cmtk-groupwise_affine - Online in the Cloud

PROGRAM:

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

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