volume_reconstruction - Volume reconstruction

       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.

CMTK 3.3.1p2                                       Feb 26 2025                          volume_reconstruction(1)

       Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R.  Maurer,  Daniel  B.
       Russakoff, and Yaroslav Halchenko

       Report bugs at http://nitrc.org/projects/cmtk/

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

http://www.fsf.org/licensing/licenses/gpl.html

       volume_reconstruction - Volume reconstruction

GlobalToolkitOptions(thesearesharedbyallCMTKtools)--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<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).

   InputOptions--exclude-first-image, -x
            Exclude 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-injection
            Use 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-kernel
            Kernel  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, -C
                 Tricubic interpolation [Thisisthedefault]--linear, -L
                 Trilinear interpolation (faster but less accurate)

            --hamming-sinc, -H
                 Hamming-windowed sinc interpolation

            --cosine-sinc, -O
                 Cosine-windowed sinc interpolation (most accurate but slowest)

       --deblurring
            Kernel 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:

            --box
                 Box-shaped kernel

            --gaussian
                 Gaussian 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, -f
            Use 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, -T
            Turn off non-linear regional intensity truncation

   OutputOptions--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, -F
            Write output images as floating point

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