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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 Wollny

COPYRIGHT

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