Provided by: cmtk_3.3.1p1+dfsg-2build1_amd64 
NAME
registration - Rigid and affine registration
SYNOPSIS
registration ReferenceImage FloatingImage
DESCRIPTION
This program performs rigid and affine image registration using multi-resolution optimization of voxel-
based image similarity measures.
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.
--xml
Write command line syntax specification in XML markup (for Slicer integration).
--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).
Automation Options
--auto-multi-levels <integer>
Automatic optimization and resolution parameter generation for <n> levels [Default: 0]
Optimization settings
--exploration <double>, -e <double>
Exploration [initial optimizer step size] [Default: 8]
--accuracy <double>, -a <double>
Accuracy [final optimizer step size] [Default: 0.1]
--stepfactor <double>, -f <double>
Factor for search step size reduction. Must be > 0.0 and < 1.0 [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]
Image resolution parameters
--sampling <double>, -s <double>
Image sampling (finest resampled image resolution) [Default: 1]
--coarsest <double>
Upper limit for image sampling in multiresolution hierarchy [Default: -1]
--omit-original-data
Do not use original data in full resolution, omit final stage in multiresolution hierarchy, thus
reducing computation time.
Transformation parameters
--dofs <integer>[,<integer>,...]
Add number of degrees of freedom [can be repeated]
--dofs-final <integer>[,<integer>,...]
Add number of degrees of freedom for final level only [can be repeated]
--no-switch, -n
Do not auto-switch reference and floating image for improved computational performance
--initxlate, -i
Initialized transformation by translating floating image FOV center onto reference image FOV center
--initial <transformation-path>
Initialize transformation from given path [Default: NONE]
--initial-is-inverse
Invert initial transformation before initializing registration
Image data
--registration-metric
Registration metric for motion estimation by image-to-image registration. Supported values: "nmi",
"mi", "cr", "msd", "ncc", where the default is "nmi", or use one of the following:
--nmi
Normalized Mutual Information metric [This is the default]
--mi Standard Mutual Information metric
--cr Correlation Ratio metric
--msd
Mean Squared Difference metric
--ncc
Normalized Cross Correlation metric
--match-histograms
Match floating image histogram to reference image histogram.
Reference Image Preprocessing
--class-ref <string>
Data class: grey (default) or label [Default: NONE]
--pad-ref <double>
Padding value [Default: disabled]
--thresh-min-ref <double>
Minimum value truncation threshold [Default: disabled]
--thresh-max-ref <double>
Maximum value truncation threshold [Default: disabled]
--prune-histogram-ref <integer>
Number of bins for histogram-based pruning [Default: disabled]
--histogram-equalization-ref
Apply histogram equalization
--sobel-filter-ref
Apply Sobel edge detection filter
--crop-index-ref <string>
Cropping region in pixel index coordinates [parsed as %d,%d,%d,%d,%d,%d for i0,j0,k0,i1,j1,k1]
[Default: NONE]
--crop-world-ref <string>
Cropping region in world coordinates [parsed as %f,%f,%f,%f,%f,%f for x0,y0,z0,x1,y1,z1] [Default:
NONE]
Floating Image Preprocessing
--class-flt <string>
Data class: grey (default) or label [Default: NONE]
--pad-flt <double>
Padding value [Default: disabled]
--thresh-min-flt <double>
Minimum value truncation threshold [Default: disabled]
--thresh-max-flt <double>
Maximum value truncation threshold [Default: disabled]
--prune-histogram-flt <integer>
Number of bins for histogram-based pruning [Default: disabled]
--histogram-equalization-flt
Apply histogram equalization
--sobel-filter-flt
Apply Sobel edge detection filter
--crop-index-flt <string>
Cropping region in pixel index coordinates [parsed as %d,%d,%d,%d,%d,%d for i0,j0,k0,i1,j1,k1]
[Default: NONE]
--crop-world-flt <string>
Cropping region in world coordinates [parsed as %f,%f,%f,%f,%f,%f for x0,y0,z0,x1,y1,z1] [Default:
NONE]
Output parameters
--outlist <string>, -o <string>
Output path for final transformation [Default: NONE]
--out-matrix <string>
Output path for final transformation in matrix format [Default: NONE]
--out-parameters <string>
Output path for final transformation in plain parameter list format [Default: NONE]
--protocol <string>, -p <string>
Optimization protocol output file name [Default: NONE]
--time <string>, -t <string>
Computation time statistics output file name [Default: NONE]
Import Results into Slicer
--out-itk <transformation-path>
Output path for final transformation in ITK format [Default: NONE]
--write-reformatted <image-path>
Write reformatted floating image. [Default: NONE]
Image/Transformation Database
--db <string>
Path to image/transformation database that should be updated with the new registration and/or
reformatted image. [Default: NONE]
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.