X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractLymphStations.ggo;h=313851473863866fbd27033961ef12deff6073b3;hb=adeedbea1fbf8bc34e2c9565867b992ad13ccc57;hp=28d78f60cd2100a6ced760a30f030838e0eebf0d;hpb=38786c4da19b87319bbe3cecc145e3d1771d10da;p=clitk.git

diff --git a/segmentation/clitkExtractLymphStations.ggo b/segmentation/clitkExtractLymphStations.ggo
index 28d78f6..3138514 100644
--- a/segmentation/clitkExtractLymphStations.ggo
+++ b/segmentation/clitkExtractLymphStations.ggo
@@ -10,18 +10,43 @@ 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 "mediastinum"   m	"Input mediastinum mask filename" string  	yes
-option "trachea"       t	"Input trachea mask filename"	  string  	yes
-option "output"        o 	"Output lungs mask filename"      string 	yes
-
-option "carenaZposition"   		c	"Sup-Inf position of the carena (in mm, with origin)" double no
-option "middleLobeBronchusZposition"   	b	"Sup-Inf position of the middle lobe bronchus (in mm, with origin)" double no
-option "spacing"     -	"Intermediate resampling spacing"         double no default="6"
-option "fuzzy1"	     -	"Fuzzy relative position threshold"	  double no default="0.6"
-
-
-
-
+option "afdb"          a	"Input Anatomical Feature DB"     string  	no
+option "input"         i	"Input filename"                  string  	no
+option "output"        o 	"Output lungs mask filename"      string 	no
+option "station"       - 	"Force to compute station even if already exist in the DB"      string 	no multiple
+option "nosupport"     -        "Do not recompute the station supports if already available"   flag off
+
+
+section "Options for Station 3A"
+option "S3A_ft_SVC"              - "Fuzzy Threshold for NotPost to SVC"         double default="0.5" no 
+option "S3A_ft_Bones"            - "Fuzzy Threshold for Post to Bones"          double default="0.5" no 
+option "S3A_t_Bones"             - "Binary HU Threshold for bones"              double default="250" no 
+option "S3A_ft_Aorta"            - "Fuzzy Threshold for NotPost to Aorta"       double default="0.5" no 
+option "S3A_ft_SubclavianArtery" - "Fuzzy Threshold for Ant to SubclavianArtery" double default="0.2" no 
+
+
+section "Options for Station 8"
+option "S8_esophagusDilatationForAnt"   - "Dilatation of esophagus, in mm, for 'anterior' limits (default=15,2,1)" double no multiple
+option "S8_esophagusDilatationForRight" - "Dilatation of esophagus, in mm, for 'right' limits (default=5,10,1)" double no multiple
+option "S8_ft_Esophagus"                - "Fuzzy Threshold for 'Post' to dilated Esophagus" double default="0.5" no 
+
+section "Options for Station 7"
+option "S7_ft_Bronchi"                    - "Fuzzy Threshold for Left/Right bronchi" double default="0.1" no 
+option "S7_ft_LeftSuperiorPulmonaryVein"  - "Fuzzy Threshold for LeftSuperiorPulmonaryVein" double default="0.3" no 
+option "S7_ft_RightSuperiorPulmonaryVein" - "Fuzzy Threshold for RightSuperiorPulmonaryVein" double default="0.2" no 
+option "S7_ft_RightPulmonaryArtery"       - "Fuzzy Threshold for RightPulmonaryArtery" double default="0.3" no 
+option "S7_ft_LeftPulmonaryArtery"        - "Fuzzy Threshold for LeftPulmonaryArtery (NOT USEFUL YET)" double default="0.5" no 
+option "S7_ft_SVC"                        - "Fuzzy Threshold for SVC" double default="0.2" no 
+option "S7_UseMostInferiorPartOnly"    - "Inferior separation with S8."  flag off
+
+section "Options for Station 2RL"
+option "S2RL_ft_CommonCarotidArtery"   - "Threshold for NotAntTo to CommonCarotidArtery"   double default="0.7" no 
+option "S2RL_ft_BrachioCephalicTrunk"  - "Threshold for NotAntTo to BrachioCephalicTrunk"  double default="0.7" no 
+option "S2RL_ft_BrachioCephalicVein"   - "Threshold for NotAntTo to BrachioCephalicVein"   double default="0.3" no 
+option "S2RL_ft_Aorta"                 - "Threshold for RightTo  to Aorta"                 double default="0.7" no 
+option "S2RL_ft_SubclavianArteryRight" - "Threshold for NotLeft  to SubclavianArteryRight" double default="0.5" no 
+option "S2RL_ft_SubclavianArteryLeft"  - "Threshold for NotRight to SubclavianArteryLeft"  double default="0.8" no