Difference between revisions of "Reg transform"

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Usage:	reg_transform [OPTIONS].
* * OPTIONS * *

	-ref <filename>
		Filename of the reference image
		The Reference image has to be specified when a cubic B-Spline parametrised control point grid is used*.
	-ref2 <filename>
		Filename of the second reference image to be used when dealing with composition

	-def <filename1> <filename2>
		Take a transformation of any recognised type* and compute the corresponding deformation field
		filename1 - Input transformation file name
		filename2 - Output deformation field file name

	-disp <filename1> <filename2>
		Take a transformation of any recognised type* and compute the corresponding displacement field
		filename1 - Input transformation file name
		filename2 - Output displacement field file name

	-flow <filename1> <filename2>
		Take a spline parametrised SVF and compute the corresponding flow field
		filename1 - Input transformation file name
		filename2 - Output flow field file name

	-comp <filename1> <filename2> <filename3>
		Compose two transformations of any recognised type* and returns a deformation field.
		Trans3(x) = Trans2(Trans1(x)).
		filename1 - Input transformation 1 file name (associated with -ref if required)
		filename2 - Input transformation 2 file name (associated with -ref2 if required)
		filename3 - Output deformation field file name

	-updSform <filename1> <filename2> <filename3>
		Update the sform of an image using an affine transformation.
		Filename1 - Image to be updated
		Filename2 - Affine transformation defined as Affine x Reference = Floating
		Filename3 - Updated image.

	-invAff <filename1> <filename2>
		Invert an affine matrix.
		filename1 - Input affine transformation file name
		filename2 - Output inverted affine transformation file name

	-invNrr <filename1> <filename2> <filename3>
		Invert a non-rigid transformation and save the result as a deformation field.
		filename1 - Input transformation file name
		filename2 - Input floating (source) image where the inverted transformation is defined
		filename3 - Output inverted transformation file name
		Note that the cubic b-spline grid parametrisations can not be inverted without approximation,
		as a result, they are converted into deformation fields before inversion.

	-half <filename1> <filename2>
		The input transformation is halfed and stored using the same transformation type.
		filename1 - Input transformation file name
		filename2 - Output transformation file name

	-makeAff <rx> <ry> <rz> <tx> <ty> <tz> <sx> <sy> <sz> <shx> <shy> <shz> <outputFilename>
		Create an affine transformation matrix

	-aff2rig <filename1> <filename2>
		Extract the rigid component from an affine transformation matrix
		filename1 - Input transformation file name
		filename2 - Output transformation file name

	-flirtAff2NR <filename1> <filename2> <filename3> <filename4>
		Convert a flirt (FSL) affine transformation to a NiftyReg affine transformation
		filename1 - Input FLIRT (FSL) affine transformation file name
		filename2 - Image used as a reference (-ref arg in FLIRT)
		filename3 - Image used as a floating (-in arg in FLIRT)
		filename4 - Output affine transformation file name


	--version		Print current source code git hash key and exit
				(3d24c3580a0cd227f30540578b3f84eca9d01e4a)
	* The supported transformation types are:
		- cubic B-Spline parametrised grid (reference image is required)
		- a dense deformation field
		- a dense displacement field
		- a cubic B-Spline parametrised stationary velocity field (reference image is required)
		- a stationary velocity deformation field
		- a stationary velocity displacement field
		- an affine matrix

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