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

LICENSE

http://www.fsf.org/licensing/licenses/gpl.html

ACKNOWLEDGMENTS

CMTK is developed with support from the NIAAA under Grant AA021697, National Consortium on Alcohol and Neurodevelopment in Adolescence (N-CANDA): Data Integration Component. From April 2009 through September 2011, CMTK development and maintenance was supported by the NIBIB under Grant EB008381.