From 183a798552699138752e8e735a868779cb65feea Mon Sep 17 00:00:00 2001 From: Simon Rit Date: Wed, 22 Jun 2011 10:35:11 +0200 Subject: [PATCH 1/1] Added ExtractBonesLower2 and FillingLevel options --- scripts/create_midP_masks.sh | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/scripts/create_midP_masks.sh b/scripts/create_midP_masks.sh index 8e4af7a..bb153c8 100755 --- a/scripts/create_midP_masks.sh +++ b/scripts/create_midP_masks.sh @@ -23,10 +23,13 @@ extract_bones() if [ x = x$ExtractBonesLower1 ]; then ExtractBonesLower1=120 fi + if [ x = x$ExtractBonesLower2 ]; then + ExtractBonesLower2=80 + fi echo "$image_name -> Extracting bones..." clitkImageConvert -i $image_name -o $mask_dir_tmp/float_$image_name -t float #clitkExtractBones -i $mask_dir_tmp/float_$image_name -o $mask_dir_tmp/bones_$image_name --lower1 120 --upper1 2000 --lower2 70 --upper2 2000 --smooth --time 0.0625 --noAutoCrop - clitkExtractBones -i $mask_dir_tmp/float_$image_name -o $mask_dir_tmp/bones_$image_name -a $afdb_name --lower1 $ExtractBonesLower1 --upper1 2000 --lower2 80 --upper2 2000 --smooth --time 0.0625 --noAutoCrop + clitkExtractBones -i $mask_dir_tmp/float_$image_name -o $mask_dir_tmp/bones_$image_name -a $afdb_name --lower1 $ExtractBonesLower1 --upper1 2000 --lower2 $ExtractBonesLower2 --upper2 2000 --smooth --time 0.0625 --noAutoCrop #clitkMorphoMath -i $mask_dir_tmp/bones_$image_name -o $mask_dir_tmp/bones_$image_name --type 2 --radius 4,4,2 } @@ -50,7 +53,10 @@ compute_motion_mask() if [ x = x$MotionMaskOffsetDetect ]; then MotionMaskOffsetDetect="0,-5,0" fi - clitkMotionMask -i $mask_dir_tmp/patient_only_$image_name -o $mask_dir_tmp/mm_$image_name --featureBones=$mask_dir_tmp/bones_$image_name --featureLungs=$mask_dir_tmp/lungs_$image_name --upperThresholdLungs -400 --fillingLevel 94 --offsetDetect 0,-5,0 --pad --writeFeature=$mask_dir_tmp/feature_$image_name $MotionMaskExtra --monitor=$mask_dir_tmp/monitor_$image_name + if [ x = x$FillingLevel ]; then + FillingLevel=94 + fi + clitkMotionMask -i $mask_dir_tmp/patient_only_$image_name -o $mask_dir_tmp/mm_$image_name --featureBones=$mask_dir_tmp/bones_$image_name --featureLungs=$mask_dir_tmp/lungs_$image_name --upperThresholdLungs -400 --fillingLevel $FillingLevel --offsetDetect 0,-5,0 --pad --writeFeature=$mask_dir_tmp/feature_$image_name $MotionMaskExtra --monitor=$mask_dir_tmp/monitor_$image_name } set_background() -- 2.45.1