permuteflipimageorientationaxes(1) [debian man page]
PERMUTEFLIPIMAGEORIENTATIONAXES(1) User Commands PERMUTEFLIPIMAGEORIENTATIONAXES(1)NAME
PermuteFlipImageOrientationAxes - part of ANTS registration suite
DESCRIPTION
Usage: ./PermuteFlipImageOrientationAxes ImageDimension inputImageFile outputImageFile xperm yperm {zperm} xflip yflip {zflip} {Fli-
pAboutOrigin}
for 3D:
./PermuteFlipImageOrientationAxes 3 in.nii out.nii 2 0 1 1 1 1
would map z=>x, x=>y, y=>z and flip each for 2D: ./PermuteFlipImageOrientationAxes 2 in.nii out.nii 1 0 1 0 would map x=>y,
y=>x and flip x
0 1 2 for permute factors gives no axis permutation 1 2 0 maps y to x, z to y and x to z the flip values are boolean - 0 1 0 would
flip the y-axis only
The FlipAboutOrigin boolean lets you flip about the coordinate set in the origin
PermuteFlipImageOrientationAxes 1.9 May 2012 PERMUTEFLIPIMAGEORIENTATIONAXES(1)
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WARPTENSORIMAGEMULTITRANSFORM(1) User Commands WARPTENSORIMAGEMULTITRANSFORM(1)NAME
WarpTensorImageMultiTransform - part of ANTS registration suite
DESCRIPTION
WarpImageMultiTransform ImageDimension moving_image output_image [-R reference_image | --tightest-bounding-box] (--reslice-by-header)
[--use-NN (use Nearest Neighbor Interpolator)][--ANTS-prefix prefix-name | --ANTS-prefix-invert prefix-name] {[deformation_field | [-i]
affine_transform_txt | --Id | [-i] --moving-image-header / -mh | [-i] --reference-image-header / -rh]} Example: Reslice the image: WarpIm-
ageMultiTransform 3 Imov.nii Iout.nii --tightest-bounding-box --reslice-by-header Reslice the image to a reference image: WarpImageMulti-
Transform 3 Imov.nii Iout.nii -R Iref.nii --tightest-bounding-box --reslice-by-header Note: -i will use the inversion of the following
affine transform. --tightest-bounding-box will be overrided by -R reference_image if given. It computes the tightest bounding box using
all the affine transformations. --Id uses the identity transform. --moving-image-header or -mh in short will use the orientation header
of the moving image file. This is typically not used with --reslice-by-header.--reference-image-header or -rh in short will use the ori-
entation header of the fixed image file. This is typically not used with --reslice-by-header.--reslice-by-header 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. --reslice-by-header is equvalient to -i -mh, or -fh -i -mh if used together with -R.
For ANTS users: To use with the deformation field and the affine transform files generated from ANTS: --ANTS-prefix prefix-name --ANTS-pre-
fix-invert prefix-name Example: 3 moving_image output_image -R reference_image --ANTS-prefix abcd.nii.gz Applies abcdWarpxvec.nii.gz/abcd-
Warpyvec.nii.gz/abcdWarpzvec.nii.gz and then abcdAffine.txt. Use this with ANTS to get the moving_image warped into the reference_image
domain. 3 reference_image output_image -R moving_image --ANTS-prefix-invert abcd.nii.gz --ANTS-invert Applies the inversion of
abcdAffine.txt and then abcdInverseWarpxvec.nii.gz/abcdInverseWarpyvec.nii.gz/abcdInverseWarpzvec.nii.gz. Use this with ANTS to get the
reference_image warped into the moving_image domain. Note: prefix name "abcd" without any extension will use ".nii.gz" by default
WarpTensorImageMultiTransform 1.9 May 2012 WARPTENSORIMAGEMULTITRANSFORM(1)
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