NAME

       WarpImageMultiTransform - part of ANTS registration suite

DESCRIPTION

       Usage:

       WarpImageMultiTransform   ImageDimension  moving_image  output_image   -R  reference_image
       --use-NN   SeriesOfTransformations--(See Below)

              SeriesOfTransformations --- WarpImageMultiTransform can apply,  via  concatenation,
              an    unlimited    number    of    transformations    to   your   data   .    Thus,
              SeriesOfTransformations may be  an Affine transform followed  by  a  warp   another
              affine and then another warp.

       Inverse affine transformations are invoked by calling
              -i MyAffine.txt

       InverseWarps are invoked by passing the InverseWarp.nii.gz
              filename (see below for a note about this).

              Example  1:  Mapping  a  warped  image  into the reference_image domain by applying
              abcdWarp.nii.gz and then abcdAffine.txt

       WarpImageMultiTransform 3 moving_image  output_image  -R  reference_image  abcdWarp.nii.gz
       abcdAffine.txt

              Example  2: To map the fixed/reference_image warped into the moving_image domain by
              applying the inversion of abcdAffine.txt and then abcdInverseWarp.nii.gz .

       WarpImageMultiTransform 3 reference_image output_image -R moving_image -i   abcdAffine.txt
       abcdInverseWarp.nii.gz

              Note  that the inverse maps (Ex. 2) are passed to this program in the reverse order
              of the forward maps (Ex. 1).

              This makes sense, geometrically ... see ANTS.pdf for visualization of this syntax.

              Compulsory arguments:

              ImageDimension: 2 or 3 (for 2 or 3 Dimensional registration)

              moving_image: the image to apply the transformation to

              output_image: the resulting image

              Optional arguments:

       -R: reference_image space that you wish to warp INTO.

       --tightest-bounding-box:  Computes  the  tightest  bounding  box  using  all  the   affine
              transformations. It will be overrided by -R reference_image if given.

       --reslice-by-header:  equivalient  to  -i  -mh, or -fh -i -mh if used together with -R. It
              uses the orientation matrix and origin encoded in the image file header.

              It can be used together with -R. This is typically not used together with any other
              transforms.

       --use-NN: Use Nearest Neighbor Interpolation.

       --use-BSpline: Use 3rd order B-Spline Interpolation.

       --use-ML  sigma:  Use  anti-aliasing  interpolation  for multi-label images, with Gaussian
              smoothing with standard deviation sigma.

              Sigma can be specified in physical or voxel units, as in Convert3D.  It  can  be  a
              scalar or a vector.

       Examples:
              --use-ML 0.4mm    -use-ML 0.8x0.8x0.8vox

       -i: will use the inversion of the following affine transform.

              Other  Example  Usages:  Reslice  the  image: WarpImageMultiTransform 3 Imov.nii.gz
              Iout.nii.gz --tightest-bounding-box --reslice-by-header  Reslice  the  image  to  a
              reference  image:  WarpImageMultiTransform 3 Imov.nii.gz Iout.nii.gz -R Iref.nii.gz
              --tightest-bounding-box --reslice-by-header

              Important Notes: Prefixname "abcd" without any  extension  will  use  ".nii.gz"  by
              default The abcdWarp and abcdInverseWarp do not exist. They are formed on the basis
              of abcd(Inverse)Warp.nii.gz when calling WarpImageMultiTransform, yet you  have  to
              use them as if they exist.