.TH volume_reconstruction "1" "Jan 25 2019" "CMTK 3.3.1p1" "The Computational Morphometry Toolkit"
.SH NAME
volume_reconstruction \- Volume reconstruction
.SH SYNOPSIS
volume_reconstruction [options] refImage xform0 inImage0 [xform1 inImage1 ...]
.SH DESCRIPTION
Iterative volume reconstruction from co-registered images using inverse interpolation or joint deblurring
.SH OPTIONS
.SS Global Toolkit Options (these are shared by all CMTK tools)
.TP 5
\fB\-\-help\fR
Write list of basic command line options to standard output.
.TP 5
\fB\-\-help-all\fR
Write complete list of basic and advanced command line options to standard output.
.TP 5
\fB\-\-wiki\fR
Write list of command line options to standard output in MediaWiki markup.
.TP 5
\fB\-\-man\fR
Write man page source in 'nroff' markup to standard output.
.TP 5
\fB\-\-version\fR
Write toolkit version to standard output.
.TP 5
\fB\-\-echo\fR
Write the current command line to standard output.
.TP 5
\fB\-\-verbose-level\fR \fI<integer>\fR
Set verbosity level.
.TP 5
\fB\-\-verbose\fR, \fB\-v\fR
Increment verbosity level by 1 (deprecated; supported for backward compatibility).
.TP 5
\fB\-\-threads\fR \fI<integer>\fR
Set maximum number of parallel threads (for POSIX threads and OpenMP).
.SS Input Options
.TP 5
\fB\-\-exclude-first-image\fR, \fB\-x\fR
Exclude first image from reconstruction as a separate registration target image)
.TP 5
\fB\-\-crop\fR \fI<string>\fR
Crop reference to pixel region x0,y0,z1:x1,y1,z1
.TP 5
\fB\-\-pass-weight\fR \fI<string>\fR, \fB\-W\fR \fI<string>\fR
Set contribution weight for a pass in the form 'pass:weight'
.SS Reconstruction Grid
.TP 5
\fB\-\-recon-grid\fR \fI<string>\fR
Define reconstruction grid as Nx,Ny,Nz:dX,dY,dZ[:Ox,Oy,Oz] (dims:pixel:offset)
.TP 5
\fB\-\-recon-grid-path\fR \fI<string>\fR, \fB\-R\fR \fI<string>\fR
Give path to grid that defines reconstructed image grid [including offset]
.B [Default: NONE]
.SS Initial Volume Injection Parameters
.TP 5
\fB\-\-isotropic-injection\fR
Use isotropic volume injection [otherwise: scaled with pass image pixel size per dimension]
.TP 5
\fB\-\-injection-kernel-sigma\fR \fI<double>\fR, \fB\-S\fR \fI<double>\fR
Standard deviation of Gaussian kernel for volume injection in multiples of pixel size in each direction.
.B [Default: 1]
.TP 5
\fB\-\-injection-kernel-radius\fR \fI<double>\fR, \fB\-r\fR \fI<double>\fR
Truncation radius factor of injection kernel. The kernel is truncated at sigma*radius, where sigma is the kernel standard deviation.
.B [Default: 2]
.SS Volume Reconstruction Options
.TP 5
\fB\-\-inverse-interpolation-kernel\fR
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:
.RS 5
.TP 5
\fB\-\-cubic\fR, \fB\-C\fR
Tricubic interpolation
\fB[This is the default]\fR
.TP 5
\fB\-\-linear\fR, \fB\-L\fR
Trilinear interpolation (faster but less accurate)
.TP 5
\fB\-\-hamming-sinc\fR, \fB\-H\fR
Hamming-windowed sinc interpolation
.TP 5
\fB\-\-cosine-sinc\fR, \fB\-O\fR
Cosine-windowed sinc interpolation (most accurate but slowest)
.RE
.TP 5
\fB\-\-deblurring\fR
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:
.RS 5
.TP 5
\fB\-\-box\fR
Box-shaped kernel
.TP 5
\fB\-\-gaussian\fR
Gaussian kernel
.RE
.TP 5
\fB\-\-psf\fR \fI<string>\fR
Explicitly set point spread function size as x,y,z. Use with 'deblurring' kernel reconstrunction.
.TP 5
\fB\-\-psf-scale\fR \fI<double>\fR
Scale point spread function size by this value. Use with 'deblurring' kernel reconstrunction.
.B [Default: 1]
.SS Optimization Parameters
.TP 5
\fB\-\-num-iterations\fR \fI<integer>\fR, \fB\-n\fR \fI<integer>\fR
Maximum number of inverse interpolation iterations
.B [Default: 20]
.TP 5
\fB\-\-fourth-order-error\fR, \fB\-f\fR
Use fourth-order (rather than second-order) error for optimization.
.SS Regularization Parameters
.TP 5
\fB\-\-l-norm-weight\fR \fI<double>\fR
Set constraint weight for Tikhonov-type L-Norm regularization (0 disables constraint)
.B [Default: 0]
.TP 5
\fB\-\-no-truncation\fR, \fB\-T\fR
Turn off non-linear regional intensity truncation
.SS Output Options
.TP 5
\fB\-\-output\fR \fI<string>\fR, \fB\-o\fR \fI<string>\fR
Output path for final reconstructed image
.B [Default: "reconstructed.nii"]
.TP 5
\fB\-\-write-injected-image\fR \fI<string>\fR
Write initial volume-injected image to this path
.B [Default: NONE]
.TP 5
\fB\-\-write-lowest-max-error-image\fR \fI<string>\fR
Optional path to write reconstructed image with lowest MAXIMUM error.
.B [Default: NONE]
.TP 5
\fB\-\-write-images-as-float\fR, \fB\-F\fR
Write output images as floating point
.SH AUTHORS
Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko
.SH LICENSE
http://www.fsf.org/licensing/licenses/gpl.html
.SH BUGS
Report bugs at http://nitrc.org/projects/cmtk/
.SH 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.