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


       volume_reconstruction - Volume reconstruction


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


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


   Global Toolkit Options (these are shared by all CMTK tools)
            Write list of basic command line options to standard output.

            Write complete list of basic and advanced command line options to standard output.

            Write list of command line options to standard output in MediaWiki markup.

            Write man page source in 'nroff' markup to standard output.

            Write toolkit version to standard output.

            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:

   Initial Volume Injection Parameters
            Use  isotropic  volume  injection  [otherwise:  scaled with pass image pixel size per

       --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
            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)

            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-shaped kernel

                 Gaussian kernel

       --psf <string>
            Explicitly set point spread function size as  x,y,z.  Use  with  'deblurring'  kernel

       --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:

       --write-images-as-float, -F
            Write output images as floating point


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



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       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.