X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractLung.ggo;h=f31f71812fa60c3bb4eca17f348c93b9f18cc9c3;hb=HEAD;hp=a5cf62a745e5e9069a5895db6d955dd2c14f7105;hpb=726fc21726f96f8f32015dda4c3b1efeb7d81851;p=clitk.git

diff --git a/segmentation/clitkExtractLung.ggo b/segmentation/clitkExtractLung.ggo
index a5cf62a..f31f718 100644
--- a/segmentation/clitkExtractLung.ggo
+++ b/segmentation/clitkExtractLung.ggo
@@ -16,9 +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"
 
@@ -31,13 +31,17 @@ option "minSize"     -	"Minimum component size in voxels"	  int		no  	default="1
 
 section "Step 2 : find trachea"
 
-option "skipslices"                  -  "Number of slices to skip before searching seed" int no default="0"
-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 (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
+option "type"                        -  "trachea finding algorithm (0: original; 1: LOLA11)" int no default="0"
+option "skipslices"                  -  "0: Number of slices to skip before searching seed" int no default="0"
+option "upperThresholdForTrachea"    -	"0: Initial upper threshold for trachea"  double	no  default="-900"
+option "multiplierForTrachea"	     -	"0: Multiplier for the region growing"    double	no  default="5"
+option "thresholdStepSizeForTrachea" -	"0: Threshold step size"	               int      no  default="64"
+option "seed"                        -	"0,1: Index of the trachea seed point (in mm  NOT IN PIXELS)"      float	no  multiple
+option "doNotCheckTracheaVolume"     -  "0,1: If set, do not check the trachea volume" flag off
+option "verboseRG"                   -  "0,1: Verbose RegionGrowing"   flag off
+option "maxElongation"               -  "1: Maximum allowed elongation of candidate regions for the trachea" float no default="0.5"
+option "numSlices"                   -  "1: Number of slices to search for trachea" int no default="50"
+option "seedPreProcessingThreshold"   -  "1: Threshold for the pre-processing step of the algorithm" int no default="-400"
 
 section "Step 3 : auto extract lung"
 
@@ -59,5 +63,9 @@ option "opencloseRadius"   	-  "OpenClose radius"	                        int no
 
 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
+#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 "removeSmallLabel"     -  "Remove small label (stomach?) before separation"  flag on
+option "noAutoCrop"	- 	"If set : do no crop final mask to BoundingBox"	                        flag 	off