various update

[clitk.git] / segmentation / clitkExtractMediastinum.ggo

diff --git a/segmentation/clitkExtractMediastinum.ggo b/segmentation/clitkExtractMediastinum.ggo
index 2f57caea2f948dab924ea1c7d8ebfcd9ae66de01..48139f50b63dc1ff7a9117dd64b9fb46bdf92f0e 100644 (file)
--- a/segmentation/clitkExtractMediastinum.ggo
+++ b/segmentation/clitkExtractMediastinum.ggo
@@ -13,24 +13,23 @@ option "verboseWarningOff" -  "Do not display warning"    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 "trachea"       t       "Input trachea mask filename"     string        yes
-option "tracheaBG"     -       "Trachea Background"              int           default="0" no
+option "input"     i   "Input CT filename"               string        yes
+option "afdb"      a   "Input Anatomical Feature DB"     string        no
+option "useBones"  -    "If set : do use bones mask (when image is not injected)"  flag        off
 
 option "output"        o       "Output lungs mask filename"      string        yes
 
 section "Step 1 : Left/Right limits with lungs"
-
 option "spacing"     - "Intermediate resampling spacing"         double no default="6"
-option "fuzzy1"             -  "Fuzzy relative position threshold"       double no default="0.6"
+option "fuzzy1"             -  "Fuzzy relative position threshold"       double no default="0.5"
 
 section "Step 2 : Ant/Post limits with bones"
-
 option "fuzzy2"             -  "Fuzzy relative position threshold"       double no default="0.6"
+option "antSpine"     -        "Distance max to anterior part of the spine in mm"  double no default="10"
+
+section "Step 3 : Inf limits with Lung"
+option "fuzzy3"             -  "Fuzzy relative position threshold"       double no default="0.05"
+
+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