mia-3drigidreg(1) | USER COMMANDS | mia-3drigidreg(1) |
NAME¶
mia-3drigidreg - Linear registration of 3D images.SYNOPSIS¶
mia-3drigidreg -i <in> -r <ref> -o <out> [options]DESCRIPTION¶
mia-3drigidreg This program implements the registration of two gray scale 3D images. The transformation is not penalized, therefore, one should only use translation, rigid, or affine transformations as target and run mia-3dnonrigidreg of nonrigid registration is to be achieved.OPTIONS¶
File I/O¶
- -i --in=(input,required)
- test image For supported file types see PLUGINS:3dimage/io
- -r --ref=(input,required)
- reference image For supported file types see PLUGINS:3dimage/io
- -o --out=(output,required)
- registered output image For supported file types see PLUGINS:3dimage/io
- -t --trans=(output)
- transformation output file name For supported file types see PLUGINS:3dtransform/io
- -c --cost=ssd
- cost function For supported plugins see PLUGINS:3dimage/cost
- -l --levels=3
- multigrid levels
- -O --optimizer=gsl:opt=simplex,step=1.0
- Optimizer used for minimization For supported plugins see PLUGINS:minimizer/singlecost
- -f --transForm=rigid
- transformation type For supported plugins see PLUGINS:3dimage/transform
Help & Info¶
- -V --verbose=warning
- verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:
info ‐ Low level messages
trace ‐ Function call trace
fail ‐ Report test failures
warning ‐ Warnings
error ‐ Report errors
debug ‐ Debug output
message ‐ Normal messages
fatal ‐ Report only fatal errors
- --copyright
- print copyright information
- -h --help
- print this help
- -? --usage
- print a short help
- --version
- print the version number and exit
Processing¶
- --threads=-1
- Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).
PLUGINS: 1d/splinebc¶
- mirror
- Spline interpolation boundary conditions that mirror on the boundary
(no parameters)
- repeat
- Spline interpolation boundary conditions that repeats the value at the boundary
(no parameters)
- zero
- Spline interpolation boundary conditions that assumes zero for values outside
(no parameters)
PLUGINS: 1d/splinekernel¶
- bspline
- B-spline kernel creation , supported parameters are:
d = 3 (int)
Spline degree. in [0, 5]
- omoms
- OMoms-spline kernel creation, supported parameters are:
d = 3 (int)
Spline degree. in [3, 3]
PLUGINS: 3dimage/cost¶
- lncc
- local normalized cross correlation with masking support., supported parameters are:
w = 5 (uint)
half width of the window used for evaluating the
localized cross correlation. in [1, 256]
- mi
- Spline parzen based mutual information., supported parameters are:
cut = 0 (float)
Percentage of pixels to cut at high and low intensities
to remove outliers. in [0, 40]
mbins = 64 (uint)
Number of histogram bins used for the moving image. in
[1, 256]
mkernel = [bspline:d=3] (factory)
Spline kernel for moving image parzen hinstogram. For
supported plug-ins see PLUGINS:1d/splinekernel
rbins = 64 (uint)
Number of histogram bins used for the reference image. in
[1, 256]
rkernel = [bspline:d=0] (factory)
Spline kernel for reference image parzen hinstogram. For
supported plug-ins see PLUGINS:1d/splinekernel
- ncc
- normalized cross correlation.
(no parameters)
- ngf
- This function evaluates the image similarity based on normalized gradient fields. Given normalized gradient fields $ _S$ of the src image and $ _R$ of the ref image various evaluators are implemented., supported parameters are:
eval = ds (dict)
plugin subtype (sq, ds,dot,cross). Supported values are:
ds ‐ square of scaled difference
dot ‐ scalar product kernel
cross ‐ cross product kernel
- ssd
- 3D image cost: sum of squared differences, supported parameters are:
autothresh = 0 (float)
Use automatic masking of the moving image by only takeing
intensity values into accound that are larger than the given threshold. in [0,
1000]
norm = 0 (bool)
Set whether the metric should be normalized by the number
of image pixels.
- ssd-automask
- 3D image cost: sum of squared differences, with automasking based on given thresholds, supported parameters are:
rthresh = 0 (double)
Threshold intensity value for reference image. in
[-1.79769e+308, 1.79769e+308]
sthresh = 0 (double)
Threshold intensity value for source image. in
[-1.79769e+308, 1.79769e+308]
PLUGINS: 3dimage/io¶
- analyze
- Analyze 7.5 image
Recognized file extensions: .HDR, .hdr
Supported element types:
unsigned 8 bit, signed 16 bit, signed 32 bit, floating
point 32 bit, floating point 64 bit
- datapool
- Virtual IO to and from the internal data pool
Recognized file extensions: .@
- dicom
- Dicom image series as 3D
Recognized file extensions: .DCM, .dcm
Supported element types:
signed 16 bit, unsigned 16 bit
- hdf5
- HDF5 3D image IO
Recognized file extensions: .H5, .h5
Supported element types:
binary data, signed 8 bit, unsigned 8 bit, signed 16 bit,
unsigned 16 bit, signed 32 bit, unsigned 32 bit, signed 64 bit, unsigned 64
bit, floating point 32 bit, floating point 64 bit
- inria
- INRIA image
Recognized file extensions: .INR, .inr
Supported element types:
signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16
bit, signed 32 bit, unsigned 32 bit, floating point 32 bit, floating point 64
bit
- mhd
- MetaIO 3D image IO using the VTK implementation (experimental).
Recognized file extensions: .MHA, .MHD, .mha, .mhd
Supported element types:
signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16
bit, signed 32 bit, unsigned 32 bit, floating point 32 bit, floating point 64
bit
- nifti
- NIFTI-1 3D image IO
Recognized file extensions: .NII, .nii
Supported element types:
signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16
bit, signed 32 bit, unsigned 32 bit, signed 64 bit, unsigned 64 bit, floating
point 32 bit, floating point 64 bit
- vff
- VFF Sun raster format
Recognized file extensions: .VFF, .vff
Supported element types:
unsigned 8 bit, signed 16 bit
- vista
- Vista 3D
Recognized file extensions: .V, .VISTA, .v, .vista
Supported element types:
binary data, signed 8 bit, unsigned 8 bit, signed 16 bit,
unsigned 16 bit, signed 32 bit, unsigned 32 bit, floating point 32 bit,
floating point 64 bit
- vti
- 3D image VTK-XML in- and output (experimental).
Recognized file extensions: .VTI, .vti
Supported element types:
signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16
bit, signed 32 bit, unsigned 32 bit, floating point 32 bit, floating point 64
bit
- vtk
- 3D VTK image legacy in- and output (experimental).
Recognized file extensions: .VTK, .VTKIMAGE, .vtk,
.vtkimage
Supported element types:
binary data, signed 8 bit, unsigned 8 bit, signed 16 bit,
unsigned 16 bit, signed 32 bit, unsigned 32 bit, floating point 32 bit,
floating point 64 bit
PLUGINS: 3dimage/transform¶
- affine
- Affine transformation (12 degrees of freedom), supported parameters are:
imgboundary = mirror (factory)
image interpolation boundary conditions. For supported
plug-ins see PLUGINS:1d/splinebc
imgkernel = [bspline:d=3] (factory)
image interpolator kernel. For supported plug-ins see
PLUGINS:1d/splinekernel
- axisrot
- Restricted rotation transformation (1 degrees of freedom). The transformation is restricted to the rotation around the given axis about the given rotation center, supported parameters are:
axis = (required, 3dfvector)
rotation axis.
imgboundary = mirror (factory)
image interpolation boundary conditions. For supported
plug-ins see PLUGINS:1d/splinebc
imgkernel = [bspline:d=3] (factory)
image interpolator kernel. For supported plug-ins see
PLUGINS:1d/splinekernel
origin = (required, 3dfvector)
center of the transformation.
- raffine
- Restricted affine transformation (3 degrees of freedom). The transformation is restricted to the rotation around the given axis and shearing along the two axis perpendicular to the given one, supported parameters are:
axis = (required, 3dfvector)
rotation axis.
imgboundary = mirror (factory)
image interpolation boundary conditions. For supported
plug-ins see PLUGINS:1d/splinebc
imgkernel = [bspline:d=3] (factory)
image interpolator kernel. For supported plug-ins see
PLUGINS:1d/splinekernel
origin = (required, 3dfvector)
center of the transformation.
- rigid
- Rigid transformation, i.e. rotation and translation (six degrees of freedom)., supported parameters are:
imgboundary = mirror (factory)
image interpolation boundary conditions. For supported
plug-ins see PLUGINS:1d/splinebc
imgkernel = [bspline:d=3] (factory)
image interpolator kernel. For supported plug-ins see
PLUGINS:1d/splinekernel
origin = [[0,0,0]] (streamable)
Relative rotation center, i.e. <0.5,0.5,0.5>
corresponds to the center of the volume.
- rotation
- Rotation transformation (three degrees of freedom)., supported parameters are:
imgboundary = mirror (factory)
image interpolation boundary conditions. For supported
plug-ins see PLUGINS:1d/splinebc
imgkernel = [bspline:d=3] (factory)
image interpolator kernel. For supported plug-ins see
PLUGINS:1d/splinekernel
origin = [[0,0,0]] (streamable)
Relative rotation center, i.e. <0.5,0.5,0.5>
corresponds to the center of the volume.
- rotbend
- Restricted transformation (4 degrees of freedom). The transformation is restricted to the rotation around the x and y axis and a bending along the x axis, independedn in each direction, with the bending increasing with the squared distance from the rotation axis., supported parameters are:
imgboundary = mirror (factory)
image interpolation boundary conditions. For supported
plug-ins see PLUGINS:1d/splinebc
imgkernel = [bspline:d=3] (factory)
image interpolator kernel. For supported plug-ins see
PLUGINS:1d/splinekernel
origin = (required, 3dfvector)
center of the transformation.
- spline
- Free-form transformation that can be described by a set of B-spline coefficients and an underlying B-spline kernel., supported parameters are:
anisorate = [[0,0,0]] (3dfvector)
anisotropic coefficient rate in pixels, nonpositive
values will be overwritten by the 'rate' value..
debug = 0 (bool)
enable additional debuging output.
imgboundary = mirror (factory)
image interpolation boundary conditions. For supported
plug-ins see PLUGINS:1d/splinebc
imgkernel = [bspline:d=3] (factory)
image interpolator kernel. For supported plug-ins see
PLUGINS:1d/splinekernel
kernel = [bspline:d=3] (factory)
transformation spline kernel. For supported plug-ins see
PLUGINS:1d/splinekernel
penalty = (factory)
transformation penalty energy term. For supported
plug-ins see PLUGINS:3dtransform/splinepenalty
rate = 10 (float)
isotropic coefficient rate in pixels. in [1, 3.40282e+38]
- translate
- Translation (three degrees of freedom), supported parameters are:
imgboundary = mirror (factory)
image interpolation boundary conditions. For supported
plug-ins see PLUGINS:1d/splinebc
imgkernel = [bspline:d=3] (factory)
image interpolator kernel. For supported plug-ins see
PLUGINS:1d/splinekernel
- vf
- This plug-in implements a transformation that defines a translation for each point of the grid defining the domain of the transformation., supported parameters are:
imgboundary = mirror (factory)
image interpolation boundary conditions. For supported
plug-ins see PLUGINS:1d/splinebc
imgkernel = [bspline:d=3] (factory)
image interpolator kernel. For supported plug-ins see
PLUGINS:1d/splinekernel
PLUGINS: 3dtransform/io¶
- bbs
- Binary (non-portable) serialized IO of 3D transformations
Recognized file extensions: .bbs
- datapool
- Virtual IO to and from the internal data pool
Recognized file extensions: .@
- vista
- Vista storage of 3D transformations
Recognized file extensions: .v, .v3dt
- xml
- XML serialized IO of 3D transformations
Recognized file extensions: .x3dt
PLUGINS: 3dtransform/splinepenalty¶
- divcurl
- divcurl penalty on the transformation, supported parameters are:
curl = 1 (float)
penalty weight on curl. in [0, 3.40282e+38]
div = 1 (float)
penalty weight on divergence. in [0, 3.40282e+38]
norm = 0 (bool)
Set to 1 if the penalty should be normalized with respect
to the image size.
weight = 1 (float)
weight of penalty energy. in [0, 3.40282e+38]
PLUGINS: minimizer/singlecost¶
- gdas
- Gradient descent with automatic step size correction., supported parameters are:
ftolr = 0 (double)
Stop if the relative change of the criterion is below..
