DESCRIPTION
COMMAND:
- ANTS
OPTIONS:
- -x, --mask-image maskFileName
- this mask -- defined in the 'fixed' image space defines the region of interest over which the registration is computed ==> above 0.1 means inside mask ==> continuous values in range [0.1,1.0] effect optimization like a probability. ==> values > 1 are treated as = 1.0
- -m, --image-metric
- The metric weights are relative to the weights on the N other metrics passed to ANTS --- N is unlimited. So, the weight, w_i on the i^{th} metric will be w_i=w_i/ ( sum_i w_i ).Intensity-Based Metrics:
- CC/cross-correlation/CrossCorrelation[fixedImage,movingImage,weight,radius/OrForMI-#histogramBins] MI/mutual-information/MutualInformation[fixedImage,movingImage,weight,radius/OrForMI-#histogramBins] SMI/spatial-mutual-information/SpatialMutualInformation[fixedImage,movingImage,weight,radius/OrForMI-#histogramBins] PR/probabilistic/Probabilistic[fixedImage,movingImage,weight,radius/OrForMI-#histogramBins] SSD
--- standard intensity difference.[fixedImage,movingImage,weight,radius/OrForMI-#histogramBins]
- MSQ/mean-squares/MeanSquares
-- demons-like, radius > 0 uses moving image gradient in metric
- deriv.[fixedImage,movingImage,weight,radius/OrForMI-#histogramBins]
- Point-Set-Based Metrics:
- PSE/point-set-expectation/PointSetExpectation[fixedImage,movingImage,fixedPoints,movingPoints,weight,pointSetPercentage,pointSetSigma,boundaryPointsOnly,kNeighborhood,
PartialMatchingIterations=100000]
- the partial matching option assumes the
- complete labeling is in the first set of label parameters ... more iterations leads to more symmetry in the matching - 0 iterations means full asymmetry
- [fixedImage,movingImage,fixedPoints,movingPoints,weight,pointSetPercentage,pointSetSigma,boundaryPointsOnly,kNeighborhood,alpha,meshResolution,splineOrder,numberOfLevels,useAnisotropicCovariances]
- -o, --output-naming
- The name for the output - a prefix or a name+type : e.g. -o OUT or -o OUT.nii or -o OUT.mha
- --R
- TODO/FIXME: the --R sets an ROI option -- it passes a vector of parameters that sets the center and bounding box
- of the region of interest for a sub-field
- registration. e.g. in 3D the option setting
- -r 10x12x15x50x50x25
- sets up a
- bounding box of size 50,50,25 with origin at 10,12,15 in voxel (should this be physical?) coordinates. <VALUES>: 0
- -i, --number-of-iterations
- number of iterations per level -- a 'vector' e.g. : 100x100x20 <VALUES>: 10x10x5
- --Restrict-Deformation
- restrict the gradient that drives the deformation by scalar factors along specified dimensions -- a TReal 'vector' of length ImageDimension to multiply against the similarity metric's gradient values --- e.g. in 3D : 0.1x1x0 --- will set the z gradient to zero and scale the x gradient by 0.1 and y by 1 (no change). Thus, you get a 2.5-Dimensional registration as there is still 3D continuity in the mapping. <VALUES>: 1x1
- -v, --verbose
- verbose output
- --use-all-metrics-for-convergence
- enable to use weighted sum of all metric terms for convergence computation. By default, only the first metric is used <VALUES>: 0
- -h
- Print the help menu (short version). <VALUES>: 0
- --help
- Print the help menu. <VALUES>: 1, 0
- -t, --transformation-model
Choose one of the following TRANSFORMATIONS:
- Diff = diffeomorphic Elast =
- Elastic
- Exp = exponential diff
- Greedy Exp = greedy exponential diff, like
- diffeomorphic demons. same parameters.
- SyN -- symmetric normalization
- DeltaTime is the integration time-discretization step - sub-voxel - n-time steps currently fixed at 2 <VALUES>: SyN[0.5]
- -r, --regularization
- REGULARIZATION[gradient-field-sigma,def-field-sigma,truncation].