X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractLung.ggo;h=98ddbd80d3dc29f1dcb53355d663a6dc7e1a4638;hb=31ae3f744e457adcd92677eaddd4c54d2702a392;hp=186508602e980191bb4b9db2e59578f06e7e5ae6;hpb=d30d301ddbebb5f290f8d9c0104dc6448ea531e1;p=clitk.git

diff --git a/segmentation/clitkExtractLung.ggo b/segmentation/clitkExtractLung.ggo
index 1865086..98ddbd8 100644
--- a/segmentation/clitkExtractLung.ggo
+++ b/segmentation/clitkExtractLung.ggo
@@ -5,6 +5,7 @@ purpose "Segment lungs in CT image. Need 'patient' mask."
 
 option "config"	        -  "Config file"		  string  	no
 option "imagetypes"     -  "Display allowed image types"  flag          off
+
 option "verbose"        v  "Verbose"			  flag		off
 option "verboseStep"    -  "Verbose each step"		  flag		off
 option "writeStep"      w  "Write image at each step"	  flag		off
@@ -15,9 +16,9 @@ option "verboseMemory"  -  "Display memory usage"         flag          off
 section "I/O"
 
 option "input"         i	"Input CT image filename"	  string  	yes
-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
+option "afdb"          a	"Output Anatomical Feature DB (Carina position)"  string  no default="default.afdb"
+option "output"        o 	"Output lungs mask filename"      string 	no default="lung.mhd"
+option "outputTrachea" t 	"Output trachea mask filename"    string 	no default="trachea.mhd"
 
 section "Step 1 : Air remove"
 
@@ -34,7 +35,7 @@ option "skipslices"                  -  "Number of slices to skip before searchi
 option "upperThresholdForTrachea"    -	"Initial upper threshold for trachea"  double	no  default="-900"
 option "multiplierForTrachea"	     -	"Multiplier for the region growing"    double	no  default="5"
 option "thresholdStepSizeForTrachea" -	"Threshold step size"	               int      no  default="64"
-option "seed"                        -	"Index of the trachea seed point"      int	no  multiple
+option "seed"                        -	"Index of the trachea seed point (in pixel, not in mm)"      int	no  multiple
 option "doNotCheckTracheaVolume"     -  "If set, do not check the trachea volume" flag off
 option "verboseRG"                   -  "Verbose RegionGrowing"   flag off
 
@@ -60,3 +61,7 @@ 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
 
+section "Step 7 : lung separation (labelling)"
+option "doNotSeparateLungs"   -  "Do not separate lungs if set"                 flag off
+
+option "noAutoCrop"	- 	"If set : do no crop final mask to BoundingBox"	                        flag 	off