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groupwise_warp - Nonrigid population registration

groupwise_warp(1) The Computational Morphometry Toolkit groupwise_warp(1)

NAME

groupwise_warp - Nonrigid population registration

SYNOPSIS

groupwise_warp [options] affineGroupRegistration

DESCRIPTION

This tool nonrigidly 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>
Override template image with given file. [Default: NONE]
--template-with-data <string>, -T <string>
Use user-supplied template images's pixel data in registration [Default: disabled]

Multuresolution Parameters

--downsample-from <integer>, -d <integer>
Initial downsampling factor [4]. [Default: 4]
--downsample-to <integer>, -D <integer>
Final downsampling factor [1]. [Default: 1]
--sampling-density <float>, -s <float>
Probabilistic sampling density [default: off]. [Default: -1]

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 ]
--no-output-average
Do not write average image.
--average-cubic
Use cubic interpolation for average image (default: linear)

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>
Set number of histogram bins for entropy evaluation. [Default: disabled]
--crop-histograms
Crop image histograms to make better use of histogram bins.
--match-histograms
Match all image histograms to template data (or first image, if no template image is given)
--repeat-match-histograms
Frequetly repeat histogram-based intensity matching to account for changing volume proportions.
--smooth-pixels <double>
Sigma of Gaussian smoothing kernel in multiples of template image pixel size [Default: disabled]
--smooth-cps <double>
Sigma of Gaussian smoothing kernel in multiples of control point delta [Default: disabled]

Transformation Parameters

--grid-spacing <double>
Control point grid spacing. [Default: 40]
--grid-spacing-fit
Use grid spacing that fits volume FOV
--refine-grid <integer>, -r <integer>
Number of times to refine transformation grid [default: 0]. [Default: 0]

Transformation Constraint Options

--zero-sum, -z
Enforce zero-sum computation.
--zero-sum-no-affine
Enforce zero-sum computation EXCLUDING affine components.
--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]
--jacobian-weight <float>, -J <float>
Weight for Jacobian volume preservation constraint [default: off] [Default: 0]
--bending-energy-weight <float>, -E <float>
Weight for grid bending energy regularization constraint [default: off] [Default: 0]

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]
--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]
--partial-gradient-thresh <float>, -p <float>
Threshold factor for partial gradient zeroing [<0 turn off] [Default: 0]
--activate-uninformative
Activate potentially uninformative control points
--disable-cp-mask <string>
Path to mask image (matching template grid) defining areas in which control points should be disabled. This guarantees that mask foreground areas remain undeformed. [Default: NONE]
--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.
Sep 11 2017 CMTK 3.3.1