antsApplyTransforms

COMMAND:

antsApplyTransforms

antsApplyTransforms, applied to an input image, transforms it according to a reference image and a transform (or a set of transforms).

OPTIONS:

-d, --dimensionality 2/3/4

This option forces the image to be treated as a specified-dimensional image. If not specified, antsWarp tries to infer the dimensionality from the input image.

-e, --input-image-type 0/1/2/3

scalar/vector/tensor/time-series

Option specifying the input image type of scalar (default), vector, tensor, or time series. <VALUES>: 0

-i, --input inputFileName

Currently, the only input objects supported are image objects. However, the current framework allows for warping of other objects such as meshes and point sets.

-r, --reference-image imageFileName

For warping input images, the reference image defines the spacing, origin, size, and direction of the output warped image.

-o, --output warpedOutputFileName

[warpedOutputFileName or compositeDisplacementField,<printOutCompositeWarpFile=0>] Linear[genericAffineTransformFile,<calculateInverse=0>]

One can either output the warped image or, if the boolean is set, one can print out the displacement field based on the composite transform and the reference image. A third option is to compose all affine transforms and (if boolean is set) calculate its inverse which is then written to an ITK file

-n, --interpolation Linear

NearestNeighbor MultiLabel[<sigma=imageSpacing>,<alpha=4.0>] Gaussian[<sigma=imageSpacing>,<alpha=1.0>] BSpline[<order=3>] CosineWindowedSinc WelchWindowedSinc HammingWindowedSinc LanczosWindowedSinc GenericLabel[<interpolator=Linear>]

Several interpolation options are available in ITK. These have all been made available.

-t, --transform transformFileName

[transformFileName,useInverse]

Several transform options are supported including all those defined in the ITK library in addition to a deformation field transform. The ordering of the transformations follows the ordering specified on the command line. An identity transform is pushed onto the transformation stack. Each new transform encountered on the command line is also pushed onto the transformation stack. Then, to warp the input object, each point comprising the input object is warped first according to the last transform pushed onto the stack followed by the second to last transform, etc. until the last transform encountered which is the identity transform. Also, it should be noted that the inverse transform can be accommodated with the usual caveat that such an inverse must be defined by the specified transform class

-f, --default-value value

Default voxel value to be used with input images only. Specifies the voxel value when the input point maps outside the output domain. With tensor input images, specifies the default voxel eigenvalues.

-z, --static-cast-for-R value

forces static cast in ReadTransform (for R)

--float

Use 'float' instead of 'double' for computations. <VALUES>: 0

-v, --verbose (0)/1

Verbose output.

-h

Print the help menu (short version).

--help

Print the help menu. <VALUES>: 1