Provided by: cmtk_3.3.1p2+dfsg-2build1_amd64 
NAME
warpx - B-spline nonrigid registration
SYNOPSIS
warpx 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]
--invert-initial
Invert given (affine) initial transformation. [This is the default]
--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: H$ ]
--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 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.