Man page - cmtk-groupwise_affine(1)

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Manual

groupwise_affine

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
Global Toolkit Options (these are shared by all CMTK tools)
Registration Metric Options
Template Image Options
Output Options
Multiresolution Parameters
Image Options and Operations
Transformation Parameters
Transformation Initialization
Optimization Parameters
AUTHORS
LICENSE
BUGS
ACKNOWLEDGMENTS

NAME

groupwise_affine - Affine population registration

SYNOPSIS

groupwise_affine [options] image0 [image1 ...]

DESCRIPTION

This tool registers a population of input images simultaneously, without a template, using either the ’congealing’ algorithm or a groupwise similarity measure based on a continuous approximation of mutual information (’RMI’).

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).

Registration Metric Options

--rmi

Use the RMI (a.k.a. regional mutual information) metric to drive the registration).

--congeal

Use the congealing algorithm using pixelwise stack entropies to drive the registration. [This is the default]

Template Image Options

--template <string> , -t <string>

Input filename for pre-defined template image. [Default: NONE]

--template-with-data <string> , -T <string>

Use user-supplied template images’s pixel data in registration [Default: disabled]

Output Options

--output-root <string> , -O <string>

Root directory for all output files. [Default: NONE]

--output <string> , -o <string>

Output filename for groupwise registration archive. [Default: groupwise.xforms ]

--output-average <string>

Output filename for registered average image. [Default: average.nii ]

--average-linear

Use linear interpolation for average image [This is the default]

--average-cubic

Use cubic interpolation for average image

--no-output-average

Do not write average image.

Multiresolution Parameters

--downsample-from <integer> , -d <integer>

Initial downsampling factor [Default: 4]

--downsample-to <integer> , -D <integer>

Final downsampling factor. [Default: 1]

--sampling-density <float> , -s <float>

Probabilistic sampling density. Legal values between 0 and 1. [Default: disabled]

Image Options and Operations

--force-background <integer> , -B <integer>

Force background pixels (outside FOV) to given (bin) value. [Default: disabled]

--histogram-bins <integer> , -H <integer>

Manually set number of histogram bins for entropy evaluation [Default: disabled]

--crop-histograms

Crop image histograms to make better use of histogram bins.

--smooth <double>

Sigma of Gaussian smoothing kernel in multiples of template image pixel size. [Default: disabled]

--match-histograms

Match all image histograms to template data (or first image, if no template image is given)

--free-and-reread

Free memory allocated for original image whenever these are not needed and re-read image files as needed. This can be useful when running on a machine with limited memory resources.

Transformation Parameters

--dofs <integer>[,<integer>,...]

Add DOFs to list [default: one pass, 6 DOF]

--zero-sum , -z

Enforce zero-sum computation.

--normal-group-first-n <integer> , -N <integer>

First N images are from the normal group and should be registered unbiased. [Default: 0]

--zero-sum-first-n <integer> , -Z <integer>

Enforce zero-sum computation for first N images. [Default: disabled]

Transformation Initialization

--align-bounding-boxes

Initially align centers of bounding boxes of all images by translations [This is the default]

--align-centers-of-mass

Initially align centers of mass by translations

--init-scales

Initialize scale factors using first-order moments

Optimization Parameters

--exploration <double> , -e <double>

Exploration of optimization in pixels [Default: 0.25]

--accuracy <double> , -a <double>

Accuracy of optimization in pixels [Default: 0.01]

--repeat-level <integer> , -r <integer>

Number of repetitions per optimization level [Default: 5]

--step-factor <double> , -S <double>

Step factor for successive optimization passes [Default: 0.5]

--delta-f-threshold <double>

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

--disable-optimization

Disable optimization and output initial configuration.

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

BUGS

Report bugs at http://nitrc.org/projects/cmtk/

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.