# 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
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
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)"
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"
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"