From 14ff5532bdc12aef0e710b204453199e6fb8402c Mon Sep 17 00:00:00 2001
From: Romulo Pinho <romulo.pinho@lyon.unicancer.fr>
Date: Thu, 8 Mar 2012 11:38:54 +0100
Subject: [PATCH] midp scripts with mask_type option

- either mm, lungs, or patient for the moment
---
 scripts/create_midP-2.0.sh       | 107 ++++++++++++++----
 scripts/create_midP_masks-2.0.sh | 181 +++++++++++++++++++++++--------
 scripts/midp_common.sh           |  22 ++--
 scripts/midp_template.conf       |   9 ++
 4 files changed, 241 insertions(+), 78 deletions(-)

diff --git a/scripts/create_midP-2.0.sh b/scripts/create_midP-2.0.sh
index 7af8b09..8830a1b 100755
--- a/scripts/create_midP-2.0.sh
+++ b/scripts/create_midP-2.0.sh
@@ -19,7 +19,7 @@
 
 ######################### includes
 
-source `dirname $0`/create_midP_masks-2.0.sh using-as-lib 2 nn
+source `dirname $0`/create_midP_masks-2.0.sh using-as-lib
 source `dirname $0`/registration.sh
 source `dirname $0`/midp_common.sh
 
@@ -85,7 +85,7 @@ registration()
         registration_elastix $reference_out $target_out $mask_ref_out $mask_targ_out $vf_out $result_out $params $log_out
       fi
 
-      motion_mask=$mask_dir/mm_$phase_nb.mhd
+      motion_mask=$mask_dir/${mask_type}_$phase_nb.mhd
 
       # combine in and out results
       out_result=$output_dir/result_${ref_phase_nb}_$phase_nb.mhd
@@ -122,7 +122,7 @@ registration()
   clitkZeroVF -i $vf_ref -o $vf_out
   abort_on_error registration $? clean_up_registration
 
-  motion_mask=$mask_dir/mm_${ref_phase_nb}.mhd
+  motion_mask=$mask_dir/${mask_type}_${ref_phase_nb}.mhd
   reference_in=$mask_dir/${banded}inside_${ref_phase_nb}.mhd
   reference_out=$mask_dir/${banded}outside_$ref_phase_nb.mhd
   out_result=$output_dir/result_${ref_phase_nb}_${ref_phase_nb}.mhd
@@ -152,6 +152,77 @@ registration()
   echo
 }
 
