Debug RTStruct conversion with empty struc

[clitk.git] / registration / clitkBLUTDIR.ggo

diff --git a/registration/clitkBLUTDIR.ggo b/registration/clitkBLUTDIR.ggo
old mode 100755 (executable)
new mode 100644 (file)
index 4d84fce..9db5646
--- a/registration/clitkBLUTDIR.ggo
+++ b/registration/clitkBLUTDIR.ggo
@@ -18,13 +18,14 @@ section "Input"
 
 option "reference"             r       "Input reference 3D image (float)"      string          yes
 option "target"                        t       "Input target    2D image (float)"      string          yes
-option "referenceMask"                 m       "Mask to placed over the reference image"                 string                no
+option "referenceMask"                 m       "Mask or labels to placed over the reference image"               string                no
 option "targetMask"            -       "Mask to placed over the target image"            string                no
 
 section "Output"
 
 option "vf"                    -       "Result DVF"                            string          yes
 option "coeff"                 -       "Result coefficient images"             string          no      
+option "coeffEveryN"           -       "Result coefficient images at every N iterations (requires --coeff and --verbose)"              int             no              default="20"
 option "output"                        o       "Deformed target image"                 string          yes
 option "before"                        -       "Difference image before (but after rigid transform)"           string          no
 option "after"                 -       "Difference image after "               string          no
@@ -33,12 +34,13 @@ option "after"                      -       "Difference image after "               string          no
 section "Transform (Note that only one of --control, --spacing is required. The other will be adjusted to fit the region and allow exact representation. SamplingFactor will be set accordingly"
 
 option "initMatrix"            -       "Prior rigid/affine transform matrix from reference to target space"    string          no      
+option "centre"   - "Centre images before starting registration (ignored if initMatrix was given)"  flag    off
 option "initCoeff"             -       "Initial coefficient image"                                             string          no
 option "order"                 -       "Spline Order FFD"                                              int       no    multiple        default="3"
 option "control"               -       "Internal control points for each dimension"                    int       no    multiple        
 option "spacing"               -       "Control point spacing for each dimension (mm)"                 double    no    multiple        
 option "samplingFactor"                -       "LUT sampling factor"                                           int       no    multiple        
-
+option "itkbspline"             -       "Use ITK BSpline instead of multilabel BLUT for debug"          flag      off
 
 section "Interpolator"
 
@@ -82,6 +84,8 @@ option "upperBound"   -       "7: The upper bound"                                                    double  no      default="0.0"
 
 section "Registration"
 
-option "levels"                -       "Number of resolution levels"                                   int     no      default="1"                                             
+option "levels"                -       "Number of resolution levels"                                   int     no      default="1"
+option "skipLastPyramidLevel"          -       "Skip full resolution pyramid level"            flag    off
 option "intermediate"          -       "Write the coefficient image of the intermediate levels (provide levels filenames)"                                     string  no      multiple                                                
 
+