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

              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