SYNOPSIS
warpx ReferenceImage FloatingImage InitialXformDESCRIPTION
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]
- --invert-initial
- Invert given (affine) initial transformation.
- --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>
- Control point grid spacing [Default: 10]
- --grid-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
- --exact-spacing
- Use exact control point spacing; do not modify spacing to fit reference image bounding box
- --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
Regularization parameters
- --jacobian-constraint-weight <float>
- Weight for Jacobian-based local volume preservation constraint [Default: 0]
- --smoothness-constraint-weight <float>
- Weight for smoothness constraint based on second-order grid bending energy. [Default: 0]
- --inverse-consistency-weight <float>
- Weight for inverse consistency constraint [Default: 0]
- --constraint-relaxation-factor <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
- --max-stepsize <double>
- Maximum optimizer step size, which determines search space exploration. [Default: -1]
- --min-stepsize <double>
- Minimum optimizer step size, which determines precision. [Default: -1]
- --stepfactor <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", "rms", "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
- --rms
- Root of Mean Squaresa metric (this is the square root of MSD)
- --msd
- Mean Squared Difference metric
- --ncc
- Normalized Cross Correlation metric
-
Floating Image Interpolation Options
- --interpolation
-
Interpolation method for floating image sampling:
Supported values: "nearest-neighbor", "linear", "cubic", "cosine-sinc", "partial-volume", "automatic", where the default is "automatic", or use one of the following:
-
- --nearest-neighbor
- Nearest neighbor interpolation (for intensity and label data)
- --linear
- Trilinear interpolation
- --cubic
- Tricubic interpolation
- --cosine-sinc
- Cosine-windowed sinc interpolation (most accurate but slowest)
- --partial-volume
- Partial volume interpolation (for label data)
- --automatic
- Select interpolation automatically based on data type: linear for grey-level data, nearest neighbor for label data. [This is the default]
-
- --match-histograms
- Match floating image histogram to reference image histogram.
- --repeat-match-histograms
- Repeat histogram matching after every level of the registration to account for volume changes. When registering masked data, it is advisable to also use the --force-outside-value option to prevent poorly matched histograms.
- --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
- --median-filter-radius-ref <integer>
- Apply median filter with given radius [Default: 0]
- --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]
- --crop-thresh-ref <double>
- Automatic cropping based on threshold [Default: disabled]
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
- --median-filter-radius-flt <integer>
- Apply median filter with given radius [Default: 0]
- --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]
- --crop-thresh-flt <double>
- Automatic cropping based on threshold [Default: disabled]
Output parameters
- --outlist <string>, -o <string>
- Output path for final transformation [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, Daniel B. Russakoff, and Yaroslav HalchenkoBUGS
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.