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mcaffine - Multi-channel affine registration


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


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


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

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

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

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

Write toolkit version to standard output.

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.

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]


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

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