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¶
- --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).
- --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]
- --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]
- --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.