X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractBones.ggo;h=fa265ef136ca924a8dd3911190950e16c2c0e6d8;hb=a24b0a699298efe54b53c53cb215455fecd633fe;hp=581392bc57db42572263cd2dff8bc99e53a5ba2e;hpb=e008d74b0ecdc4ca2eaae8c429901a78f9ef5c31;p=clitk.git

diff --git a/segmentation/clitkExtractBones.ggo b/segmentation/clitkExtractBones.ggo
index 581392b..fa265ef 100644
--- a/segmentation/clitkExtractBones.ggo
+++ b/segmentation/clitkExtractBones.ggo
@@ -15,7 +15,16 @@ section "I/O"
 
 option "input"		i	"Input image filename"		  string  	yes
 option "output"    	o   	"Output image filename"		  string 	yes
-option "like"    	l   	"Resample like this image"	  string 	no
+option "afdb"           a	"Output Anatomical Feature DB (Carina position)"  string  no
+
+section "Smoothing (curvature anistropic diffusion)"
+
+option "smooth"			-	"smooth input image"			flag 	 	off
+option "spacing"		-	"Use image spacing"			flag 	 	off
+option "cond"			-	"Conductance parameter" 			double no	default="3.0"
+option "time"			-	"Time step (0.125 for 2D and 0.0625 for 3D)" 	double no	default="0.0625"
+option "iter"			-	"Iterations" 				double no	default="5"
+
 
 section "Initial connected component labelling (CCL)"
 
@@ -31,4 +40,8 @@ option "upper2"		-	"Upper threshold for RG"		double	no 	default="1500"
 option "radius2"	-	"Neighborhood radius"			int	no 	multiple	default="1" 
 option "sampleRate2"	-	"Sample rate of label image for RG: number of voxels to skip between seeds"	int	no 	default="0" 
 
-option "autoCrop"	- 	"Crop final mask to BoundingBox"        flag 	off
+section "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 "noAutoCrop"	- 	"If set : do no crop final mask to BoundingBox"	                        flag 	on