SYNOPSIS

xform2scalar InputImage XformList

DESCRIPTION

This tool extracts scalar measures from transformations and deformation fields, sampled at grid locations, and writes the results to an image. Examples of supported scalar measures are: x,y,z component of the transformation, magnitude of the transformation, and Jacobian determinants.

OPTIONS

Global Toolkit Options (these are shared by all CMTK tools)

--help

Write list of basic command line options to standard output.

--help-all

Write complete list of basic and advanced command line options to standard output.

--wiki

Write list of command line options to standard output in MediaWiki markup.

--man

Write man page source in 'nroff' markup to standard output.

--xml

Write command line syntax specification in XML markup (for Slicer integration).

--version

Write toolkit version to standard output.

--echo

Write the current command line to standard output.

--verbose-level <integer>

Set verbosity level.

--verbose, -v

Increment verbosity level by 1 (deprecated; supported for backward compatibility).

--threads <integer>

Set maximum number of parallel threads (for POSIX threads and OpenMP).

Operating Options

--mode

Mode of operation: type of scalar measure to be extracted. Supported values: "x-component", "y-component", "z-component", "magnitude", where the default is "magnitude", or use one of the following:

--x-component

X component of transformation vector.

--y-component

Y component of transformation vector.

--z-component

Z component of transformation vector.

--magnitude

Magnitude of the transformation vector. [This is the default]

--warp-only, -w

Output warp component only (excluding affine).

Output Options

--type

Scalar data type of output image. Supported values: "float", "double", where the default is "double", or use one of the following:

--float

Single-precision float.

--double

Double-precision float. [This is the default]

--output <image-path>, -o <image-path>

Output path for image with extracted scalar data. [Default: NONE]

AUTHORS

Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko

LICENSE

http://www.fsf.org/licensing/licenses/gpl.html

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.