SYNOPSIS
volume_reconstruction [options] refImage xform0 inImage0 [xform1 inImage1 ...]DESCRIPTION
Iterative volume reconstruction from coregistered images using inverse interpolation or joint deblurringOPTIONS
Global Toolkit Options (these are shared by all CMTK tools)
 help
 Write list of basic command line options to standard output.
 helpall
 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.
 verboselevel <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
 excludefirstimage, 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
 passweight <string>, W <string>
 Set contribution weight for a pass in the form 'pass:weight'
Reconstruction Grid
 recongrid <string>
 Define reconstruction grid as Nx,Ny,Nz:dX,dY,dZ[:Ox,Oy,Oz] (dims:pixel:offset)
 recongridpath <string>, R <string>
 Give path to grid that defines reconstructed image grid [including offset] [Default: NONE]
Initial Volume Injection Parameters
 isotropicinjection
 Use isotropic volume injection [otherwise: scaled with pass image pixel size per dimension]
 injectionkernelsigma <double>, S <double>
 Standard deviation of Gaussian kernel for volume injection in multiples of pixel size in each direction. [Default: 1]
 injectionkernelradius <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
 inverseinterpolationkernel

Kernel for the inverse interpolation reconstruction
Supported values: "cubic", "linear", "hammingsinc", "cosinesinc", 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)
 hammingsinc, H
 Hammingwindowed sinc interpolation
 cosinesinc, O
 Cosinewindowed 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
 Boxshaped kernel
 gaussian
 Gaussian kernel

 psf <string>
 Explicitly set point spread function size as x,y,z. Use with 'deblurring' kernel reconstrunction.
 psfscale <double>
 Scale point spread function size by this value. Use with 'deblurring' kernel reconstrunction. [Default: 1]
Optimization Parameters
 numiterations <integer>, n <integer>
 Maximum number of inverse interpolation iterations [Default: 20]
 fourthordererror, f
 Use fourthorder (rather than secondorder) error for optimization.
Regularization Parameters
 lnormweight <double>
 Set constraint weight for Tikhonovtype LNorm regularization (0 disables constraint) [Default: 0]
 notruncation, T
 Turn off nonlinear regional intensity truncation
Output Options
 output <string>, o <string>
 Output path for final reconstructed image [Default: reconstructed.nii]
 writeinjectedimage <string>
 Write initial volumeinjected image to this path [Default: NONE]
 writelowestmaxerrorimage <string>
 Optional path to write reconstructed image with lowest MAXIMUM error. [Default: NONE]
 writeimagesasfloat, 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 HalchenkoBUGS
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 (NCANDA): Data Integration Component. From April 2009 through September 2011, CMTK development and maintenance was supported by the NIBIB under Grant EB008381.