Output of minctracc -help

Command-specific options:
---Transformation maps one to volume two---
Initial transformation information.
 -no_clobber:        Do not overwrite output file (default).
 -clobber:           Overwrite output file.
 -transformation:    Initial world transformation. (Default = identity).
 -est_center:        use center estimated from Principal axis trans.
 -est_scales:        use scales estimated from Principal axis trans.
 -est_rotations:     use rotations estimated from Principal axis trans.
 -est_translations:  use translations estimated from Principal axis trans.
 -center:            Force center of rotation and scale.
		Default value: 0 0 0
Output transformation type. Default = -procrustes.
 -pat:               principal axis transformation matrix (input matrix ignored).
 -lsq6:              6 parameter transformation (3 translation, 3 rotation, scale=1.0).
 -lsq7:              7 parameter transformation (lsq6 + 1 global scale, same as -procrustes).
 -lsq9:              9 parameter transformation (lsq6 + 3 scales).
 -lsq12:             full 12 parameter transformation (lsq9 + 3 shears).
 -lsq:               full 12 parameter transformation (same as -lsq12).
 -procrustes:        procrustes transformation (3 trans, 3 rots, 1 scale), same as -lsq7.
 -forward:           Recover forward transformation (source -> model, default).
 -invert:            Recover inverted transformation (model -> source).
Options for mask volumes.
 -model_mask:        Specifies a binary mask file for the target.
 -source_mask:       Specifies a binary mask file for the source.
Interpolation options.
 -trilinear:         Do trilinear interpolation
 -tricubic:          Do tricubic interpolation
 -nearest_neighbour: Do nearest neighbour interpolation
Optimization objective functions. (default = -xcorr)
 -xcorr:             Use cross correlation.
 -zscore:            Use normalized difference.
 -ssc:               Use stochastic sign change.
 -vr:                Use variance of ratio vol1/vol2
 -groups:            Number of groups for ratio calculations.
		Default value: 16
 -threshold:         Lower limit for voxel threshold
		Default value: 0 0
 -speckle:           percent speckle noise to add to source
		Default value: 5

Options for optimization.
 -tol:               Stopping criteria tolerance
		Default value: 0.005
 -simplex:           Radius of simplex volume.
		Default value: 20
Options for measurement comparison.
 -matlab:            Output selected objective function value curves.
 -measure:           Output value of each obj. func. for given x-form.
Options for 3D lattice (default = target).
 -step:              Step size along each dimension (X, Y, Z)
		Default value: 4 4 4
 -xstep:             Step size along the column dimension
		Default value: 4
 -ystep:             Step size along the row dimension
		Default value: 4
 -zstep:             Step size along the slice dimension
		Default value: 4
Options for logging progress. Default = -verbose 1.
 -verbose:           Write messages indicating progress
		Default value: 1
 -quiet:             Do not write log messages
 -debug:             Print out debug info.
Generic options for all commands:
 -help:              Print summary of command-line options and abort
Usage: minctracc [<options>] <sourcefile> <targetfile> <output transfile>
       minctracc [-help]