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


volume_reconstruction - Volume reconstruction


volume_reconstruction [options] refImage xform0 inImage0 [xform1 inImage1 ...]


Iterative volume reconstruction from co-registered images using inverse interpolation or joint deblurring


Global Toolkit Options (these are shared by all CMTK tools)

Write list of basic command line options to standard output.
Write complete list of basic and advanced command line options to standard output.
Write list of command line options to standard output in MediaWiki markup.
Write man page source in 'nroff' markup to standard output.
Write toolkit version to standard output.
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

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

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)
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-shaped kernel
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


Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko



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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.
Jan 25 2019 CMTK 3.3.1p1