antsApplyTransforms - part of ANTS registration suite
- antsApplyTransforms
- antsApplyTransforms, applied to an input image, transforms it according to
a reference image and a transform (or a set of transforms).
-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
0/1/2/3/4/5
- scalar/vector/tensor/time-series/multichannel/five-dimensional
- Option specifying the input image type of scalar (default), vector,
tensor, time series, or multi-channel. A time series image is a scalar
image defined by an additional dimension for the time component whereas a
multi-channel image is a vector image with only spatial dimensions.
Five-dimensionalimages are e.g., AFNI stats image. <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.
- -u, --output-data-type
char
- uchar short int float double default
- Output image data type. This is a direct typecast; output values are not
rescaled. Default is to use the internal data type (float or double).
uchar is unsigned char; others are signed. WARNING: Outputs will be
incorrect (overflowed/reinterpreted) if values exceed the range allowed by
your choice. Note that some pixel types are not supported by some image
formats. e.g. int is not supported by jpg.
- -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