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

   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 <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).

   Input Options
       --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'

   Reconstruction Grid
       --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]

   Initial Volume Injection Parameters
       --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]

   Volume Reconstruction Options
       --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 [This is the default]

            --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]

   Optimization Parameters
       --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.

   Regularization Parameters
       --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

   Output Options
       --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

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.