composemultitransform(1) [debian man page]

COMPOSEMULTITRANSFORM(1)					   User Commands					  COMPOSEMULTITRANSFORM(1)

NAME

       ComposeMultiTransform - part of ANTS registration suite

DESCRIPTION

       ComposeMultiTransform ImageDimension output_field [-R reference_image] {[deformation_field | [-i] affine_transform_txt ]}

	      Usage has the same form as WarpImageMultiTransform

	      For Example:

       ./ComposeMultiTransform Dimension  outwarp.nii	-R template.nii   ExistingWarp.nii  ExistingAffine.nii

	      or for an inverse mapping :

       ./ComposeMultiTransform Dimension  outwarp.nii	-R template.nii   -i ExistingAffine.nii ExistingInverseWarp.nii

	      recalling that the -i option takes the inverse of the affine mapping

       Or:  to	compose multiple affine text file into one: ComposeMultiTransform ImageDimension output_affine_txt [-R reference_affine_txt] {[-i]
       affine_transform_txt} This will be evoked if a text file is given as the second parameter. In this case	reference_affine_txt  is  used	to
       define  the  center  of the output affine.  The default reference is the first given affine text file. This ignores all non-txt files among
       the following parameters.

ComposeMultiTransform 1.9					     May 2012						  COMPOSEMULTITRANSFORM(1)

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)