volume_reconstruction(1)			       The Computational Morphometry Toolkit				  volume_reconstruction(1)

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, and Daniel B. Russakoff

LICENSE

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

BUGS

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

ACKNOWLEDGMENTS

       From April 2009 through September 2011, CMTK Development and Maintenance was supported by the National Institute of Biomedical Imaging  and
       Bioengineering under Grant No.R01 EB008381 (PI: Torsten Rohlfing).

CMTK 2.2.2							    Jul 20 2012 					  volume_reconstruction(1)