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¶
- --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.
- --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]
- --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, and Daniel B. Russakoff
LICENSE¶
http://www.fsf.org/licensing/licenses/gpl.html
BUGS¶
Report bugs at
http://nitrc.org/projects/cmtk/
ACKNOWLEDGMENTS¶
From April 2009 through September 2011, CMTK Development and Maintenance was
supported by the National Institute of Biomedical Imaging and Bioengineering
under Grant No.R01 EB008381 (PI: Torsten Rohlfing).