NAME¶
symplx - Symmetry plane computation
SYNOPSIS¶
symplx 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¶
- --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]
- --fix-offset
- Fix symmetry plane offset. Reduces computation time and forces symmetry
plane to cross center of mass, but may lead to less-than-accurate
result.
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.