DESCRIPTIONCompute 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.
Global Toolkit Options (these are shared by all CMTK tools)
- Write list of basic command line options to standard output.
- Write complete list of basic and advanced command line options to standard output.
- Write list of command line options to standard output in MediaWiki markup.
- Write man page source in 'nroff' markup to standard output.
- Write command line syntax specification in XML markup (for Slicer integration).
- Write toolkit version to standard output.
- 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).
- --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 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:
- Approximately axial symmetry
- Approximately coronal symmetry
- Approximately sagittal symmetry [This is the default]
- Approximately XY plane symmetry
- Approximately XZ plane symmetry
- Approximately YZ plane symmetry [This is the default]
- --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]
- --min-value <float>
- Force minumum data value. [Default: disabled]
- --max-value <float>
- Force maximum data value. [Default: disabled]
Output of Images
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 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]
AUTHORSTorsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko
BUGSReport bugs at http://nitrc.org/projects/cmtk/
ACKNOWLEDGMENTSCMTK 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.