.TH mk_phantom_3d "1" "Jan 25 2019" "CMTK 3.3.1p1" "The Computational Morphometry Toolkit"
.SH NAME
mk_phantom_3d \- Generate phantom image
.SH SYNOPSIS
mk_phantom_3d [options] command0 [command1 ...]
	 sphere x,y,z radius value
	 box x0,y0,z0 x1,y1,z1 value

.SH DESCRIPTION
Generate 3D digital phantom images using a selection of drawing commands
.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 Main Options
.TP 5
\fB\-\-dims\fR \fI<string>\fR, \fB\-D\fR \fI<string>\fR
Set dimensions in voxels
.TP 5
\fB\-\-voxel\fR \fI<string>\fR, \fB\-V\fR \fI<string>\fR
Set voxel size in [mm]
.TP 5
\fB\-\-coordinates\fR
Coordinate specification mode.
Supported values: "indexed", "absolute", "relative", where the default is "indexed", or use one of the following:
.RS 5
.TP 5
\fB\-\-indexed\fR
Use grid indexes to specify coordinates. For each dimension, the valid value range is [0,Dims-1].
\fB[This is the default]\fR
.TP 5
\fB\-\-absolute\fR
Use absolute volume coordinates. For each dimension, the valid range is [0,FOV].
.TP 5
\fB\-\-relative\fR
Use relative volume coordinates. For each dimension, the valid range is [0,1].
.RE
.TP 5
\fB\-\-char\fR, \fB\-c\fR
8 bits, signed
.TP 5
\fB\-\-byte\fR, \fB\-b\fR
8 bits, unsigned
.TP 5
\fB\-\-short\fR, \fB\-s\fR
16 bits, signed
.TP 5
\fB\-\-ushort\fR, \fB\-u\fR
16 bits, unsigned
\fB[This is the default]\fR
.TP 5
\fB\-\-int\fR, \fB\-i\fR
32 bits signed
.TP 5
\fB\-\-float\fR, \fB\-f\fR
32 bits floating point
.TP 5
\fB\-\-double\fR, \fB\-d\fR
64 bits floating point

.TP 5
\fB\-\-bg\fR \fI<double>\fR, \fB\-B\fR \fI<double>\fR
Set the image background value (use to initialize newly created image).
.B [Default: 0]
.TP 5
\fB\-\-import\fR \fI<string>\fR, \fB\-I\fR \fI<string>\fR
Import image
.B [Default: NONE]
.TP 5
\fB\-\-import-grid\fR \fI<string>\fR
Import image grid only, ignore data
.B [Default: disabled]
.TP 5
\fB\-\-outfile\fR \fI<string>\fR, \fB\-o\fR \fI<string>\fR
File name for output image
.B [Default: "phantom.nii"]
.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.