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cmtk-registration - Online in the Cloud

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This is the command cmtk-registration that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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

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