Man page - cmtk-volume_reconstruction(1)

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Manual

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, 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.

Feb 26 2025

CMTK 3.3.1p2