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WarpImageMultiTransform
Langue: en
Version: June 2010 (ubuntu - 24/10/10)
Section: 1 (Commandes utilisateur)
Sommaire
NAME
WarpImageMultiTransform - part of ANTS registration suiteDESCRIPTION
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.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre