Merge branch 'master' of tux.creatis.insa-lyon.fr:clitk

[clitk.git] / segmentation / clitkExtractLung.ggo

diff --git a/segmentation/clitkExtractLung.ggo b/segmentation/clitkExtractLung.ggo
index 186508602e980191bb4b9db2e59578f06e7e5ae6..0cae0f89ad0a926ba70e365d0e0e779e56b06435 100644 (file)
--- a/segmentation/clitkExtractLung.ggo
+++ b/segmentation/clitkExtractLung.ggo
@@ -5,6 +5,7 @@ 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
@@ -15,9 +16,9 @@ option "verboseMemory"  -  "Display memory usage"         flag          off
 section "I/O"
 
 option "input"         i       "Input CT image filename"         string        yes
-option "afdb"          a       "Output Anatomical Feature DB (Carina position)"  string  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"
 
@@ -30,13 +31,17 @@ option "minSize"     -      "Minimum component size in voxels"        int           no      default="1
 
 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 "doNotCheckTracheaVolume"     -  "If set, do not check the trachea volume" flag off
-option "verboseRG"                   -  "Verbose RegionGrowing"   flag off
+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"
 
@@ -60,3 +65,7 @@ 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