mcaffine - Multi-channel affine registration
mcaffine [options] refChannel0 [refChannel1 ...] -- fltChannel0
[fltChannel1 ...]
Multi-channel affine image registration using histogram-based or
covariance-based joint entropy measures
- --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.
- --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).
- --out-archive
<string>, -o <string>
- Output archive path. [Default: NONE]
- --initial-xform
<string>
- Optional path of a file with the initial transformation. [Default:
NONE]
- --downsample-from
<integer>, -d <integer>
- Initial downsampling factor [1]. [Default: 1]
- --downsample-to
<integer>, -D <integer>
- Final downsampling factor [1]. Factor 0 is full resolution with smoothing
turned off [Default: 1]
- --smooth
<float>
- Sigma of Gaussian smoothing kernel in multiples of template image pixel
size [default: off] ) [Default: 0]
- --downsample-average
<boolean>
- Downsample using sliding-window averaging [default: off] ) [Default:
0]
- --dofs
<integer>[,<integer>,...]
- Set sequence of numbers of DOFs for optimization schedule [can be
repeated]. Supported values are: 0, 3, 6, 7, 9, 12.
- --nmi
- Use normalized mutual information metric [default] [This is the
default]
- --mi
- Use standard mutual information metric
- --histograms,
-H
- Use multi-dimensional histograms to compute entropies [default] [This
is the default]
- --covariance,
-C
- Use covariance matrix determinants to compute entropies
- --cubic,
-c
- Use cubic interpolation [default: linear]
- --initial-step-size
<double>
- Initial optimizer step size in pixels. [Default: 1]
- --final-step-size
<double>
- Initial optimizer step size in pixels. [Default: 0.125]
- --delta-f-threshold
<double>
- Optional threshold to terminate optimization (level) if relative change of
target function drops below this value. [Default: 0]
- --crop-reference-from-index
<string>
- Crop reference image from index x,y,z. [Default: NONE]
- --crop-reference-to-index
<string>
- Crop reference image to index x,y,z. [Default: NONE]
Torsten Rohlfing, with contributions from Michael P. Hasak, Greg
Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko
http://www.fsf.org/licensing/licenses/gpl.html
Report bugs at http://nitrc.org/projects/cmtk/
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.