+registration_no_motion_mask()
+{
+  echo
+  echo "----------- Registration Without Motion Masks ------------"
+  start=`date`
+  echo "start: $start"
+  echo
+
+  mkdir -p $vf_dir
+  mkdir -p $output_dir
+
+  # banded images may be created as separate files,
+  # with the specified preffix, which is interesting for debugging. 
+  # if blank, it means that the original images (those without bands) 
+  # will be used (see create_midP_masks-2.0.sh for details).
+  banded=""
+
+  # params read from conf file
+  use_coeffs=1
+  params="$nb_iter $nb_samples $sampling_algo $nb_hist_bins $nb_levels $bspline_spacing $metric $optimizer $interpolator"
+
+  # register all phases to the reference
+  for i in $( seq 0 $((${#phase_files[@]} - 1))); do
+    phase_file=${phase_files[$i]}
+    phase_nb=${phase_nbs[$i]}
+    
+    if [ "$phase_nb" != "$ref_phase_nb" ]; then
+      # params
+      reference=$mask_dir/patient_$ref_phase_nb.mhd
+      target=$mask_dir/patient_$phase_nb.mhd
+      mask_ref=$mask_dir/patient_mask_$ref_phase_nb.mhd
+      mask_targ=$mask_dir/patient_mask_$phase_nb.mhd
+      vf=$vf_dir/vf_${ref_phase_nb}_$phase_nb.mhd
+      result=$output_dir/result_${ref_phase_nb}_$phase_nb.mhd
+      log=$log_dir/log_${ref_phase_nb}_$phase_nb.log
+      if [ $use_coeffs = 1 ]; then
+        init_coeff=$coeff_in # empty at first iteration
+        coeff=$vf_dir/coeff_${ref_phase_nb}_$phase_nb.mhd
+      fi
+
+      # registration
+      if [ "$method" == "blutdir" ]; then
+        registration_blutdir $reference $target $mask_ref $mask_targ $vf $result $params $log $coeff 
+      elif [ "$method" == "elastix" ]; then
+        registration_elastix $reference $target $mask_ref $mask_targ $vf $result $params $log
+      fi
+
+      # save for later...
+      vf_ref=$vf
+    fi
+  done
+
+  clitkZeroVF -i $vf_ref -o $vf_dir/vf_${ref_phase_nb}_${ref_phase_nb}.mhd
+
+  # create 4D vf
+  create_mhd_4D_pattern.sh $vf_dir/vf_${ref_phase_nb}_
+
+  # create 4D coeffs
+  create_mhd_4D_pattern.sh $vf_dir/coeff_${ref_phase_nb}_ _0
+
+  # create 4D result image
+  create_mhd_4D_pattern.sh $output_dir/result_${ref_phase_nb}_
+
+  echo
+  echo "-------- Registration done ! --------"
+  end=`date`
+  echo "start: $start"
+  echo "end: $end"
+  echo
+}
+
 midp()
 {
   echo
@@ -250,20 +321,14 @@ midp_in_out()
   coeff_midp_in=$midp_dir/coeff_inside_midp_$phase_nb.mhd
   coeff_midp_out=$midp_dir/coeff_outside_midp_$phase_nb.mhd
   # average the vf's from reference phase to phase
-  # clitkAverageTemporalDimension -i $vf_dir/vf_inside_${ref_phase_nb}_4D.mhd -o $vf_midp_in
-  #clitkAverageTemporalDimension -i $vf_dir/coeff_inside_${ref_phase_nb}_4D_0.mhd -o $coeff_midp_in
   average_temporal_dimension $vf_dir/coeff_inside_${ref_phase_nb}_4D_0.mhd $coeff_midp_in
   abort_on_error midp $? clean_up_midp
-  # clitkAverageTemporalDimension -i $vf_dir/vf_outside_${ref_phase_nb}_4D.mhd -o $vf_midp_out
-  #clitkAverageTemporalDimension -i $vf_dir/coeff_outside_${ref_phase_nb}_4D_0.mhd -o $coeff_midp_out
   average_temporal_dimension $vf_dir/coeff_outside_${ref_phase_nb}_4D_0.mhd $coeff_midp_out
   abort_on_error midp $? clean_up_midp
 
   # invert the vf 
-  # clitkInvertVF -i $vf_midp_in -o $vf_midp_in
   clitkInvertVF -i $coeff_midp_in -o $vf_midp_in --type 1 --like $ref_phase_file
   abort_on_error midp $? clean_up_midp
-  # clitkInvertVF -i $vf_midp_out -o $vf_midp_out
   clitkInvertVF -i $coeff_midp_out -o $vf_midp_out --type 1 --like $ref_phase_file
   abort_on_error midp $? clean_up_midp
 
@@ -271,10 +336,8 @@ midp_in_out()
   ref_vf_midp_in=$vf_midp_in
   ref_vf_midp_out=$vf_midp_out
   vf_midp=$midp_dir/vf_midp_$phase_nb.mhd
-  #clitkCombineImage -i $vf_midp_in -j $vf_midp_out -o $vf_midp -m $mask_dir/mm_$phase_nb.mhd
-  combine_image $vf_midp_in $vf_midp_out $vf_midp $mask_dir/mm_$phase_nb.mhd
+  combine_image $vf_midp_in $vf_midp_out $vf_midp $mask_dir/${mask_type}_$phase_nb.mhd
   clitkZeroVF -i $vf_midp -o vf_zero.mhd
-  #clitkCombineImage -i $vf_midp -j vf_zero.mhd -o $vf_midp -m $mask_dir/patient_mask_$phase_nb.mhd
   combine_image $vf_midp vf_zero.mhd $vf_midp $mask_dir/patient_mask_$phase_nb.mhd
 
