.TH volume_injection "1" "Nov 13 2020" "CMTK 3.3.1p1" "The Computational Morphometry Toolkit"
.SH NAME
volume_injection \- Volume injection
.SH SYNOPSIS
volume_injection [options] refImage xform0 inImage0 [xform1 inImage1 ...]
.SH DESCRIPTION
Reconstruction a high-resolution volume from multiple co-registered (low-resolution) images using forward volume injection
.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\-\-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 Options
.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]
.TP 5
\fB\-\-crop\fR \fI<string>\fR
Crop reference to pixel region x0,y0,z1:x1,y1,z1
.SS Volume Injection Options
.TP 5
\fB\-\-isotropic-injection\fR
Use isotropic volume injection [default: scaled with pass image pixel size per dimension]
.TP 5
\fB\-\-injection-kernel-sigma\fR \fI<double>\fR, \fB\-S\fR \fI<double>\fR
Gauss contribution
.B [Default: 1]
.TP 5
\fB\-\-injection-kernel-radius\fR \fI<integer>\fR, \fB\-r\fR \fI<integer>\fR
VolumeInjectionRadius of affected pixel
.B [Default: 0]
.SS Output Options
.TP 5
\fB\-\-output\fR \fI<string>\fR, \fB\-o\fR \fI<string>\fR
Output image path
.B [Default: "volume_injection.nii"]
.TP 5
\fB\-\-write-images-as-float\fR, \fB\-F\fR
Write output images as floating point [default: same as input]
.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.