trusty (1) WarpImageMultiTransform.1.gz

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.