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)