--- name: "cmtk-groupwise_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-groupwise_warp" --- # cmtk-groupwise\_warp(1) Nonrigid population registration ## NAME groupwise\_warp - Nonrigid population registration ## SYNOPSIS groupwise\_warp \[options\] affineGroupRegistration ## DESCRIPTION This tool nonrigidly registers a population of input images simultaneously, without a template, using either the 'congealing' algorithm or a groupwise similarity measure based on a continuous approximation of mutual information ('RMI'). ## 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. - **--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). ### Registration Metric Options - **--rmi** Use the RMI (a.k.a. regional mutual information) metric to drive the registration). - **--congeal** Use the congealing algorithm using pixelwise stack entropies to drive the registration. **\[This is the default\]** ### Template Image Options - **--template** *\*, **-t** *\* Override template image with given file. **\[Default: NONE\]** - **--template-with-data** *\*, **-T** *\* Use user-supplied template images's pixel data in registration **\[Default: disabled\]** ### Multuresolution Parameters - **--downsample-from** *\*, **-d** *\* Initial downsampling factor \[4\]. **\[Default: 4\]** - **--downsample-to** *\*, **-D** *\* Final downsampling factor \[1\]. **\[Default: 1\]** - **--sampling-density** *\*, **-s** *\* Probabilistic sampling density \[default: off\]. **\[Default: -1\]** ### Output Options - **--output-root** *\*, **-O** *\* Root directory for all output files. **\[Default: NONE\]** - **--output** *\*, **-o** *\* Output filename for groupwise registration archive. **\[Default: groupwise.xforms \]** - **--output-average** *\* Output filename for registered average image. **\[Default: average.nii \]** - **--no-output-average** Do not write average image. - **--average-cubic** Use cubic interpolation for average image (default: linear) ### Image Options and Operations - **--force-background** *\*, **-B** *\* Force background pixels (outside FOV) to given (bin) value. **\[Default: disabled\]** - **--histogram-bins** *\*, **-H** *\* Set number of histogram bins for entropy evaluation. **\[Default: disabled\]** - **--crop-histograms** Crop image histograms to make better use of histogram bins. - **--match-histograms** Match all image histograms to template data (or first image, if no template image is given) - **--repeat-match-histograms** Frequetly repeat histogram-based intensity matching to account for changing volume proportions. - **--smooth-pixels** *\* Sigma of Gaussian smoothing kernel in multiples of template image pixel size **\[Default: disabled\]** - **--smooth-cps** *\* Sigma of Gaussian smoothing kernel in multiples of control point delta **\[Default: disabled\]** ### Transformation Parameters - **--grid-spacing** *\* Control point grid spacing. **\[Default: 40\]** - **--grid-spacing-fit** Use grid spacing that fits volume FOV - **--refine-grid** *\*, **-r** *\* Number of times to refine transformation grid \[default: 0\]. **\[Default: 0\]** ### Transformation Constraint Options - **--zero-sum**, **-z** Enforce zero-sum computation. - **--zero-sum-no-affine** Enforce zero-sum computation EXCLUDING affine components. - **--normal-group-first-n** *\*, **-N** *\* First N images are from the normal group and should be registered unbiased. **\[Default: 0\]** - **--zero-sum-first-n** *\*, **-Z** *\* Enforce zero-sum computation for first N images. **\[Default: disabled\]** - **--jacobian-weight** *\*, **-J** *\* Weight for Jacobian volume preservation constraint \[default: off\] **\[Default: 0\]** - **--bending-energy-weight** *\*, **-E** *\* Weight for grid bending energy regularization constraint \[default: off\] **\[Default: 0\]** ### Optimization Parameters - **--exploration** *\*, **-e** *\* Exploration of optimization in pixels **\[Default: 0.25\]** - **--accuracy** *\*, **-a** *\* Accuracy of optimization in pixels **\[Default: 0.01\]** - **--step-factor** *\*, **-S** *\* Step factor for successive optimization passes **\[Default: 0.5\]** - **--delta-f-threshold** *\* Optional threshold to terminate optimization (level) if relative change of target function drops below this value. **\[Default: 0\]** - **--partial-gradient-thresh** *\*, **-p** *\* Threshold factor for partial gradient zeroing \[\<0 turn off\] **\[Default: 0\]** - **--activate-uninformative** Activate potentially uninformative control points - **--disable-cp-mask** *\* Path to mask image (matching template grid) defining areas in which control points should be disabled. This guarantees that mask foreground areas remain undeformed. **\[Default: NONE\]** - **--disable-optimization** Disable optimization and output initial configuration. ## 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.