   # create the midp by warping the reference phase with the reference vf
@@ -303,10 +366,8 @@ midp_in_out()
 
       # combine in and out VF's
       vf_midp=$midp_dir/vf_midp_$phase_nb.mhd
-      #clitkCombineImage -i $vf_midp_in -j $vf_midp_out -o $vf_midp -m $mask_dir/mm_$phase_nb.mhd
-      combine_image $vf_midp_in $vf_midp_out $vf_midp $mask_dir/mm_$phase_nb.mhd
+      combine_image $vf_midp_in $vf_midp_out $vf_midp $mask_dir/${mask_type}_$phase_nb.mhd
       clitkZeroVF -i $vf_midp -o vf_zero.mhd
-      #clitkCombineImage -i $vf_midp -j vf_zero.mhd -o $vf_midp -m $mask_dir/patient_mask_$phase_nb.mhd
       combine_image $vf_midp vf_zero.mhd $vf_midp $mask_dir/patient_mask_$phase_nb.mhd
       
       midp=$midp_dir/midp_$phase_nb.mhd
@@ -327,7 +388,6 @@ midp_in_out()
   create_mhd_4D_pattern.sh $midp_dir/vf_outside_midp_
 
   echo "Calculating midp_avg.mhd..."
-  #clitkAverageTemporalDimension -i $midp_dir/midp_4D.mhd -o $midp_dir/midp_avg.mhd
   average_temporal_dimension $midp_dir/midp_4D.mhd $midp_dir/midp_avg.mhd
   abort_on_error midp $? clean_up_midp
 
@@ -335,9 +395,6 @@ midp_in_out()
   clitkMedianTemporalDimension -i $midp_dir/midp_4D.mhd -o $midp_dir/midp_med.mhd
   abort_on_error midp $? clean_up_midp
 
-  # clean-up
-  #rm $midp_dir/vf_*
-      
   echo
   echo "-------- Mid-position done ! --------"
   end=`date`
@@ -374,14 +431,20 @@ mask_dir="MASK-${mask_interpolation_spacing}mm-$mask_interpolation_algorithm"
 extract_4d_phases_ref $mhd4d $ref_phase
 
 if [ "$step" == "mask" -o "$step" == "all" ]; then
-  motion_mask $mhd4d $mask_interpolation_spacing $mask_interpolation_algorithm 
+    motion_mask $mhd4d $mask_type $mask_interpolation_spacing $mask_interpolation_algorithm 
 fi 
 
 if [ "$step" == "registration" -o "$step" == "all" ]; then
-  registration
+  if [ "$mask_type" == "mm" ]; then
+    registration
+  elif [ "$mask_type" == "lungs" ]; then
+    registration
+  elif [ "$mask_type" == "patient" ]; then
+    registration_no_motion_mask
+    midp_combined_vf=1
+  fi
 fi 
 
-midp_combined_vf=0
 if [ "$step" == "midp" -o "$step" == "all" ]; then
   if [ $midp_combined_vf = 0 ]; then
     midp_in_out
diff --git a/scripts/create_midP_masks-2.0.sh b/scripts/create_midP_masks-2.0.sh
index 292ff3c..6fa7476 100755
--- a/scripts/create_midP_masks-2.0.sh
+++ b/scripts/create_midP_masks-2.0.sh
@@ -1,4 +1,4 @@
-#! /bin/bash 
+#! /bin/bash -x
   
 ###############################################################################
 #
@@ -54,6 +54,7 @@ resample()
   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
+  clitkResampleImage -i $mask_dir_tmp/bones_$phase_nb.mhd -o $mask_dir_tmp/bones_$phase_nb.mhd --like $mask_dir_tmp/patient_$phase_nb.mhd
 }
 
 compute_motion_mask()
@@ -65,7 +66,8 @@ compute_motion_mask()
     FillingLevel=94
   fi
 
