X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractLung.ggo;h=ddc1fe71bb1c9a1b33b5c3cfa26651193bf837b0;hb=3c89981c4f78fe15b1087f40e51e37c0c1fb087c;hp=08f066a60f8fa4ec0bf04e52cc67c9858f195f3c;hpb=6e16222234a90c6079a8f4696c92de7349a496bb;p=clitk.git

diff --git a/segmentation/clitkExtractLung.ggo b/segmentation/clitkExtractLung.ggo
index 08f066a..ddc1fe7 100644
--- a/segmentation/clitkExtractLung.ggo
+++ b/segmentation/clitkExtractLung.ggo
@@ -14,8 +14,7 @@ option "verboseWarningOff" -  "Do not display warning"    flag          off
 section "I/O"
 
 option "input"         i	"Input CT image filename"	  string  	yes
-option "patient"       p	"Input patient mask filename"	  string  	yes
-option "patientBG"   -	"Patient Background"              int           default="0" no
+option "afdb"          a	"Output Anatomical Feature DB (Carina position)"  string  no
 option "output"        o 	"Output lungs mask filename"      string 	yes
 option "outputTrachea" t 	"Output trachea mask filename"    string 	no
 
@@ -50,3 +49,11 @@ option "remove3"     -	"Labels not to keep in lungs mask (trachea)"    int		no
 option "firstKeep3"  -	"First label to keep"			  int		no  	default="1"
 option "lastKeep3"   -	"Last label to keep"		          int		no  	default="2"
 
+section "Step 5 : [optional] openclose"
+option "openclose"		-  "Perform an OpenClose operation"		flag off
+option "opencloseRadius"   	-  "OpenClose radius"	                        int no default="1"
+
+section "Step 6 : fill holes"
+option "doNotFillHoles"		-  "Do not fill holes if set"                 flag on
+option "dir"    	        d  "Directions (axes) to perform filling (defaults to 2,1,0)"	int multiple no
+