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
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"
option "upperBound" - "7: The upper bound" double no default="0.0"
-Section "Registration"
+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
+