-  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 
+  #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
+  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 --featureBones $mask_dir_tmp/bones_$phase_nb.mhd --fillingLevel $FillingLevel --offsetDetect $MotionMaskOffsetDetect --pad --writeFeature $mask_dir_tmp/feature_$phase_nb.mhd $MotionMaskExtra  
   #--monitor=$mask_dir_tmp/monitor_$phase_nb.mhd
 }
 
@@ -96,8 +98,8 @@ create_banded_mask()
   clitkImageArithm -i $input_mask -j $input_dir/band1_$input_base -o $output_mask -t 0
   clitkImageArithm -i $output_mask -j $input_dir/band2_$input_base -o $output_mask -t 0
   # combine bands with image
-  clitkCombineImage -i $input_dir/short_band1_$input_base -j $input -m $input_dir/band1_$input_base -o $output
-  clitkCombineImage -i $input_dir/short_band2_$input_base -j $output -m $input_dir/band2_$input_base -o $output
+  combine_image $input_dir/short_band1_$input_base $input $output $input_dir/band1_$input_base
+  combine_image $input_dir/short_band2_$input_base $output $output $input_dir/band2_$input_base
 
   # clean-up
   rm `echo $input_dir/extra?_$input_base | sed 's:.mhd:.*:g'`
@@ -107,7 +109,30 @@ create_banded_mask()
 
 create_registration_masks()
 {
-  # extract inside and outside lung regions from the patient image, 
+  # extract inside and outside regions from the patient image, 
+  # using the motion mask computed previously
+  echo "$phase_file -> Setting Background..."
+  clitkSetBackground -i $mask_dir_tmp/patient_$phase_nb.mhd -o $mask_dir_tmp/inside_$phase_nb.mhd --mask $mask_dir_tmp/${mask_type}_$phase_nb.mhd --outsideValue -1200
+  clitkSetBackground -i $mask_dir_tmp/patient_$phase_nb.mhd -o $mask_dir_tmp/outside_$phase_nb.mhd --mask $mask_dir_tmp/${mask_type}_$phase_nb.mhd --outsideValue -1200 --fg
+
+  # the registration masks for inside (and outside) region correspond
+  # to the motion mask (and its complement) plus extra grey value bands,
+  # obtained with morphological dilations.
+  # 
+  echo "$phase_file -> Creating registration masks..."
+  # inside
+  clitkMorphoMath -i $mask_dir_tmp/${mask_type}_$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 $mask_dir_tmp/${mask_type}_$phase_nb.mhd $mask_dir_tmp/banded_inside_$phase_nb.mhd $mask_dir_tmp/banded_mask_inside_$phase_nb.mhd 4
+  # outside 
+  clitkBinarizeImage -i $mask_dir_tmp/outside_$phase_nb.mhd -o $mask_dir_tmp/${mask_type}_outside_$phase_nb.mhd -l -999 -u 4000 --mode both 
+  #clitkExtractPatient -i $mask_dir_tmp/outside_$phase_nb.mhd -o $mask_dir_tmp/${mask_type}_outside_$phase_nb.mhd --noAutoCrop
+  clitkMorphoMath -i $mask_dir_tmp/${mask_type}_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 $mask_dir_tmp/${mask_type}_outside_$phase_nb.mhd $mask_dir_tmp/banded_outside_$phase_nb.mhd $mask_dir_tmp/banded_mask_outside_$phase_nb.mhd 4
+}
+
+create_registration_motion_masks()
+{
+  # extract inside and outside regions from the patient image, 
   # using the motion mask computed previously
   echo "$phase_file -> Setting Background..."
   clitkSetBackground -i $mask_dir_tmp/patient_$phase_nb.mhd -o $mask_dir_tmp/inside_$phase_nb.mhd --mask $mask_dir_tmp/mm_$phase_nb.mhd --outsideValue -1200
@@ -127,10 +152,32 @@ create_registration_masks()
   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
 }
 
