--- /dev/null
+#File clitkBSplineDeformableRegistration.ggo
+#Author: Jef Vandemeulebroucke <jefvdmb@gmail.com>
+#Date : Tue 15 July 2008 16.35
+
+Package "clitk"
+Version "Register 2 images using optimized ITK FFD (high memory requirements) or BLUT FFD. Both implementations are provided, mainly for debugging purposes.."
+
+option "config" - "Config file" string no
+
+
+section "Run Time"
+
+option "verbose" v "Verbose" flag off
+option "threads" - "Number of threads to use for intensive algorithms (default=min(cores,8))" int no
+
+
+section "Input"
+
+option "reference" r "Input reference 3D image (float)" string yes
+option "target" t "Input target 2D image (float)" string yes
+option "mask" m "Mask to placed over the reference image" string no
+
+
+section "Output"
+
+option "vf" - "Result DVF" string yes
+option "coeff" - "Result coefficient images" string no multiple
+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 for BLUT FFD 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 "init" - "Initial coefficient images" string no multiple
+option "rigid" - "Prior rigid transform matrix from reference to target space" 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 "wlut" - "With LUT for BSpline calculation" flag off
+option "samplingFactor" - "LUT sampling factor" int no multiple
+
+
+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 "Metric (optimized, threaded (opt) versions are marked *)"
+
+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="9"
+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)" 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 (rigid=true; FFD=false)" flag off
+
+
+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="7"
+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+1 high precision) " double no default="1e+7"
+option "maxIt" - "0-7: Maximum number of iterations" int no default="500"
+option "maxLineIt" - "1,2: Maximum number of line iterations" int no default="50"
+option "maxEval" - "6,7: Maximum number of evaluations" int no default="500"
+option "maxCorr" - "7: 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 default="0.0"
+option "upperBound" - "7: The upper bound" double no default="0.0"
+
+
+Section "Registration"
+
+option "levels" - "Number of resolution levels" int no default="1"
+
+
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff