NAME¶
registrationx - Rigid and affine registration
SYNOPSIS¶
registrationx ReferenceImage FloatingImage
DESCRIPTION¶
This program performs rigid and affine image registration using multi-resolution
optimization of voxel-based image similarity measures.
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).
Automation Options¶
- --auto-multi-levels <integer>
- Automatic optimization and resolution parameter generation
for <n> levels [Default: 0]
Optimization settings¶
- --max-stepsize <double>
- Maximum optimizer step size, which determines search space
exploration. [Default: 8]
- --min-stepsize <double>
- Minimum optimizer step size, which determines precision.
[Default: 0.1]
- --stepfactor <double>
- Factor for search step size reduction. Must be > 0.0 and
< 1.0 [Default: 0.5]
- --delta-f-threshold <double>
- Optional threshold to terminate optimization (level) if
relative change of target function drops below this value. [Default:
0]
Image resolution parameters¶
- --sampling <double>, -s
<double>
- Image sampling (finest resampled image resolution)
[Default: 1]
- --coarsest <double>
- Upper limit for image sampling in multiresolution hierarchy
[Default: -1]
- --omit-original-data
- Do not use original data in full resolution, omit final
stage in multiresolution hierarchy, thus reducing computation time.
- --dofs
<integer>[,<integer>,...]
- Add number of degrees of freedom. This can be 3
(translation), 6 (rigid: translation and rotation), 7 (rigid plus global
scale), 9 (rigid plus anisotropic scales), 12 (rigid plus scales plus
shears), or 603 (rigid plus shears, but no scale). This option can be
repeated, in which case DOFs are used for successive optimization runs in
the order that they appear.
- --dofs-final
<integer>[,<integer>,...]
- Add number of degrees of freedom for final level only [can
be repeated]
- --symmetric
- Use symmetric registration functional to simultaneously
estimate forward and inverse transformation. This increases ragistration
time substantially but produces a result that is invariant under exchange
of fixed and moving image. It may also be more robust and/or more accurate
than forward-only registration.
- --restrict-in-plane
- Restrict the affine trasnformation to be in-plane for
planes perpendicular to a given coordinate axis. Supported values:
"xy", "xz", "yz", "none", where
the default is "none", or use one of the following:
- --xy
- Transformation restricted to in-plane for 'xy' plane
(perpendicular to z coordinate axis).
- --xz
- Transformation restricted to in-plane for 'xz' plane
(perpendicular to y coordinate axis).
- --yz
- Transformation restricted to in-plane for 'yz' plane
(perpendicular to x coordinate axis).
- --none
- Full 3D affine transformation is computed. [This is the
default]
- --init
- Select initializer for the affine trasnformation. Supported
values: "none", "fov", "com",
"pax", "physical", where the default is
"fov", or use one of the following:
- --none
- Use input transformation, or identity transformation if
none was provided.
- --fov
- Align centers of field of view (or crop regions) using a
translation. [This is the default]
- --com
- Align centers of mass using a translation.
- --pax
- Align images by rotation using principal axes and
translation using centers of mass.
- --physical
- Align images by rotation using direction vectors stored in
input images and translation using image origins.
- --initial <transformation-path>
- Initialize transformation from given path [Default:
NONE]
- --initial-is-inverse
- Invert initial transformation before initializing
registration
Image data¶
- --registration-metric
- Registration metric for motion estimation by image-to-image
registration. Supported values: "nmi", "mi",
"cr", "rms", "msd", "ncc", where
the default is "nmi", or use one of the following:
- --nmi
- Normalized Mutual Information metric [This is the
default]
- --mi
- Standard Mutual Information metric
- --cr
- Correlation Ratio metric
- --rms
- Root of Mean Squaresa metric (this is the square root of
MSD)
- --msd
- Mean Squared Difference metric
- --ncc
- Normalized Cross Correlation metric
Floating Image Interpolation Options¶
- --interpolation
- Interpolation method for floating image sampling: Supported
values: "nearest-neighbor", "linear",
"cubic", "cosine-sinc", "partial-volume",
"automatic", where the default is "automatic", or use
one of the following:
- --nearest-neighbor
- Nearest neighbor interpolation (for intensity and label
data)
- --linear
- Trilinear interpolation
- --cubic
- Tricubic interpolation
- --cosine-sinc
- Cosine-windowed sinc interpolation (most accurate but
slowest)
- --partial-volume
- Partial volume interpolation (for label data)
- --automatic
- Select interpolation automatically based on data type:
linear for grey-level data, nearest neighbor for label data. [This is
the default]
- --match-histograms
- Match floating image histogram to reference image
histogram.
- --force-outside-value <double>
- Force values outside field of view to this value rather
than drop incomplete pixel pairs [Default: disabled]
Reference Image Preprocessing¶
- --class-ref <string>
- Data class: grey (default) or label [Default:
NONE]
- --pad-ref <double>
- Padding value [Default: disabled]
- --thresh-min-ref <double>
- Minimum value truncation threshold [Default:
disabled]
- --thresh-max-ref <double>
- Maximum value truncation threshold [Default:
disabled]
- --prune-histogram-ref <integer>
- Number of bins for histogram-based pruning [Default:
disabled]
- --histogram-equalization-ref
- Apply histogram equalization
- --median-filter-radius-ref
<integer>
- Apply median filter with given radius [Default:
0]
- --sobel-filter-ref
- Apply Sobel edge detection filter
- --crop-index-ref <string>
- Cropping region in pixel index coordinates [parsed as
%d,%d,%d,%d,%d,%d for i0,j0,k0,i1,j1,k1] [Default: NONE]
- --crop-world-ref <string>
- Cropping region in world coordinates [parsed as
%f,%f,%f,%f,%f,%f for x0,y0,z0,x1,y1,z1] [Default: NONE]
- --crop-thresh-ref <double>
- Automatic cropping based on threshold [Default:
disabled]
Floating Image Preprocessing¶
- --class-flt <string>
- Data class: grey (default) or label [Default:
NONE]
- --pad-flt <double>
- Padding value [Default: disabled]
- --thresh-min-flt <double>
- Minimum value truncation threshold [Default:
disabled]
- --thresh-max-flt <double>
- Maximum value truncation threshold [Default:
disabled]
- --prune-histogram-flt <integer>
- Number of bins for histogram-based pruning [Default:
disabled]
- --histogram-equalization-flt
- Apply histogram equalization
- --median-filter-radius-flt
<integer>
- Apply median filter with given radius [Default:
0]
- --sobel-filter-flt
- Apply Sobel edge detection filter
- --crop-index-flt <string>
- Cropping region in pixel index coordinates [parsed as
%d,%d,%d,%d,%d,%d for i0,j0,k0,i1,j1,k1] [Default: NONE]
- --crop-world-flt <string>
- Cropping region in world coordinates [parsed as
%f,%f,%f,%f,%f,%f for x0,y0,z0,x1,y1,z1] [Default: NONE]
- --crop-thresh-flt <double>
- Automatic cropping based on threshold [Default:
disabled]
Output parameters¶
- --output <string>, -o
<string>
- Output path for final transformation [Default:
NONE]
- --write-matrix <string>
- Output path for final transformation in matrix format
[Default: NONE]
- --write-parameters <string>
- Output path for final transformation in plain parameter
list format [Default: NONE]
- --write-protocol <string>
- Optimization protocol output file name [Default:
NONE]
- --write-time <string>
- Computation time statistics output file name [Default:
NONE]
Import Results into Slicer¶
- --write-itk <transformation-path>
- Output path for final transformation in ITK format
[Default: NONE]
- --write-reformatted <image-path>
- Write reformatted floating image. [Default:
NONE]
- --db <string>
- Path to image/transformation database that should be
updated with the new registration and/or reformatted image. [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).