#File clitkExtractBones.ggo
package "clitkExtractBones"
version "1.0"
purpose "Extract bony anatomy through thresholding and connected component labelling. Resample mask afterwards (interp= NN) to match another one (like)"

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
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 "input"		i	"Input image filename"		  string  	yes
option "output"    	o   	"Output image filename"		  string 	yes
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)"

option "lower1"			-	"Lower threshold for CCL"			double	no default="100" 
option "upper1"			-	"Upper threshold for CCL"			double	no default="1500" 
option "minSize"		-	"Minimal Component Size for CCL"		int 	no default="100" 
option "full"			-	"Use full connectivity (one side is enough)"	flag	off 

section "Neighborhood Connected Region Growing (RG)"

option "lower2"		-	"Lower threshold for RG"		double	no	default="10" 
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" 

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 	off