Man page - cmtk-volume_reconstruction(1)

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Manual

volume_reconstruction

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
Global Toolkit Options (these are shared by all CMTK tools)
Input Options
Reconstruction Grid
Initial Volume Injection Parameters
Volume Reconstruction Options
Optimization Parameters
Regularization Parameters
Output Options
AUTHORS
LICENSE
BUGS
ACKNOWLEDGMENTS

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.