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 "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)"
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 off