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cmtk-warp(1) [debian man page]

warp(1) 					       The Computational Morphometry Toolkit						   warp(1)

NAME
warp - B-spline nonrigid registration SYNOPSIS
warp ReferenceImage FloatingImage InitialXform DESCRIPTION
This program performs nonrigid image registration using multi-resolution optimization of voxel-based image similarity measures and a multi- resolution B-spline transformation model. 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). Transformation import/export --initial <transformation-path> Initialize transformation from given path [Default: NONE] --write-itk-xform <transformation-path> Output path for final transformation in ITK format [Default: NONE] --write-reformatted <image-path> Write reformatted floating image. [Default: NONE] Transformation parameters --grid-spacing <double>, -g <double> Control point grid spacing [Default: 15] --exact-spacing Use exact control point spacing; do not modify spacing to fit reference image bounding box --refine <integer> Number of refinements (control point grid resolution levels) [Default: 0] --delay-refine Delay control point grid refinement; first switch to next higher image resolution --ignore-edge <integer> Ignore n control point layers along each image face [Default: 0] --restrict <string> Restrict deformation to coordinate dimension(s) [one or more of 'x','y','z'] [Default: NONE] --no-adaptive-fix Disable adaptive fixing of control points; optimize all deformation parameters --adaptive-fix-thresh <float> Threshold factor for entropy criterion to fix local control points [Default: 0.5] --accurate Accurate computation mode: may give slightly better results after substantially longer computation [This is the default] --fast Fast computation mode: may give slightly worse results than accurate mode, but saves substantial CPU time --switch, -S Switch reference and floating image Regularization parameters --jacobian-weight <float> Weight for Jacobian-based local volume preservation constraint [Default: 0] --energy-weight <float> Weight for grid bending energy constraint [Default: 0] --rigidity-weight <float> Weight for local rigidity constraint [Default: 0] --ic-weight <float> Weight for inverse consistency constraint [Default: 0] --relax <float> Weight relaxation factor for alternating under-constrained iterations [Default: -1] --relax-to-unfold Before each resolution level, regularize negative-Jacobian areas of the deformation to unfold them. Optimization parameters --exploration <double>, -e <double> Search space exploration (initial step size) [Default: -1] --accuracy <double>, -a <double> Search accuracy (initial step size) [Default: -1] --stepfactor <double>, -f <double> Factor for search step size reduction. Must be > 0.0 and < 1.0 [default: 0.5] [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] --no-maxnorm Use Euclid norm for gradient normalication in optimization, rather than maximum norm 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 for final registration stage. 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. --force-outside-value <double> Force values outside field of view to this value rather than drop incomplete pixel pairs [Default: disabled] 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] --protocol <string>, -p <string> Optimization protocol output file name [Default: NONE] --time <string>, -t <string> Computation time statistics output file name [Default: NONE] --output-intermediate Write transformation for each level [default: only write final transformation] 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, 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). CMTK 2.2.2 Jul 20 2012 warp(1)

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