.TH warp "1" "Jan 25 2019" "CMTK 3.3.1p1" "The Computational Morphometry Toolkit" .SH NAME warp \- B-spline nonrigid registration .SH SYNOPSIS \fBwarp\fR ReferenceImage FloatingImage InitialXform .SH 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. .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\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\fR Set maximum number of parallel threads (for POSIX threads and OpenMP). .SS Transformation import/export .TP 5 \fB\-\-initial\fR \fI\fR Initialize transformation from given path .B [Default: NONE] .TP 5 \fB\-\-write-itk-xform\fR \fI\fR Output path for final transformation in ITK format .B [Default: NONE] .TP 5 \fB\-\-write-reformatted\fR \fI\fR Write reformatted floating image. .B [Default: NONE] .SS Transformation parameters .TP 5 \fB\-\-grid-spacing\fR \fI\fR, \fB\-g\fR \fI\fR Control point grid spacing .B [Default: 15] .TP 5 \fB\-\-exact-spacing\fR Use exact control point spacing; do not modify spacing to fit reference image bounding box .TP 5 \fB\-\-refine\fR \fI\fR Number of refinements (control point grid resolution levels) .B [Default: 0] .TP 5 \fB\-\-delay-refine\fR Delay control point grid refinement; first switch to next higher image resolution .TP 5 \fB\-\-ignore-edge\fR \fI\fR Ignore n control point layers along each image face .B [Default: 0] .TP 5 \fB\-\-restrict\fR \fI\fR Restrict deformation to coordinate dimension(s) [one or more of 'x','y','z'] .B [Default: NONE] .TP 5 \fB\-\-no-adaptive-fix\fR Disable adaptive fixing of control points; optimize all deformation parameters .TP 5 \fB\-\-adaptive-fix-thresh\fR \fI\fR Threshold factor for entropy criterion to fix local control points .B [Default: 0.5] .TP 5 \fB\-\-accurate\fR Accurate computation mode: may give slightly better results after substantially longer computation \fB[This is the default]\fR .TP 5 \fB\-\-fast\fR Fast computation mode: may give slightly worse results than accurate mode, but saves substantial CPU time .TP 5 \fB\-\-switch\fR, \fB\-S\fR Switch reference and floating image .SS Regularization parameters .TP 5 \fB\-\-jacobian-weight\fR \fI\fR Weight for Jacobian-based local volume preservation constraint .B [Default: 0] .TP 5 \fB\-\-energy-weight\fR \fI\fR Weight for grid bending energy constraint .B [Default: 0] .TP 5 \fB\-\-rigidity-weight\fR \fI\fR Weight for local rigidity constraint .B [Default: 0] .TP 5 \fB\-\-ic-weight\fR \fI\fR Weight for inverse consistency constraint .B [Default: 0] .TP 5 \fB\-\-relax\fR \fI\fR Weight relaxation factor for alternating under-constrained iterations .B [Default: -1] .TP 5 \fB\-\-relax-to-unfold\fR Before each resolution level, regularize negative-Jacobian areas of the deformation to unfold them. .SS Optimization parameters .TP 5 \fB\-\-exploration\fR \fI\fR, \fB\-e\fR \fI\fR Search space exploration (initial step size) .B [Default: -1] .TP 5 \fB\-\-accuracy\fR \fI\fR, \fB\-a\fR \fI\fR Search accuracy (initial step size) .B [Default: -1] .TP 5 \fB\-\-stepfactor\fR \fI\fR, \fB\-f\fR \fI\fR Factor for search step size reduction. Must be > 0.0 and < 1.0 [default: 0.5] .B [Default: 0.5] .TP 5 \fB\-\-delta-f-threshold\fR \fI\fR Optional threshold to terminate optimization (level) if relative change of target function drops below this value. .B [Default: 0] .TP 5 \fB\-\-no-maxnorm\fR Use Euclid norm for gradient normalication in optimization, rather than maximum norm .SS Image resolution parameters .TP 5 \fB\-\-sampling\fR \fI\fR, \fB\-s\fR \fI\fR Image sampling (finest resampled image resolution) .B [Default: -1] .TP 5 \fB\-\-coarsest\fR \fI\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 for final registration stage. .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. .TP 5 \fB\-\-force-outside-value\fR \fI\fR Force values outside field of view to this value rather than drop incomplete pixel pairs .B [Default: disabled] .SS Reference Image Preprocessing .TP 5 \fB\-\-class-ref\fR \fI\fR Data class: grey (default) or label .B [Default: NONE] .TP 5 \fB\-\-pad-ref\fR \fI\fR Padding value .B [Default: disabled] .TP 5 \fB\-\-thresh-min-ref\fR \fI\fR Minimum value truncation threshold .B [Default: disabled] .TP 5 \fB\-\-thresh-max-ref\fR \fI\fR Maximum value truncation threshold .B [Default: disabled] .TP 5 \fB\-\-prune-histogram-ref\fR \fI\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\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\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\fR Data class: grey (default) or label .B [Default: NONE] .TP 5 \fB\-\-pad-flt\fR \fI\fR Padding value .B [Default: disabled] .TP 5 \fB\-\-thresh-min-flt\fR \fI\fR Minimum value truncation threshold .B [Default: disabled] .TP 5 \fB\-\-thresh-max-flt\fR \fI\fR Maximum value truncation threshold .B [Default: disabled] .TP 5 \fB\-\-prune-histogram-flt\fR \fI\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\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\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\fR, \fB\-o\fR \fI\fR Output path for final transformation .B [Default: NONE] .TP 5 \fB\-\-protocol\fR \fI\fR, \fB\-p\fR \fI\fR Optimization protocol output file name .B [Default: NONE] .TP 5 \fB\-\-time\fR \fI\fR, \fB\-t\fR \fI\fR Computation time statistics output file name .B [Default: NONE] .TP 5 \fB\-\-output-intermediate\fR Write transformation for each level [default: only write final transformation] .SS Image/Transformation Database .TP 5 \fB\-\-db\fR \fI\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.