.TH registration "1" "Jan 25 2019" "CMTK 3.3.1p1" "The Computational Morphometry Toolkit"
.SH NAME
registration \- Rigid and affine registration
.SH SYNOPSIS
\fBregistration\fR ReferenceImage FloatingImage 
.SH DESCRIPTION
This program performs rigid and affine image registration using multi-resolution optimization of voxel-based image similarity measures.
.SH OPTIONS
.SS Global Toolkit Options (these are shared by all CMTK tools)
.TP 5
\fB\-\-help\fR
Write list of basic command line options to standard output.
.TP 5
\fB\-\-help-all\fR
Write complete list of basic and advanced command line options to standard output.
.TP 5
\fB\-\-wiki\fR
Write list of command line options to standard output in MediaWiki markup.
.TP 5
\fB\-\-man\fR
Write man page source in 'nroff' markup to standard output.
.TP 5
\fB\-\-xml\fR
Write command line syntax specification in XML markup (for Slicer integration).
.TP 5
\fB\-\-version\fR
Write toolkit version to standard output.
.TP 5
\fB\-\-echo\fR
Write the current command line to standard output.
.TP 5
\fB\-\-verbose-level\fR \fI<integer>\fR
Set verbosity level.
.TP 5
\fB\-\-verbose\fR, \fB\-v\fR
Increment verbosity level by 1 (deprecated; supported for backward compatibility).
.TP 5
\fB\-\-threads\fR \fI<integer>\fR
Set maximum number of parallel threads (for POSIX threads and OpenMP).
.SS Automation Options
.TP 5
\fB\-\-auto-multi-levels\fR \fI<integer>\fR
Automatic optimization and resolution parameter generation for <n> levels
.B [Default: 0]
.SS Optimization settings
.TP 5
\fB\-\-exploration\fR \fI<double>\fR, \fB\-e\fR \fI<double>\fR
Exploration [initial optimizer step size]
.B [Default: 8]
.TP 5
\fB\-\-accuracy\fR \fI<double>\fR, \fB\-a\fR \fI<double>\fR
Accuracy [final optimizer step size]
.B [Default: 0.1]
.TP 5
\fB\-\-stepfactor\fR \fI<double>\fR, \fB\-f\fR \fI<double>\fR
Factor for search step size reduction. Must be > 0.0 and < 1.0
.B [Default: 0.5]
.TP 5
\fB\-\-delta-f-threshold\fR \fI<double>\fR
Optional threshold to terminate optimization (level) if relative change of target function drops below this value.
.B [Default: 0]
.SS Image resolution parameters
.TP 5
\fB\-\-sampling\fR \fI<double>\fR, \fB\-s\fR \fI<double>\fR
Image sampling (finest resampled image resolution)
.B [Default: 1]
.TP 5
\fB\-\-coarsest\fR \fI<double>\fR
Upper limit for image sampling in multiresolution hierarchy
.B [Default: -1]
.TP 5
\fB\-\-omit-original-data\fR
Do not use original data in full resolution, omit final stage in multiresolution hierarchy, thus reducing computation time.
.SS Transformation parameters
.TP 5
\fB\-\-dofs\fR \fI<integer>[,<integer>,...]\fR
Add number of degrees of freedom [can be repeated]
.TP 5
\fB\-\-dofs-final\fR \fI<integer>[,<integer>,...]\fR
Add number of degrees of freedom for final level only [can be repeated]
.TP 5
\fB\-\-no-switch\fR, \fB\-n\fR
Do not auto-switch reference and floating image for improved computational performance
.TP 5
\fB\-\-initxlate\fR, \fB\-i\fR
Initialized transformation by translating floating image FOV center onto reference image FOV center
.TP 5
\fB\-\-initial\fR \fI<transformation-path>\fR
Initialize transformation from given path
.B [Default: NONE]
.TP 5
\fB\-\-initial-is-inverse\fR
Invert initial transformation before initializing registration
.SS Image data
.TP 5
\fB\-\-registration-metric\fR
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:
.RS 5
.TP 5
\fB\-\-nmi\fR
Normalized Mutual Information metric
\fB[This is the default]\fR
.TP 5
\fB\-\-mi\fR
Standard Mutual Information metric
.TP 5
\fB\-\-cr\fR
Correlation Ratio metric
.TP 5
\fB\-\-msd\fR
Mean Squared Difference metric
.TP 5
\fB\-\-ncc\fR
Normalized Cross Correlation metric
.RE
.TP 5
\fB\-\-match-histograms\fR
Match floating image histogram to reference image histogram.
