Provided by: cmtk_3.3.1p2+dfsg-2build1_amd64

**NAME**

volume_reconstruction - Volume reconstruction

**SYNOPSIS**

volume_reconstruction [options] refImage xform0 inImage0 [xform1 inImage1 ...]

**DESCRIPTION**

Iterative volume reconstruction from co-registered images using inverse interpolation or joint deblurring

**OPTIONS**

GlobalToolkitOptions(thesearesharedbyallCMTKtools)--helpWrite list of basic command line options to standard output.--help-allWrite complete list of basic and advanced command line options to standard output.--wikiWrite list of command line options to standard output in MediaWiki markup.--manWrite man page source in 'nroff' markup to standard output.--versionWrite toolkit version to standard output.--echoWrite the current command line to standard output.--verbose-level<integer>Set verbosity level.--verbose,-vIncrement verbosity level by 1 (deprecated; supported for backward compatibility).--threads<integer>Set maximum number of parallel threads (for POSIX threads and OpenMP).InputOptions--exclude-first-image,-xExclude first image from reconstruction as a separate registration target image)--crop<string>Crop reference to pixel region x0,y0,z1:x1,y1,z1--pass-weight<string>,-W<string>Set contribution weight for a pass in the form 'pass:weight'ReconstructionGrid--recon-grid<string>Define reconstruction grid as Nx,Ny,Nz:dX,dY,dZ[:Ox,Oy,Oz] (dims:pixel:offset)--recon-grid-path<string>,-R<string>Give path to grid that defines reconstructed image grid [including offset][Default:NONE]InitialVolumeInjectionParameters--isotropic-injectionUse isotropic volume injection [otherwise: scaled with pass image pixel size per dimension]--injection-kernel-sigma<double>,-S<double>Standard deviation of Gaussian kernel for volume injection in multiples of pixel size in each direction.[Default:1]--injection-kernel-radius<double>,-r<double>Truncation radius factor of injection kernel. The kernel is truncated at sigma*radius, where sigma is the kernel standard deviation.[Default:2]VolumeReconstructionOptions--inverse-interpolation-kernelKernel for the inverse interpolation reconstruction Supported values: "cubic", "linear", "hamming-sinc", "cosine-sinc", where the default is "cubic", or use one of the following:--cubic,-CTricubic interpolation[Thisisthedefault]--linear,-LTrilinear interpolation (faster but less accurate)--hamming-sinc,-HHamming-windowed sinc interpolation--cosine-sinc,-OCosine-windowed sinc interpolation (most accurate but slowest)--deblurringKernel shape to approximate the point spread function for joint deblurring reconstruction (selecting one of these disables inverse interpolation reconstruction) Supported values: "box", "gaussian", or use one of the following:--boxBox-shaped kernel--gaussianGaussian kernel--psf<string>Explicitly set point spread function size as x,y,z. Use with 'deblurring' kernel reconstrunction.--psf-scale<double>Scale point spread function size by this value. Use with 'deblurring' kernel reconstrunction.[Default:1]OptimizationParameters--num-iterations<integer>,-n<integer>Maximum number of inverse interpolation iterations[Default:20]--fourth-order-error,-fUse fourth-order (rather than second-order) error for optimization.RegularizationParameters--l-norm-weight<double>Set constraint weight for Tikhonov-type L-Norm regularization (0 disables constraint)[Default:0]--no-truncation,-TTurn off non-linear regional intensity truncationOutputOptions--output<string>,-o<string>Output path for final reconstructed image[Default:reconstructed.nii]--write-injected-image<string>Write initial volume-injected image to this path[Default:NONE]--write-lowest-max-error-image<string>Optional path to write reconstructed image with lowest MAXIMUM error.[Default:NONE]--write-images-as-float,-FWrite output images as floating point

**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.