+create_registration_lung_masks()
+{
+  # extract inside and outside lung regions from the patient image, 
+  # using the motion mask computed previously
+  echo "$phase_file -> Setting Background..."
+  clitkSetBackground -i $mask_dir_tmp/patient_$phase_nb.mhd -o $mask_dir_tmp/inside_$phase_nb.mhd --mask $mask_dir_tmp/lungs_$phase_nb.mhd --outsideValue -1200
+  clitkSetBackground -i $mask_dir_tmp/patient_$phase_nb.mhd -o $mask_dir_tmp/outside_$phase_nb.mhd --mask $mask_dir_tmp/lungs_$phase_nb.mhd --outsideValue -1200 --fg
+
+  # the registration masks for inside (and outside) region correspond
+  # to the motion mask (and its complement) plus extra grey value bands,
+  # obtained with morphological dilations.
+  # 
+  echo "$phase_file -> Creating registration masks..."
+  # inside
+  clitkMorphoMath -i $mask_dir_tmp/lungs_$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 $mask_dir_tmp/lungs_$phase_nb.mhd $mask_dir_tmp/banded_inside_$phase_nb.mhd $mask_dir_tmp/banded_mask_inside_$phase_nb.mhd 4
+  # outside 
+  clitkBinarizeImage -i $mask_dir_tmp/outside_$phase_nb.mhd -o $mask_dir_tmp/lungs_outside_$phase_nb.mhd -l -999 -u 4000 --mode both 
+  clitkMorphoMath -i $mask_dir_tmp/lungs_outside_$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 $mask_dir_tmp/lungs_outside_$phase_nb.mhd $mask_dir_tmp/banded_outside_$phase_nb.mhd $mask_dir_tmp/banded_mask_outside_$phase_nb.mhd 4
+}
+
 mm_preprocessing()
 {
   extract_patient
-  # extract_bones
+  extract_bones
   extract_lungs
   # remove_tmp_masks 1
   if [ $resample_spacing -ne 0 ] ; then 
@@ -142,7 +189,13 @@ mm_postprocessing()
 {
   # remove_tmp_masks 2
   # remove_tmp_masks 3
+
   create_registration_masks
+#   if [ "$mask_type" == "mm" ]; then
+#     create_registration_motion_masks
+#   elif [ "$mask_type" == "lungs" ]; then
+#     create_registration_lung_masks
+#   fi
 }
 
 wait_mm_creation()
@@ -163,13 +216,42 @@ wait_mm_creation()
     # the check assumes that the inside and outside masks are the key files to exist.
     do_mm=0
     nb_phases=${#phase_nbs[@]}
-    nb_in_masks=`ls $mask_dir/mask_in*.mhd | wc -l`
-    nb_out_masks=`ls $mask_dir/mask_out*.mhd | wc -l`
-    if [ $nb_in_masks != $nb_phases -o $nb_out_masks != $nb_phases ]; then
-      # if the mask dir is invalid, remove it and recreate all masks, just in case.
-      rm -fr $mask_dir 2> /dev/null
-      do_mm=1
+    if [ "$mask_type" == "patient" ]; then
+      nb_masks=`ls $mask_dir/lungs_*.mhd | wc -l`
+      if [ $nb_masks != $nb_phases ]; then
+        # if the mask dir is invalid, remove it and recreate all masks, just in case.
+        rm -fr $mask_dir 2> /dev/null
+        do_mm=1
+      fi
+    else
+      nb_mm_masks=`ls $mask_dir/${mask_type}_outside*.mhd | wc -l`
+      nb_in_masks=`ls $mask_dir/mask_in*.mhd | wc -l`
+      nb_out_masks=`ls $mask_dir/mask_out*.mhd | wc -l`
+      if [ $nb_mm_masks != $nb_phases -o $nb_in_masks != $nb_phases -o $nb_out_masks != $nb_phases ]; then
+        # if the mask dir is invalid, remove it and recreate all masks, just in case.
+        rm -fr $mask_dir 2> /dev/null
+        do_mm=1
+      fi
     fi
+#     elif [ "$mask_type" == "lungs" ]; then
+#       nb_mm_masks=`ls $mask_dir/lungs_outside*.mhd | wc -l`
+#       nb_in_masks=`ls $mask_dir/mask_in*.mhd | wc -l`
+#       nb_out_masks=`ls $mask_dir/mask_out*.mhd | wc -l`
+#       if [ $nb_mm_masks != $nb_phases -o $nb_in_masks != $nb_phases -o $nb_out_masks != $nb_phases ]; then
+#         # if the mask dir is invalid, remove it and recreate all masks, just in case.
+#         rm -fr $mask_dir 2> /dev/null
+#         do_mm=1
+#       fi
+#     elif [ "$mask_type" == "mm" ]; then
+#       nb_mm_masks=`ls $mask_dir/mm_outside*.mhd | wc -l`
+#       nb_in_masks=`ls $mask_dir/mask_in*.mhd | wc -l`
+#       nb_out_masks=`ls $mask_dir/mask_out*.mhd | wc -l`
+#       if [ $nb_mm_masks != $nb_phases -o $nb_in_masks != $nb_phases -o $nb_out_masks != $nb_phases ]; then
+#         # if the mask dir is invalid, remove it and recreate all masks, just in case.
+#         rm -fr $mask_dir 2> /dev/null
+#         do_mm=1
+#       fi
+#     fi
   fi
   