.SS Reference Image Preprocessing
.TP 5
\fB\-\-class-ref\fR \fI<string>\fR
Data class: grey (default) or label
.B [Default: NONE]
.TP 5
\fB\-\-pad-ref\fR \fI<double>\fR
Padding value
.B [Default: disabled]
.TP 5
\fB\-\-thresh-min-ref\fR \fI<double>\fR
Minimum value truncation threshold
.B [Default: disabled]
.TP 5
\fB\-\-thresh-max-ref\fR \fI<double>\fR
Maximum value truncation threshold
.B [Default: disabled]
.TP 5
\fB\-\-prune-histogram-ref\fR \fI<integer>\fR
Number of bins for histogram-based pruning
.B [Default: disabled]
.TP 5
\fB\-\-histogram-equalization-ref\fR
Apply histogram equalization
.TP 5
\fB\-\-sobel-filter-ref\fR
Apply Sobel edge detection filter
.TP 5
\fB\-\-crop-index-ref\fR \fI<string>\fR
Cropping region in pixel index coordinates [parsed as %d,%d,%d,%d,%d,%d for i0,j0,k0,i1,j1,k1]
.B [Default: NONE]
.TP 5
\fB\-\-crop-world-ref\fR \fI<string>\fR
Cropping region in world coordinates [parsed as %f,%f,%f,%f,%f,%f for x0,y0,z0,x1,y1,z1]
.B [Default: NONE]
.SS Floating Image Preprocessing
.TP 5
\fB\-\-class-flt\fR \fI<string>\fR
Data class: grey (default) or label
.B [Default: NONE]
.TP 5
\fB\-\-pad-flt\fR \fI<double>\fR
Padding value
.B [Default: disabled]
.TP 5
\fB\-\-thresh-min-flt\fR \fI<double>\fR
Minimum value truncation threshold
.B [Default: disabled]
.TP 5
\fB\-\-thresh-max-flt\fR \fI<double>\fR
Maximum value truncation threshold
.B [Default: disabled]
.TP 5
\fB\-\-prune-histogram-flt\fR \fI<integer>\fR
Number of bins for histogram-based pruning
.B [Default: disabled]
.TP 5
\fB\-\-histogram-equalization-flt\fR
Apply histogram equalization
.TP 5
\fB\-\-sobel-filter-flt\fR
Apply Sobel edge detection filter
.TP 5
\fB\-\-crop-index-flt\fR \fI<string>\fR
Cropping region in pixel index coordinates [parsed as %d,%d,%d,%d,%d,%d for i0,j0,k0,i1,j1,k1]
.B [Default: NONE]
.TP 5
\fB\-\-crop-world-flt\fR \fI<string>\fR
Cropping region in world coordinates [parsed as %f,%f,%f,%f,%f,%f for x0,y0,z0,x1,y1,z1]
.B [Default: NONE]
.SS Output parameters
.TP 5
\fB\-\-outlist\fR \fI<string>\fR, \fB\-o\fR \fI<string>\fR
Output path for final transformation
.B [Default: NONE]
.TP 5
\fB\-\-out-matrix\fR \fI<string>\fR
Output path for final transformation in matrix format
.B [Default: NONE]
.TP 5
\fB\-\-out-parameters\fR \fI<string>\fR
Output path for final transformation in plain parameter list format
.B [Default: NONE]
.TP 5
\fB\-\-protocol\fR \fI<string>\fR, \fB\-p\fR \fI<string>\fR
Optimization protocol output file name
.B [Default: NONE]
.TP 5
\fB\-\-time\fR \fI<string>\fR, \fB\-t\fR \fI<string>\fR
Computation time statistics output file name
.B [Default: NONE]
.SS Import Results into Slicer
.TP 5
\fB\-\-out-itk\fR \fI<transformation-path>\fR
Output path for final transformation in ITK format
.B [Default: NONE]
.TP 5
\fB\-\-write-reformatted\fR \fI<image-path>\fR
Write reformatted floating image.
.B [Default: NONE]
.SS Image/Transformation Database
.TP 5
\fB\-\-db\fR \fI<string>\fR
Path to image/transformation database that should be updated with the new registration and/or reformatted image.
.B [Default: NONE]
.SH AUTHORS
Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko
.SH LICENSE
http://www.fsf.org/licensing/licenses/gpl.html
.SH BUGS
Report bugs at http://nitrc.org/projects/cmtk/
.SH 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.