_$phase_nb.mhd
+      clitkCombineImage -i $result_in -j $result_out -m $motion_mask -o $out_result
+      abort_on_error registration $? clean_up_registration
+
+      # combine in and out vf
       vf_result=$vf_dir/vf_${ref_phase_nb}_$phase_nb.mhd
       clitkCombineImage -i $vf_in -j $vf_out -m $motion_mask -o $vf_result
       abort_on_error registration $? clean_up_registration
@@ -103,6 +109,10 @@ registration()
   # create 4D vf
   create_mhd_4D_pattern.sh $vf_dir/vf_${ref_phase_nb}_
 
+  # create 4D result image
+  create_mhd_4D_pattern.sh $output_dir/result_inside_${ref_phase_nb}_
+  create_mhd_4D_pattern.sh $output_dir/result_${ref_phase_nb}_
+
   echo
   echo "-------- Registration done ! --------"
   end=`date`
-- 
2.45.1