.TH xform2dfield "1" "Jan 25 2019" "CMTK 3.3.1p1" "The Computational Morphometry Toolkit"
.SH NAME
xform2dfield \- Transformation to Deformation Field
.SH SYNOPSIS
\fBxform2dfield\fR OutputPath ReferenceImage XformList 
.SH DESCRIPTION
Convert parametric rigid or nonrigid transformation to deformation field, sampled at pixel locations of a given reference image
.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\-\-mask\fR, \fB\-m\fR
Use reference image pixels as a binary mask.
.TP 5
\fB\-\-target-image-fsl\fR \fI<string>\fR
Path to optional target image to be used in FSL. This is the image that the transformation (and thus the created deformation field) maps to. When creating a deformation field to be used with FSL's "applywarp" tool, is may be necessary to determine whether the x coordinate of the resulting deformation vectors has to be flipped.
.B [Default: disabled]
.TP 5
\fB\-\-inversion-tolerance-factor\fR \fI<double>\fR
Factor for numerical tolerance of B-spline inversion [multiples of minimum grid pixel size; default=0.1]
.B [Default: 0.1]
.TP 5
\fB\-\-downsample\fR \fI<string>\fR
Downsample grid by factors 'x,y,z' or by single factor 'xyz'
.B [Default: NONE]
.TP 5
\fB\-\-output-absolute\fR
Make output deformation field with absolute target location vectors, rather than relative offset vectors.
.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.