Reg aladin

Usage

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Block Matching algorithm for global registration.
Based on Ourselin et al., "Reconstructing a 3D structure from serial histological sections",
Image and Vision Computing, 2001
This code has been written by Marc Modat (m.modat@ucl.ac.uk) and Pankaj Daga,
for any comment, please contact them.
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Usage:	reg_aladin -ref <filename> -flo <filename> [OPTIONS].
	-ref <filename>	Reference image filename (also called Target or Fixed) (mandatory)
	-flo <filename>	Floating image filename (also called Source or moving) (mandatory)

* * OPTIONS * *
	-noSym 			The symmetric version of the algorithm is used by default. Use this flag to disable it.
	-rigOnly		To perform a rigid registration only. (Rigid+affine by default)
	-affDirect		Directly optimize 12 DoF affine. (Default is rigid initially then affine)
	-aff <filename>		Filename which contains the output affine transformation. [outputAffine.txt]
	-inaff <filename>	Filename which contains an input affine transformation. (Affine*Reference=Floating) [none]
	-rmask <filename>	Filename of a mask image in the reference space.
	-fmask <filename>	Filename of a mask image in the floating space. (Only used when symmetric turned on)
	-res <filename>		Filename of the resampled image. [outputResult.nii]
	-maxit <int>		Maximal number of iterations of the trimmed least square approach to perform per level. [5]
	-ln <int>		Number of levels to use to generate the pyramids for the coarse-to-fine approach. [3]
	-lp <int>		Number of levels to use to run the registration once the pyramids have been created. [ln]
	-smooR <float>		Standard deviation in mm (voxel if negative) of the Gaussian kernel used to smooth the Reference image. [0]
	-smooF <float>		Standard deviation in mm (voxel if negative) of the Gaussian kernel used to smooth the Floating image. [0]
	-refLowThr <float>	Lower threshold value applied to the reference image. [0]
	-refUpThr <float>	Upper threshold value applied to the reference image. [0]
	-floLowThr <float>	Lower threshold value applied to the floating image. [0]
	-floUpThr <float>	Upper threshold value applied to the floating image. [0]
	-nac			Use the nifti header origin to initialise the transformation. (Image centres are used by default)
	-cog			Use the input masks centre of mass to initialise the transformation. (Image centres are used by default)
	-interp			Interpolation order to use internally to warp the floating image.
	-iso			Make floating and reference images isotropic if required.
	-pv <int>		Percentage of blocks to use in the optimisation scheme. [50]
	-pi <int>		Percentage of blocks to consider as inlier in the optimisation scheme. [50]
	-speeeeed		Go faster
	-omp <int>		Number of thread to use with OpenMP. [8]
	-voff			Turns verbose off [on]

	--version		Print current source code git hash key and exit
				(3d24c3580a0cd227f30540578b3f84eca9d01e4a)
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