*** empty log message ***

[clitk.git] / segmentation / clitkExtractLung.ggo

diff --git a/segmentation/clitkExtractLung.ggo b/segmentation/clitkExtractLung.ggo
index e91a2eaed9c79344301337273ca49f55369acd47..ddc1fe71bb1c9a1b33b5c3cfa26651193bf837b0 100644 (file)
--- a/segmentation/clitkExtractLung.ggo
+++ b/segmentation/clitkExtractLung.ggo
@@ -14,9 +14,7 @@ option "verboseWarningOff" -  "Do not display warning"    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 "afdb"          a       "Output Anatomical Feature DB (Carina position)"    string      no
+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
 
@@ -51,3 +49,11 @@ option "remove3"     -       "Labels not to keep in lungs mask (trachea)"    int             no
 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
+