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 CT image filename" string yes
-option "patient" p "Input patient mask filename" string yes
-option "patientBG" - "Patient Background" int default="0" 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"
-option "lower" - "Initial lower threshold" double no
-option "upper" - "Initial upper threshold" double no default="-300"
+option "lower" - "Initial lower threshold" int no
+option "upper" - "Initial upper threshold" int no default="-300"
option "minSize" - "Minimum component size in voxels" int no default="100"
-option "remove1" - "Labels not to keep in air mask (lungs)" int no multiple default="2"
-option "firstKeep1" - "First label to keep" int no default="1"
-option "lastKeep1" - "Last label to keep" int no
+#option "remove1" - "Labels not to keep in air mask (lungs)" int no multiple default="2"
+#option "firstKeep1" - "First label to keep" int no default="1"
+#option "lastKeep1" - "Last label to keep" int no
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" int no multiple
+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 pixel, not in mm)" int 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"
option "bins" - "Number of bins to use for the Otsu thresholding" int no default="500"
-option "remove2" - "Labels not to keep in air mask (gas)" int no multiple
-option "firstKeep2" - "First label to keep" int no default="1"
-option "lastKeep2" - "Last label to keep" int no
+# option "remove2" - "Labels not to keep in air mask (gas)" int no multiple
+# option "firstKeep2" - "First label to keep" int no default="1"
+# option "lastKeep2" - "Last label to keep" int no
section "Step 4 : remove trachea"
option "radius" - "Radius for dilation" int no default="1"
-option "remove3" - "Labels not to keep in lungs mask (trachea)" int no multiple
-option "firstKeep3" - "First label to keep" int no default="1"
-option "lastKeep3" - "Last label to keep" int no default="2"
+# option "remove3" - "Labels not to keep in lungs mask (trachea)" int no multiple
+# option "firstKeep3" - "First label to keep" int no default="1"
+# option "lastKeep3" - "Last label to keep" int no default="2"
+
+section "Step 5 : [optional] openclose"
+option "openclose" - "Perform an OpenClose operation" flag off
+option "opencloseRadius" - "OpenClose radius" int no default="1"
+
+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
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff