X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractLung.ggo;h=0cae0f89ad0a926ba70e365d0e0e779e56b06435;hb=b2fd61648c05339dd302e102361c22c4b11d48ff;hp=08f066a60f8fa4ec0bf04e52cc67c9858f195f3c;hpb=6e16222234a90c6079a8f4696c92de7349a496bb;p=clitk.git diff --git a/segmentation/clitkExtractLung.ggo b/segmentation/clitkExtractLung.ggo index 08f066a..0cae0f8 100644 --- a/segmentation/clitkExtractLung.ggo +++ b/segmentation/clitkExtractLung.ggo @@ -5,48 +5,67 @@ purpose "Segment lungs in CT image. Need 'patient' mask." 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