in [0, INF]
max-step = 2 (double)
Minimal absolute step size. in [1, INF]
maxiter = 200 (uint)
Stopping criterion: the maximum number of iterations. in
[1, 2147483647]
min-step = 0.1 (double)
Maximal absolute step size. in [1e-10, INF]
xtola = 0.01 (double)
Stop if the inf-norm of the change applied to x is below
this value.. in [0, INF]
- gdsq
- Gradient descent with quadratic step estimation, supported parameters are:
ftolr = 0 (double)
Stop if the relative change of the criterion is below..
in [0, INF]
gtola = 0 (double)
Stop if the inf-norm of the gradient is below this
value.. in [0, INF]
maxiter = 100 (uint)
Stopping criterion: the maximum number of iterations. in
[1, 2147483647]
scale = 2 (double)
Fallback fixed step size scaling. in [1, INF]
step = 0.1 (double)
Initial step size. in [0, INF]
xtola = 0 (double)
Stop if the inf-norm of x-update is below this value.. in
[0, INF]
- gsl
- optimizer plugin based on the multimin optimizers ofthe GNU Scientific Library (GSL) https://www.gnu.org/software/gsl/, supported parameters are:
eps = 0.01 (double)
gradient based optimizers: stop when |grad| < eps,
simplex: stop when simplex size < eps.. in [1e-10, 10]
iter = 100 (int)
maximum number of iterations. in [1, 2147483647]
opt = gd (dict)
Specific optimizer to be used.. Supported values are:
bfgs ‐
Broyden-Fletcher-Goldfarb-Shann
bfgs2 ‐ Broyden-Fletcher-Goldfarb-Shann
(most efficient version)
cg-fr ‐ Flecher-Reeves conjugate gradient
algorithm
gd ‐ Gradient descent.
simplex ‐ Simplex algorithm of Nelder and
Mead
cg-pr ‐ Polak-Ribiere conjugate gradient
algorithm
step = 0.001 (double)
initial step size. in [0, 10]
tol = 0.1 (double)
some tolerance parameter. in [0.001, 10]
- nlopt
- Minimizer algorithms using the NLOPT library, for a description of the optimizers please see 'http://ab-initio.mit.edu/wiki/index.php/NLopt_Algorithms', supported parameters are:
ftola = 0 (double)
Stopping criterion: the absolute change of the objective
value is below this value. in [0, INF]
ftolr = 0 (double)
Stopping criterion: the relative change of the objective
value is below this value. in [0, INF]
higher = inf (double)
Higher boundary (equal for all parameters). in [INF, INF]
local-opt = none (dict)
local minimization algorithm that may be required for the
main minimization algorithm.. Supported values are:
gn-orig-direct-l ‐ Dividing Rectangles
(original implementation, locally biased)
gn-direct-l-noscal ‐ Dividing Rectangles
(unscaled, locally biased)
gn-isres ‐ Improved Stochastic Ranking
Evolution Strategy
ld-tnewton ‐ Truncated Newton
gn-direct-l-rand ‐ Dividing Rectangles
(locally biased, randomized)
ln-newuoa ‐ Derivative-free Unconstrained
Optimization by Iteratively Constructed Quadratic Approximation
gn-direct-l-rand-noscale ‐ Dividing
Rectangles (unscaled, locally biased, randomized)
gn-orig-direct ‐ Dividing Rectangles
(original implementation)
ld-tnewton-precond ‐ Preconditioned
Truncated Newton
ld-tnewton-restart ‐ Truncated Newton with
steepest-descent restarting
gn-direct ‐ Dividing Rectangles
ln-neldermead ‐ Nelder-Mead simplex
algorithm
ln-cobyla ‐ Constrained Optimization BY
Linear Approximation
gn-crs2-lm ‐ Controlled Random Search with
Local Mutation
ld-var2 ‐ Shifted Limited-Memory
Variable-Metric, Rank 2
ld-var1 ‐ Shifted Limited-Memory
Variable-Metric, Rank 1
ld-mma ‐ Method of Moving Asymptotes
ld-lbfgs-nocedal ‐ None
ld-lbfgs ‐ Low-storage BFGS
gn-direct-l ‐ Dividing Rectangles (locally
biased)
none ‐ don't specify algorithm
ln-bobyqa ‐ Derivative-free
