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ANTS(1) - Linux man page online | User commands

Part of ANTS registration suite.

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August 2017
ANTS(1) User Commands ANTS(1)

NAME

ANTS - part of ANTS registration suite

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,movingIm‐ age,weight,radius/OrForMI-#histogramBins] MI/mutual-information/MutualInforma‐ tion[fixedImage,movingImage,weight,radius/OrForMI-#histogramBins] SMI/spa‐ tial-mutual-information/SpatialMutualInformation[fixedImage,movingIm‐ age,weight,radius/OrForMI-#histogramBins] PR/probabilistic/Probabilistic[fixedIm‐ age,movingImage,weight,radius/OrForMI-#histogramBins] SSD --- standard intensity difference.[fixedImage,movingImage,weight,radius/OrForMI-#his‐ togramBins] 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,fixed‐ Points,movingPoints,weight,pointSetPercentage,pointSetSigma,boundary‐ PointsOnly,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,pointSetPercent‐ age,pointSetSigma,boundaryPointsOnly,kNeighborhood,alpha,meshResolution,spline‐ Order,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 TRANSFORMATION[gradient-step-length,number-of-time-steps,DeltaTime,symmetry-type]. 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]. Choose one of the following REGULARIZATIONS: Gauss = gaussian DMFFD = directly manipulated free form deformation <VALUES>: Gauss[3,0.5] -a, --initial-affine use the input file as the initial affine parameter -F, --fixed-image-initial-affine use the input file as the initial affine parameter for the fixed image --fixed-image-initial-affine-ref-image reference space for using the input file as the initial affine parameter for the fixed image -T, --geodesic = 0 / 1 / 2, 0 = not time-dependent, 1 = asymmetric , 2 = symmetric -G, --go-faster true / false -- if true, SyN is faster but loses some accuracy wrt inverse-identity constraint, see Avants MIA 2008. <VALUES>: false --continue-affine true (default) | false, do (not) perform affine given the initial affine parameters <VALUES>: true --number-of-affine-iterations number of iterations per level -- a 'vector' e.g. : 100x100x20 <VALUES>: 10000x10000x10000 --use-NN use nearest neighbor interpolation <VALUES>: 0 --use-Histogram-Matching use histogram matching of moving to fixed image <VALUES>: 0 --affine-metric-type MI: mutual information (default), MSQ: mean square error, SSD, CC: Normalized cor‐ relation, CCH: Histogram-based correlation coefficient (not recommended), GD: gra‐ dient difference (not recommended) <VALUES>: MI --MI-option option of mutual information: MI_bins x MI_samples (default: 32x32000) <VALUES>: 32x5000 --rigid-affine use rigid transformation : true / false(default) <VALUES>: false --do-rigid use rigid transformation : true / false(default) <VALUES>: false --affine-gradient-descent-option option of gradient descent in affine transformation: maximum_step_length x relax‐ ation_factor x minimum_step_length x translation_scales <VALUES>: 0.1x0.5x1.e-4x1.e-4 --use-rotation-header use rotation matrix in image headers: true (default) / false <VALUES>: false --ignore-void-origin ignore the apparently unmatched origins (when use-rotation-header is false and the rotation matrix is identity: true (default) / false <VALUES>: false --gaussian-smoothing-sigmas At each resolution level the image is subsampled and smoothed by Gaussian convolu‐ tion. This option allows the user to override the default smoothing by specifying sigma values (in mm) for smoothing both fixed and moving images for each resolution level. <VALUES>: --subsampling-factors At each resolution level the image is subsampled and smoothed by Gaussian convolu‐ tion. This option allows the user to override the default subsampling by specifying the subsampling factor for both fixed and moving images for each resolution level. <VALUES>:
ANTS 2.2.0 August 2017 ANTS(1)
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