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
              abcdWarpxvec.nii.gz/abcdWarpyvec.nii.gz/abcdWarpzvec.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
              abcdInverseWarpxvec.nii.gz/abcdInverseWarpyvec.nii.gz/abcdInverseWarpzvec.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.

       -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)Warpxvec/yvec/zvec.nii.gz  when calling ./WarpImageMultiTransform,
              yet you have to use them as if they exist.