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 symmetry 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 "initial-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: 4095]

       --write-marked <image-path>
            File name for output image with marked symmetry plane.  [Default: NONE]

       --write-aligned <image-path>
            File name for symmetry plane-aligned output image.  [Default: NONE]

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

       --write-subtract <image-path>
            File name for mirror subtraction image.  [Default: NONE]

       --write-mirror <image-path>
            File name for image mirrored w.r.t. symmetry plane.  [Default: NONE]

   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, Daniel B. Russakoff, and Yaroslav Halchenko

LICENSE

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

BUGS

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

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.