plucky (1) antsApplyTransforms.1.gz

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