   if [ $do_mm = 1 ]; then
@@ -210,10 +292,11 @@ wait_mm_creation()
 motion_mask()
 {
   #set cmd line variables
-  mhd4d=`basename $1`
-  if [ $# -eq 3 ] ; then
-    resample_spacing=$2
-    resample_algo=$3
+  local mhd4d=`basename $1`
+  mask_type=$2
+  if [ $# -eq 4 ] ; then
+    resample_spacing=$3
+    resample_algo=$4
   else
     resample_spacing=0
     resample_algo=0
@@ -267,33 +350,36 @@ motion_mask()
       abort_on_error mm_preprocessing $ret clean_up_masks
     done
 
-    # single-threaded motion mask calc
-    for i in $( seq 0 $((${#phase_nbs[@]} - 1))); do
-      phase_nb=${phase_nbs[$i]}
-      phase_file=${phase_files[$i]}
-
-      check_threads 1
-      echo "$phase_file -> Computing motion mask..."
-      compute_motion_mask > $mask_log_dir/motion_mask_$phase_file.log
-      abort_on_error compute_motion_mask $? clean_up_masks
-    done
+    if [ "$mask_type" == "mm" ]; then
+      # single-threaded motion mask calc
+      for i in $( seq 0 $((${#phase_nbs[@]} - 1))); do
+        phase_nb=${phase_nbs[$i]}
+        phase_file=${phase_files[$i]}
+
+        check_threads 1
+        echo "$phase_file -> Computing motion mask..."
+        compute_motion_mask > $mask_log_dir/motion_mask_$phase_file.log
+        abort_on_error compute_motion_mask $? clean_up_masks
+      done
+    fi
 
     # multi-threaded post-processing of motion mask calcs
-    pids=( )
-    for i in $( seq 0 $((${#phase_nbs[@]} - 1))); do
-      phase_nb=${phase_nbs[$i]}
-      phase_file=${phase_files[$i]}
-
-      check_threads $MAX_THREADS 
-      mm_postprocessing &
-      pids=( "${pids[@]}" "$!" )
-    done
-  
-    wait_pids ${pids[@]}
-    for ret in $ret_codes; do
-      abort_on_error mm_postprocessing $ret clean_up_masks
-    done
-
+    if [ "$mask_type" != "patient" ]; then
+      pids=( )
+      for i in $( seq 0 $((${#phase_nbs[@]} - 1))); do
+        phase_nb=${phase_nbs[$i]}
+        phase_file=${phase_files[$i]}
+
+        check_threads $MAX_THREADS 
+        mm_postprocessing &
+        pids=( "${pids[@]}" "$!" )
+      done
+    
+      wait_pids ${pids[@]}
+      for ret in $ret_codes; do
+        abort_on_error mm_postprocessing $ret clean_up_masks
+      done
+    fi
 
