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

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.