# file clitkAffineRegistration.ggo package "clitk" version "1.0" purpose "Perform an affine registration between two images." option "config" - "Config file" string no section "Run Time" option "verbose" v "Verbose" flag off 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 (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 "referenceMask" m "Mask to placed over the reference image" string no option "targetMask" - "Mask to placed over the target image" string no section "Output" option "output" o "Transformed object image filename" string no option "checker_after" - "Checherboard representation of the transformed object image and reference image" string no option "checker_before" - "Checherboard representation of the object image and reference image" string no option "after" - "Difference between the reference image and the transformed object" string no option "before" - "Difference between the reference image and the original object image" string no option "matrix" - "Affine matrix (reference to object space) filename " string no section "Interpolator" option "interp" - "Interpolation: 0=NN, 1=Linear, 2=BSpline, 3=BLUT" int no default="1" option "interpOrder" - "Order if BLUT or BSpline (0-5)" int no default="3" option "interpSF" - "Sampling factor if BLUT" int no default="20" section "Transform (Input and Output transformation parameters map the physical space of the fixed or reference image into the physical space of the moving or object image. Positive rotations result in a counter-clockwise rotation for the moving image. Positive translations result in shift along the negative axis for the moving image.)" option "transform" - "Type: 0=Identity, 1=Translation, 2=Rigid, 3=Affine" int no default="2" 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" - "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 "metric" - "Type: 0=Mean-Squares*, 1=Normalized CC*, 2=Histogram CC, 3=Gradient-Difference, 4=Viola-Wells MI, 5=Histogram MI, 6=Mattes' MI*, 7=Normalized MI, 8=CR, 9=SSD for BLUT FFD**" int no default="0" option "samples" - "Specify fraction [0, 1] of samples of the reference image used for the metric (* only). Use high fraction for detailed images (eg. 0.2, 0.5), for smooth images 0.01 might be enough." float no default="1" option "intThreshold" - "Fixed image samples intensity threshold (* only; caution with --normalize)" float no option "subtractMean" - "1: Subtract mean for NCC calculation (narrows optimal)" flag on 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 (affine=true; FFD=false)" flag on section "Preprocessing" option "normalize" - "Normalize images before registration (not necessary for metric 1,2,5,6,8; caution with --intThreshold)" flag off option "blur" - "Blur images before registration, use Gaussian with std dev (none by default) " float no default="0.0" section "Optimizer" option "optimizer" - "0=Simplex, 1=Powell, 2=FRPR, 3=Regular Step GD, 4=VersorRigid3D, 5=Conjugated Gradient, 6=L-BFGS, 7=L-BFGS-B" int no default="0" option "delta" - "0: Initial delta, otherwise automatic" double no option "step" - "1,2,3,4: Initial stepsize (to be multiplied with the gradient)" double no default="2.0" option "relax" - "3,4: Relaxation of the stepsize (multiplied each time the gradient changes sign)" double no default="0.7" option "valueTol" - "0,1,2: Tolerance on the function" double no default="0.01" option "stepTol" - "0,1,3,4: Tolerance on the step size" double no default="0.1" option "gradTol" - "3,4,6,7: Tolerance on the (projected) gradient magnitude (7: 1=low->1e-10=high precision)" double no default="1e-5" option "lineAcc" - "6: Line accuracy (eg: high=0.1, low=0.9)" double no default="0.9" option "convFactor" - "7: Convergence factor: terminate if factor*machine_precision>reduction in cost (1e+12 low, 1e+7 moderate and 1e+1 high precision) " double no default="1e+12" option "maxIt" - "0-7: Maximum number of iterations" int no default="500" option "maxLineIt" - "Maximum number of line iterations" int no default="50" option "maxEval" - "Maximum number of evaluations" int no default="500" option "maxCorr" - "Maximum number of corrections" int no default="5" option "selectBound" - "7: Select the type of bound: 0=none, 1=u, 2=u&l, 3=l" int no default="0" 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 "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" option "dec" - "Decrement factor (:) previous step/tol = new step/tol at next resolution level" float no default="4"