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.