Bound-constrained Optimization
ln-sbplx ‐ Subplex variant of
Nelder-Mead
ln-newuoa-bound ‐ Derivative-free
Bound-constrained Optimization by Iteratively Constructed Quadratic
Approximation
ln-praxis ‐ Gradient-free Local
Optimization via the Principal-Axis Method
gn-direct-noscal ‐ Dividing Rectangles
(unscaled)
ld-tnewton-precond-restart ‐ Preconditioned
Truncated Newton with steepest-descent restarting
lower = -inf (double)
Lower boundary (equal for all parameters). in [INF, INF]
maxiter = 100 (int)
Stopping criterion: the maximum number of iterations. in
[1, 2147483647]
opt = ld-lbfgs (dict)
main minimization algorithm. Supported values are:
gn-orig-direct-l ‐ Dividing Rectangles
(original implementation, locally biased)
g-mlsl-lds ‐ Multi-Level Single-Linkage
(low-discrepancy-sequence, require local gradient based optimization and
bounds)
gn-direct-l-noscal ‐ Dividing Rectangles
(unscaled, locally biased)
gn-isres ‐ Improved Stochastic Ranking
Evolution Strategy
ld-tnewton ‐ Truncated Newton
gn-direct-l-rand ‐ Dividing Rectangles
(locally biased, randomized)
ln-newuoa ‐ Derivative-free Unconstrained
Optimization by Iteratively Constructed Quadratic Approximation
gn-direct-l-rand-noscale ‐ Dividing
Rectangles (unscaled, locally biased, randomized)
gn-orig-direct ‐ Dividing Rectangles
(original implementation)
ld-tnewton-precond ‐ Preconditioned
Truncated Newton
ld-tnewton-restart ‐ Truncated Newton with
steepest-descent restarting
gn-direct ‐ Dividing Rectangles
auglag-eq ‐ Augmented Lagrangian algorithm
with equality constraints only
ln-neldermead ‐ Nelder-Mead simplex
algorithm
ln-cobyla ‐ Constrained Optimization BY
Linear Approximation
gn-crs2-lm ‐ Controlled Random Search with
Local Mutation
ld-var2 ‐ Shifted Limited-Memory
Variable-Metric, Rank 2
ld-var1 ‐ Shifted Limited-Memory
Variable-Metric, Rank 1
ld-mma ‐ Method of Moving Asymptotes
ld-lbfgs-nocedal ‐ None
g-mlsl ‐ Multi-Level Single-Linkage
(require local optimization and bounds)
ld-lbfgs ‐ Low-storage BFGS
gn-direct-l ‐ Dividing Rectangles (locally
biased)
ln-bobyqa ‐ Derivative-free
Bound-constrained Optimization
ln-sbplx ‐ Subplex variant of
Nelder-Mead
ln-newuoa-bound ‐ Derivative-free
Bound-constrained Optimization by Iteratively Constructed Quadratic
Approximation
auglag ‐ Augmented Lagrangian
algorithm
ln-praxis ‐ Gradient-free Local
Optimization via the Principal-Axis Method
gn-direct-noscal ‐ Dividing Rectangles
(unscaled)
ld-tnewton-precond-restart ‐ Preconditioned
Truncated Newton with steepest-descent restarting
ld-slsqp ‐ Sequential Least-Squares
Quadratic Programming
step = 0 (double)
Initial step size for gradient free methods. in [0, INF]
stop = -inf (double)
Stopping criterion: function value falls below this
value. in [INF, INF]
xtola = 0 (double)
Stopping criterion: the absolute change of all x-values
is below this value. in [0, INF]
xtolr = 0 (double)
Stopping criterion: the relative change of all x-values
is below this value. in [0, INF]
EXAMPLE¶
Register image test.v to image ref.v affine and write the registered image to reg.v. Use two multiresolution levels and ssd as cost function.mia-3drigidreg -i test.v -r ref.v -o reg.v -l 2 -f affine -c
ssd
AUTHOR(s)¶
Gert WollnyCOPYRIGHT¶
This software is Copyright (c) 1999‐2013 Leipzig, Germany and Madrid, Spain. It comes with ABSOLUTELY NO WARRANTY and you may redistribute it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 (or later). For more information run the program with the option '--copyright'.17 October 2014 | 2.0.10 |