EnglishFrenchSpanish

Ad


OnWorks favicon

cmtk-warpx - Online in the Cloud

Run cmtk-warpx in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command cmtk-warpx that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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.

--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 Halchenko

Use cmtk-warpx online using onworks.net services


Free Servers & Workstations

Download Windows & Linux apps

  • 1
    deep-clean
    deep-clean
    A Kotlin script that nukes all build
    caches from Gradle/Android projects.
    Useful when Gradle or the IDE let you
    down. The script has been tested on
    macOS, but ...
    Download deep-clean
  • 2
    Eclipse Checkstyle Plug-in
    Eclipse Checkstyle Plug-in
    The Eclipse Checkstyle plug-in
    integrates the Checkstyle Java code
    auditor into the Eclipse IDE. The
    plug-in provides real-time feedback to
    the user about viol...
    Download Eclipse Checkstyle Plug-in
  • 3
    AstrOrzPlayer
    AstrOrzPlayer
    AstrOrz Player is a free media player
    software, part based on WMP and VLC. The
    player is in a minimalist style, with
    more than ten theme colors, and can also
    b...
    Download AstrOrzPlayer
  • 4
    movistartv
    movistartv
    Kodi Movistar+ TV es un ADDON para XBMC/
    Kodi que permite disponer de un
    decodificador de los servicios IPTV de
    Movistar integrado en uno de los
    mediacenters ma...
    Download movistartv
  • 5
    Code::Blocks
    Code::Blocks
    Code::Blocks is a free, open-source,
    cross-platform C, C++ and Fortran IDE
    built to meet the most demanding needs
    of its users. It is designed to be very
    extens...
    Download Code::Blocks
  • 6
    Amidst
    Amidst
    Amidst or Advanced Minecraft Interface
    and Data/Structure Tracking is a tool to
    display an overview of a Minecraft
    world, without actually creating it. It
    can ...
    Download Amidst
  • More »

Linux commands

Ad