groupwise_affine(1) 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

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.