.TH unwarp_image_phantom "1" "Jul 20 2012" "CMTK 2.2.2" "The Computational Morphometry Toolkit"
.SH NAME
unwarp_image_phantom \- Unwarp T1-weighted MR image using a phantom description
.SH SYNOPSIS
\fBunwarp_image_phantom\fR InputPhantom InputImage OutputXform 
.SH DESCRIPTION
This tool computes a  B-spline free-form deformation to unwarp an image. The transformation is based on expected and detected landmarks in an image of a structural phantom acquired on the same scanner. Use the 'detect_adni_phantom' tool to detect landmarks of the ADNI Phantom in an image and generate a phantom description file suitable for use with this tool.
.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 Fitting Options
.TP 5
\fB\-\-levels\fR \fI<integer>\fR
Number of levels in the multi-level B-spline approximation procedure.
.B [Default: 1]
.TP 5
\fB\-\-no-fit-affine\fR
Disable fitting of affine transformation to initialize spline. Instead, fit spline directly. This usually gives worse results and is discouraged.
.SS Output Options
.TP 5
\fB\-\-final-cp-spacing\fR \fI<double>\fR
Final control point grid spacing of the output B-spline transformation.
.B [Default: 0]
.TP 5
\fB\-\-final-cp-dims\fR \fI<string>\fR
Final control point grid dimensions (i.e., number of control points) of the output B-spline transformation. To be provided as 'dimX,dimY,dimZ'.
.B [Default: NONE]
.SH AUTHORS
Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, and Daniel B. Russakoff
.SH LICENSE
http://www.fsf.org/licensing/licenses/gpl.html
.SH BUGS
Report bugs at http://nitrc.org/projects/cmtk/
.SH ACKNOWLEDGMENTS
From April 2009 through September 2011, CMTK Development and Maintenance was supported by the National Institute of Biomedical Imaging and Bioengineering under Grant No.R01 EB008381 (PI: Torsten Rohlfing).