     # rename tmp mask directory after mask creation
     check_threads 1
@@ -313,8 +399,9 @@ motion_mask()
 # main  #
 #################
 
-if [ $# -ne 3 -a $# -ne 1 ]; then
-  echo "Usage: $0 CT_4D [RESAMPLE_SPACING RESAMPLE_ALGORITHM]"
+if [ $# -ne 4 -a $# -ne 2 -a $# -ne 1 ]; then
+  echo "Usage: $0 CT_4D TYPE [RESAMPLE_SPACING RESAMPLE_ALGORITHM]"
+  echo "  TYPE: \"motion\" (traditional motion masks); \"lungs\" (lung masks); \"patient\" (patient mask only)"
   exit -1
 fi
 
@@ -325,9 +412,11 @@ fi
 #
 
 if [ $1 != "using-as-lib" ]; then
-  if [ $# -eq 3 ] ; then
-    motion_mask $1 $2 $3
+  if [ $# -eq 4 ] ; then
+    motion_mask $1 $2 $3 $4
+  elif [ $# -eq 2 ] ; then
+    motion_mask $1 $2
   else
-    motion_mask $1
+    motion_mask $1 all
   fi
 fi
diff --git a/scripts/midp_common.sh b/scripts/midp_common.sh
index 16535a1..1ac9529 100755
--- a/scripts/midp_common.sh
+++ b/scripts/midp_common.sh
@@ -18,9 +18,9 @@ abort_on_error()
 {
   if [ $2 != 0 ]; then
     echo Aborted at $1 with code $2
-    if [ $# = 3 ]; then
-      eval $3
-    fi
+    #if [ $# = 3 ]; then
+    #  eval $3
+    #fi
 
     exit $2
   fi
@@ -179,12 +179,14 @@ extract_4d_phases_ref()
 combine_image()
 {
 #  eg: -i $result_in -j $result_out -o $out_result -m $motion_mask
+  local tmp1=$RANDOM
+  local tmp2=$RANDOM
 
-  clitkSetBackground -i $1 -o temp1.mhd -m $4
-  clitkSetBackground -i $2 -o temp2.mhd -m $4 --fg
+  clitkSetBackground -i $1 -o $tmp1.mhd -m $4
+  clitkSetBackground -i $2 -o $tmp2.mhd -m $4 --fg
 
-  clitkImageArithm -i temp1.mhd -j temp2.mhd -o $3
-  rm temp?.*
+  clitkImageArithm -i $tmp1.mhd -j $tmp2.mhd -o $3
+  rm $tmp1.* $tmp2.*
 }
 
 # 
@@ -192,8 +194,8 @@ combine_image()
 average_temporal_dimension()
 {
   # eg: -i $midp_dir/midp_4D.mhd -o $midp_dir/midp_avg.mhd
-
-  local tot=tot.mhd
+  local tmp=$RANDOM
+  local tot=$tmp.mhd
 
   local dir=`dirname $1` 
   local first=`grep raw $1 | sed 's/raw/mhd/g' | head -n 1`
@@ -205,5 +207,5 @@ average_temporal_dimension()
   done
 
   clitkImageArithm -i $tot -o $2 -t 11 -s $nbphases
-  rm tot.*
+  rm $tmp.*
 }
diff --git a/scripts/midp_template.conf b/scripts/midp_template.conf
index 8fde2c8..be3e0aa 100644
--- a/scripts/midp_template.conf
+++ b/scripts/midp_template.conf
@@ -18,6 +18,15 @@ log_dir="<LOGDIR>"
 # midp depends on registration, which depends on mask
 step="all"
 
+# indicate if midp images are computed with the in and out
+# VFs combined
+midp_combined_vf=0
+
+# indicate which masks are used in the registration (mm, lungs, patient). if
+# "patient", only the patient mask is used, and midp_combined_vf is
+# set to 1.
+mask_type="<TYPE>"
+
 # mask parameters
 #
 # interpolation algorithm for resampling (see clitkResampleImage)
-- 
2.47.1