sympl(1)					       The Computational Morphometry Toolkit						  sympl(1)

NAME

       sympl - Symmetry plane computation

SYNOPSIS

       sympl InputImage

DESCRIPTION

       Compute	the  approximate symmetry plane of an image to determine, for example, the mid-sagittal plane in human brain images. Various forms
       of output are supported, e.g., writing the input image with the symmetry plane drawn into it, or the input image realigned along the symme-
       try plane.

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).

   Optimization
       --accuracy <double>, -a <double>
	    Accuracy (final optimization step size in [mm].  [Default: 0.1]

       --sampling <double>, -s <double>
	    Resampled  image resolution. This is the resolution [in mm] of the first (finest) resampled image in the multi-scale pyramid, which is
	    derived directly from the original full-resolution images.	[Default: 1]

       --levels <integer>, -l <integer>
	    Number of resolution levels. The algorithm will create (levels-1) resampled images with increasingly coarse resolution and	use  these
	    in successive order of increasing resolution before using the original images at the final level.  [Default: 4]

   Initial approximate symmetry plane orientation
       --initial-plane
	    Initial  orientation  of symmetry plane. This should be the closest orthogonal plane to the expected actual symmetry plane.  Supported
	    values: "initial-axial", "initial-coronal", "initial-sagittal", "initial-xy", "initial-xz", "initial-yz", where the default  is  "ini-
	    tial-sagittal", or use one of the following:

	    --initial-axial
		 Approximately axial symmetry

	    --initial-coronal
		 Approximately coronal symmetry

	    --initial-sagittal
		 Approximately sagittal symmetry [This is the default]

	    --initial-xy
		 Approximately XY plane symmetry

	    --initial-xz
		 Approximately XZ plane symmetry

	    --initial-yz
		 Approximately YZ plane symmetry [This is the default]

   Pre-computed symmetry
       --output-only <string>
	    Give symmetry parameters [Rho Theta Phi] as option, skip search.  [Default: disabled]

       --output-only-file <string>
	    Read symmetry parameters from file, skip search.  [Default: disabled]

   Data pre-processing
       --min-value <float>
	    Force minumum data value.  [Default: disabled]

       --max-value <float>
	    Force maximum data value.  [Default: disabled]

   Output of Images
       --interpolation
	    Interpolation  method  used for reformatted output data Supported values: "linear", "cubic", "sinc", where the default is "linear", or
	    use one of the following:

	    --linear, -L
		 Use linear image interpolation for output.  [This is the default]

	    --cubic, -C
		 Use cubic image interpolation for output.

	    --sinc, -S
		 Use cosine-windowed sinc image interpolation for output.

       --pad-out <double>, -P <double>
	    Padding value for output images.  [Default: disabled]

       --mark-value <double>
	    Data value to mark (draw) symmetry plane.  [Default: disabled]

       --write-marked <image-path>
	    File name for output image with marked symmetry plane.  [Default: disabled]

       --write-aligned <image-path>
	    File name for symmetry plane-aligned output image.	[Default: disabled]

       --mark-aligned
	    Mark symmetry plane in aligned output image.

       --write-subtract <image-path>
	    File name for mirror subtraction image.  [Default: disabled]

       --write-mirror <image-path>
	    File name for image mirrored w.r.t. symmetry plane.  [Default: disabled]

   Output of Parameters
       --outfile <path>, -o <path>
	    File name for symmetry plane parameter output.  [Default: NONE]

       --write-xform <transformation-path>
	    Write affine alignment transformation to file [Default: NONE]

AUTHORS

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

LICENSE

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

BUGS

       Report bugs at http://nitrc.org/projects/cmtk/

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).

CMTK 2.2.2							    Jul 20 2012 							  sympl(1)