--- name: "cmtk-warp" section: "1" platform: "linux" package: "cmtk" version: "3.3.1p2+dfsg-3" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/cmtk-warp" --- # cmtk-warp(1) B-spline nonrigid registration ## 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** *\* Set verbosity level. - **--verbose**, **-v** Increment verbosity level by 1 (deprecated; supported for backward compatibility). - **--threads** *\* Set maximum number of parallel threads (for POSIX threads and OpenMP). ### Transformation import/export - **--initial** *\* Initialize transformation from given path **\[Default: NONE\]** - **--write-itk-xform** *\* Output path for final transformation in ITK format **\[Default: NONE\]** - **--write-reformatted** *\* Write reformatted floating image. **\[Default: NONE\]** ### Transformation parameters - **--grid-spacing** *\*, **-g** *\* Control point grid spacing **\[Default: 15\]** - **--exact-spacing** Use exact control point spacing; do not modify spacing to fit reference image bounding box - **--refine** *\* 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** *\* Ignore n control point layers along each image face **\[Default: 0\]** - **--restrict** *\* 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** *\* 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** *\* Weight for Jacobian-based local volume preservation constraint **\[Default: 0\]** - **--energy-weight** *\* Weight for grid bending energy constraint **\[Default: 0\]** - **--rigidity-weight** *\* Weight for local rigidity constraint **\[Default: 0\]** - **--ic-weight** *\* Weight for inverse consistency constraint **\[Default: 0\]** - **--relax** *\* 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** *\*, **-e** *\* Search space exploration (initial step size) **\[Default: -1\]** - **--accuracy** *\*, **-a** *\* Search accuracy (initial step size) **\[Default: -1\]** - **--stepfactor** *\*, **-f** *\* Factor for search step size reduction. Must be \> 0.0 and \< 1.0 \[default: 0.5\] **\[Default: 0.5\]** - **--delta-f-threshold** *\* 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** *\*, **-s** *\* Image sampling (finest resampled image resolution) **\[Default: -1\]** - **--coarsest** *\* 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** *\* Force values outside field of view to this value rather than drop incomplete pixel pairs **\[Default: disabled\]** ### Reference Image Preprocessing - **--class-ref** *\* Data class: grey (default) or label **\[Default: NONE\]** - **--pad-ref** *\* Padding value **\[Default: disabled\]** - **--thresh-min-ref** *\* Minimum value truncation threshold **\[Default: disabled\]** - **--thresh-max-ref** *\* Maximum value truncation threshold **\[Default: disabled\]** - **--prune-histogram-ref** *\* 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** *\* 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** *\* 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** *\* Data class: grey (default) or label **\[Default: NONE\]** - **--pad-flt** *\* Padding value **\[Default: disabled\]** - **--thresh-min-flt** *\* Minimum value truncation threshold **\[Default: disabled\]** - **--thresh-max-flt** *\* Maximum value truncation threshold **\[Default: disabled\]** - **--prune-histogram-flt** *\* 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** *\* 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** *\* 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** *\*, **-o** *\* Output path for final transformation **\[Default: NONE\]** - **--protocol** *\*, **-p** *\* Optimization protocol output file name **\[Default: NONE\]** - **--time** *\*, **-t** *\* Computation time statistics output file name **\[Default: NONE\]** - **--output-intermediate** Write transformation for each level \[default: only write final transformation\] ### Image/Transformation Database - **--db** *\* 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.