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PROGRAM:

NAME


mcaffine - Multi-channel affine registration

SYNOPSIS


mcaffine [options] refChannel0 [refChannel1 ...] -- fltChannel0 [fltChannel1 ...]

DESCRIPTION


Multi-channel affine image registration using histogram-based or covariance-based joint
entropy measures

OPTIONS


Global Toolkit Options (these are shared by all CMTK tools)
--help
Write list of basic command line options to standard output.

--help-all
Write complete list of basic and advanced command line options to standard output.

--wiki
Write list of command line options to standard output in MediaWiki markup.

--man
Write man page source in 'nroff' markup to standard output.

--version
Write toolkit version to standard output.

--echo
Write the current command line to standard output.

--verbose-level <integer>
Set verbosity level.

--verbose, -v
Increment verbosity level by 1 (deprecated; supported for backward compatibility).

--threads <integer>
Set maximum number of parallel threads (for POSIX threads and OpenMP).

Main Options
--out-archive <string>, -o <string>
Output archive path. [Default: NONE]

--initial-xform <string>
Optional path of a file with the initial transformation. [Default: NONE]

--downsample-from <integer>, -d <integer>
Initial downsampling factor [1]. [Default: 1]

--downsample-to <integer>, -D <integer>
Final downsampling factor [1]. Factor 0 is full resolution with smoothing turned off
[Default: 1]

--smooth <float>
Sigma of Gaussian smoothing kernel in multiples of template image pixel size
[default: off] ) [Default: 0]

--downsample-average <boolean>
Downsample using sliding-window averaging [default: off] ) [Default: 0]

--dofs <integer>[,<integer>,...]
Set sequence of numbers of DOFs for optimization schedule [can be repeated].
Supported values are: 0, 3, 6, 7, 9, 12.

--nmi
Use normalized mutual information metric [default] [This is the default]

--mi Use standard mutual information metric

--histograms, -H
Use multi-dimensional histograms to compute entropies [default] [This is the default]

--covariance, -C
Use covariance matrix determinants to compute entropies

--cubic, -c
Use cubic interpolation [default: linear]

--initial-step-size <double>
Initial optimizer step size in pixels. [Default: 1]

--final-step-size <double>
Initial optimizer step size in pixels. [Default: 0.125]

--delta-f-threshold <double>
Optional threshold to terminate optimization (level) if relative change of target
function drops below this value. [Default: 0]

--crop-reference-from-index <string>
Crop reference image from index x,y,z. [Default: NONE]

--crop-reference-to-index <string>
Crop reference image to index x,y,z. [Default: NONE]

AUTHORS


Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R.
Maurer, Daniel B. Russakoff, and Yaroslav Halchenko

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