warp: Voxel-based affine image registration.

(see also affine registration tool)
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Syntax:
	warp [options] floating.study reference.study
or
	warp [options] input.list

where [options] is one or more from:

Flags:
 --copyright
	Print copyright message.
 --copyright-vtk
	CopyrightVTK

	-v, --verbose
		Output diagnostic information (default)
	-q, --quiet
		Suppress all diagnostic output
	-S, --switch
		Exchange floating and reference image.

	--exchange
		Force exchange of floating and reference image.

Input and output control:
	-o <dir>, --outlist <dir>
		Output studylist containing registration.
	--output-intermediate
		Output intermediate studylists by level (level-##.list).
	--initial <dir>
		Read initial transformation from studylist in <dir>.
	-t <file>, --time <file>
		Time output file (default: none.)
	-p <file>, --protocol <file>
		Protocol output file (default: none)

Registration control:
	-s <realval>, --sampling <realval>
		Maximum (finest) resampled resolution in mm (default: 1.0)
	-c <realval>, --coarsest <realval>
		Minimum (coarsest) image resolution in mm (default: none)
	--use-original-data
		Do final registration using original image data
	--omit-original-data
		Do final registration using data at resolution given with
		-s or --sampling
	-a <realval>, --accuracy <realval>
		Minimum registration stepsize in mm (default: 0.1)
	-e <realval>, --exploration <realval>
		Initial stepsize (exploration) in mm (default: 4.0)
	-f <realval>, --stepfactor <realval>
		Factor between two successive step sizes (default: 0.5)
		Value must be between 0 and 1.
	-m <n>, --metric <n>
		Metric: 0 = normalized mutual information (default),
		        1 = mutual information,
		        2 = correlation ratio (experimental).
		        3 = masked NMI (experimental).
		        4 = mean squared difference.

		        5 = normalized cross correlation.

	--jacobian-weight <realval>
		Relative weight of Jacobian constraint (default: 0).
	--rigidity-weight <realval>
		Relative weight of rigidity constraint (default: 0).
	--rigidity-weight-map <filename>
		Pixelwise map of weights of rigidity constraint (multiplied by --rigidity-weight value) (default: 0).
	--energy-weight <realval>
		Relative weight of smoothness constraint (default: 0).
	--landmark-weight <realval>
		Relative weight of landmark error from (default: 0).
	--ic-weight <realval>
		Absolute weight of inverse consistency weight (default: 0).

Optimization. One or none of the following:
	-l, --linesearch
		Linesearch optimizer (default).

	-b, --bestneighbour
		Best neighbour search
	--adaptive-fix / --no-adaptive-fix
		Adaptive control point pixing
	--adaptive-fix-thresh factor
		Set control point fixing threshold factor [0.5]
	--powell
		Powell-optimization (experimental)
	--maxnorm
		Use maximum norm for updates (default: on)
	--no-maxnorm
		Use Euclid norm for updates (default: off)
	--adaptive-fix
		Fix control points adaptively.
	--no-adaptive-fix
		Do not fix control points adaptively.
	--ignore-edge <int>
		Fix <int> outer layers of the control point grid.

Deformation grid control:
	--spline
		B-spline deformation (default)
	--linear
		Locally linear deformation
	-g <realval>, --grid-spacing <realval>
		Initial resolution of warp grip.
	--refine <n>
		Refine control point grid n times.
	--delay <n>
		Only refine grid after running current level with old grid.
	--fast
		Fast but (potentially) inaccurate computation.
	--accurate
		Slow but (potentially) more accurate computation.
	--no-delay-refine
		Refine grid immediately when movin to next image resolution.
	--ignore-edge <intval>
		Fix positions of given number of outer control point planes
		(default = 0)

Image data control:
	--sobel0, --sobel1
		Apply 3-D Sobel edge operator to reference (floating).
	--hist-eq0, --hist-eq1
		Apply histogram euqalization to reference (floating).
	--pad0 <realval>, --pad1 <realval>
		<realval> is padding value; voxels are ignored.
	--prune-histogram0 <int>, --prune-histogram1 <int>
		<int> is number of histogram bins for which to prune intensity range.
	--class0 [grey|label|binary], --class1 [grey|label|binary]
		Set class of image data for reference (floating) image.

Specialties:
	--threads <intval>|auto
		Run <intval> threads in parallel on multi-processor machines.
		If 'auto' is given as the number of threads the program will
		determine the number of available CPUs installed and will use
		that number as the (maximum) number of threads.
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