X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractMediastinum.ggo;h=bbb473dae195f85c2893ffd5ef71cab2530bf522;hb=fa358ee6738c92950cd9e6c45f55dda6e9b4576e;hp=4a42029569271ce141b3ae2739ddfdc9782211a7;hpb=44ebb81a500e42cf19964d209e14a59812a0dd4d;p=clitk.git

diff --git a/segmentation/clitkExtractMediastinum.ggo b/segmentation/clitkExtractMediastinum.ggo
index 4a42029..bbb473d 100644
--- a/segmentation/clitkExtractMediastinum.ggo
+++ b/segmentation/clitkExtractMediastinum.ggo
@@ -10,29 +10,29 @@ option "verboseStep"    -  "Verbose each step"		  flag		off
 option "writeStep"      w  "Write image at each step"	  flag		off
 option "verboseOption"  -  "Display options values"       flag          off
 option "verboseWarningOff" -  "Do not display warning"    flag          off
+option "verboseMemory"  -  "Display memory usage"         flag          off
 
 section "I/O"
 
-option "patient"       p	"Input patient mask filename"	  string  	yes
-option "patientBG"     -	"Patient Background"              int           default="0" no
-option "bones"         b	"Input bones mask filename"	  string  	yes
-option "bonesBG"       -	"Bones Background"                int           default="0" no
-option "lung"          l	"Input lung mask filename"	  string  	yes
-option "lungBG"        -	"Lung Background"                 int           default="0" no
-option "lungLeft"      -	"Lung Left value"                 int           default="1" no
-option "lungRight"     -	"Lung Right value"                int           default="2" no
-option "trachea"       t	"Input trachea mask filename"	  string  	yes
-option "tracheaBG"     -	"Trachea Background"              int           default="0" no
-option "afdb"          a	"Input Anatomical Feature DB"     string  	no
-
-option "output"        o 	"Output lungs mask filename"      string 	yes
-
-section "Step 1 : Left/Right limits with lungs"
+option "input"     i	"Input CT filename"               string  	yes
+option "output"    o 	"Output lungs mask filename"      string 	yes
+option "afdb"      a	"Input Anatomical Feature DB (needs Patient, Lungs, Trachea, VertebralBody)"     string  	no
+option "useBones"  -    "If set : do use bones mask (when image is not injected)"  flag	off
+option "maxAntSpine"  - "Distance max to anterior part of the VertebralBody (spine) in mm"  double no default="10"
+
 option "spacing"     -	"Intermediate resampling spacing"         double no default="6"
-option "fuzzy1"	     -	"Fuzzy relative position threshold"	  double no default="0.4"
+option "ft_LR_lungs"	     -	"RelPos LR limits lungs"	  double no default="0.3"
+option "ft_bones"	     -	"RelPos AP limits bones"	  double no default="0.6"
+option "ft_inf_lungs"	     -	"RelPos inf limits bones"	  double no default="0.05"
+option "ft_ant_sternum"	     -	"RelPos ant limits sternum"	  double no default="0.5"
+
+#section "Step 1 : Left/Right limits with lungs"
 
 section "Step 2 : Ant/Post limits with bones"
-option "fuzzy2"	     -	"Fuzzy relative position threshold"	  double no default="0.6"
+#option "antSpine"     -	"Distance max to anterior part of the spine in mm"  double no default="10"
+
+#section "Step 3 : Inf limits with Lung"
 
-section "Step 3 : Inf limits with Lung"
-option "fuzzy3"	     -	"Fuzzy relative position threshold"	  double no default="0.2"
+# section "Step x : threshold for removing bones and injected parts"
+# option "upper"  - "Upper threshold" double no default="150"
+# option "lower"  - "Lower threshold" double no default="-200"
\ No newline at end of file