Debug RTStruct conversion with empty struc

[clitk.git] / registration / clitkAffineRegistration.ggo

diff --git a/registration/clitkAffineRegistration.ggo b/registration/clitkAffineRegistration.ggo
index 6c9f439c2b131ede716dc6828bd922b80e66a13c..a5d03855baeda66222ffa60e0692d69b62b6d867 100644 (file)
--- a/registration/clitkAffineRegistration.ggo
+++ b/registration/clitkAffineRegistration.ggo
@@ -1,7 +1,7 @@
 # file clitkAffineRegistration.ggo
 package "clitk"
 version "1.0"
-purpose "Compute an affine registration between two images." 
+purpose "Perform an affine registration between two images." 
 
 option "config"                -       "Config file"                   string          no
 
@@ -12,7 +12,7 @@ option "gradient"     -       "If verbose, show gradient at each iteration"   flag    off
 option "threads"       -       "Number of threads to use  (default=min(#cores,8))"     int      no
 
 
-section "Input (Both images have to be of the same dimension (2 or 3D). For 2D-3D registrations, give the 2D image a third dimension of 1 and set it to the reference image.)"
+section "Input (Both images have to be of the same dimension (2 or 3D). For 2D-3D (non-projective) registrations, give the 2D image a third dimension of 1 and set it to the reference image.)"
 
 option "reference"     i       "Reference or fixed image filename"             string  yes
 option "target"        j       "Target or moving image filename"               string  yes
@@ -42,8 +42,8 @@ option "transform"  - "Type: 0=Identity, 1=Translation, 2=Rigid, 3=Affine" int n
 option "transX"     x "1-3: Initial translation in mm along the X axis"  float no  default="0.0"
 option "transY"     y "1-3: Initial translation in mm along the Y axis"  float no  default="0.0"
 option "transZ"     z "1-3: Initial translation in mm along the Z axis"  float no  default="0.0"
-option "initMatrix" - "2-3: Initial matrix (reference to object space) filename " string  no
-option "moment"     - "2-3: Initialize translation by aligning the center of gravities for the respective intensities" flag off
+option "initMatrix" - "1-3: Initial matrix (reference to object space) filename " string  no
+option "moment"     - "1-3: Initialize translation by aligning the center of gravities for the respective intensities" flag off
 
 section "Metric (optimized, threaded versions are available for *, compile ITK with REVIEW and OPT_REGISTRATION enabled)"
 
@@ -54,7 +54,7 @@ option "subtractMean" -       "1: Subtract mean for NCC calculation (narrows opt
 option "bins"          -       "2,5-8: Number of histogram bins"                                                                       int     no      default="50"
 option "random"        -       "4,6: Samples should be taken randomly, otherwise uniformly"                                            flag    off     
 option "stdDev"                -       "4: specify the standard deviation in mm of the gaussian kernels for both PDF estimations"              float   no      default="0.4"   
-option "explicitPDFDerivatives"        -       "6: Calculate PDF derivatives explicitly (rigid=true; FFD=false)"                               flag    on
+option "explicitPDFDerivatives"        -       "6: Calculate PDF derivatives explicitly (affine=true; FFD=false)"                              flag    on
 
 
 section "Preprocessing"
@@ -82,7 +82,7 @@ option "selectBound"  -       "7: Select the type of bound: 0=none, 1=u, 2=u&l, 3=l"
 option "lowerBound"    -       "7: The lower bound"                                                    double  no      
 option "upperBound"    -       "7: The upper bound"                                                    double  no      
 
-option "rWeight"       -       "Weight of 1° of rotation during optimisation (high weight, less change)"            float   no      default="50.0"
+option "rWeight"       -       "Weight of 1° of rotation during optimisation (high weight, less change)"              float   no      default="50.0"
 option "tWeight"       -       "Weight of 1mm of translation  during optimisation (high weight, less change)"          float   no      default="1.0"
 option "levels"                -       "Number of resolution levels"                                                           int     no      default="1"                                             
 option "inc"           -       "Increment factor (x)  previous step/tol = new step/tol at next resolution level"       float   no      default="1.2"