NAME

       antsApplyTransforms - part of ANTS registration suite

DESCRIPTION

   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

              Sets  the  dimensionality of transforms and scalar inputs.dimensional image. This will be the same
              dimension as used in antsRegistration. This does not change for multi-valued inputs,  use  the  -e
              option for time series and other multi-component images.

       -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

       --time-index <timeIndex>

              Time index to extract from time series input (-e 3). This selects a single slice from time  series
              input without reading the entire dataset into memory.

       -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

antsApplyTransforms 2.5.4+dfsg                    February 2025                           ANTSAPPLYTRANSFORMS(1)