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PROGRAM:

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

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