itk4 Renaming

[clitk.git] / segmentation / clitkExtractMediastinum.ggo

diff --git a/segmentation/clitkExtractMediastinum.ggo b/segmentation/clitkExtractMediastinum.ggo
index 490c673c60401d778071e3e1931fc055feee9122..bbb473dae195f85c2893ffd5ef71cab2530bf522 100644 (file)
--- a/segmentation/clitkExtractMediastinum.ggo
+++ b/segmentation/clitkExtractMediastinum.ggo
@@ -10,25 +10,29 @@ 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 "patient"       p       "Input patient mask filename"     string        yes
-option "patientBG"     -       "Patient Background"              int           default="0" no
-option "bones"         b       "Input bones mask filename"       string        yes
-option "bonesBG"       -       "Bones Background"                int           default="0" no
-option "lung"          l       "Input lung mask filename"        string        yes
-option "lungBG"        -       "Lung Background"                 int           default="0" no
-option "lungLeft"      -       "Lung Left value"                 int           default="1" no
-option "lungRight"     -       "Lung Right value"                int           default="2" no
-
-option "output"        o       "Output lungs mask filename"      string        yes
-
-section "Step 1 : Left/Right limits with lungs"
+option "input"     i   "Input CT filename"               string        yes
+option "output"    o   "Output lungs mask filename"      string        yes
+option "afdb"      a   "Input Anatomical Feature DB (needs Patient, Lungs, Trachea, VertebralBody)"     string         no
+option "useBones"  -    "If set : do use bones mask (when image is not injected)"  flag        off
+option "maxAntSpine"  - "Distance max to anterior part of the VertebralBody (spine) in mm"  double no default="10"
 
 option "spacing"     - "Intermediate resampling spacing"         double no default="6"
-option "fuzzy1"             -  "Fuzzy relative position threshold"       double no default="0.6"
+option "ft_LR_lungs"        -  "RelPos LR limits lungs"          double no default="0.3"
+option "ft_bones"           -  "RelPos AP limits bones"          double no default="0.6"
+option "ft_inf_lungs"       -  "RelPos inf limits bones"         double no default="0.05"
+option "ft_ant_sternum"             -  "RelPos ant limits sternum"       double no default="0.5"
+
+#section "Step 1 : Left/Right limits with lungs"
 
 section "Step 2 : Ant/Post limits with bones"
+#option "antSpine"     -       "Distance max to anterior part of the spine in mm"  double no default="10"
+
+#section "Step 3 : Inf limits with Lung"
 
-option "fuzzy2"             -  "Fuzzy relative position threshold"       double no default="0.6"
+# section "Step x : threshold for removing bones and injected parts"
+# option "upper"  - "Upper threshold" double no default="150"
+# option "lower"  - "Lower threshold" double no default="-200"
\ No newline at end of file