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transformix(1) [debian man page]

TRANSFORMIX(1)							   User Commands						    TRANSFORMIX(1)

transformix - apply geometric transform to an image SYNOPSIS
transformix mandatory-args [optional-args] DESCRIPTION
transformix applies a transform on an input image and/or generates a deformation field. The transform is specified in the transform-param- eter file. OPTIONS
Call transformix from the command line with mandatory arguments: -out output directory -tp transform-parameter file, only 1 Optional extra commands: -in input image to deform -def file containing input-image points the point are transformed according to the specified transform-parameter file use "-def all" to transform all points from the input-image, which effectively generates a deformation field. -jac use "-jac all" to generate an image with the determinant of the spatial Jacobian -jacmat use "-jacmat all" to generate an image with the spatial Jacobian matrix at each voxel -priority set the process priority to high or belownormal (Windows only) -threads set the maximum number of threads of transformix At least one of the options "-in", "-def", "-jac", or "-jacmat" should be given. The transform-parameter file must contain all the information necessary for transformix to run properly. That includes which transform to use, with which parameters, etc. For a usable transform-parameter file, see the output of elastix. SEE ALSO
elastix(1) Check the website, or mail transformix version: 4.400 December 2010 TRANSFORMIX(1)

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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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