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