mia-3drigidreg(1) Linear registration of 3D images.

SYNOPSIS

mia-3drigidreg -i <in-image> -r <ref-image> -o <out-image> [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-image=(input, required); io
test image For supported file types see PLUGINS:3dimage/io
-r --ref-image=(input, required); io
reference image For supported file types see PLUGINS:3dimage/io
-o --out-image=(output, required); io
registered output image For supported file types see PLUGINS:3dimage/io
-t --transformation=(output); io
transformation output file name For supported file types see PLUGINS:3dtransform/io
-c --cost=ssd
cost functioncost function For supported plugins see PLUGINS:3dimage/cost
-l --levels=3
multigrid levelsmultigrid levels
-O --optimizer=gsl:opt=simplex,step=1.0
Optimizer used for minimizationOptimizer used for minimization For supported plugins see PLUGINS:minimizer/singlecost
-f --transForm=rigid
transformation typetransformation 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).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 in [0, 5]
Spline degree.

omoms
OMoms-spline kernel creation, supported parameters are:

d = 3; int in [3, 3]
Spline degree.

PLUGINS: 3dimage/cost

lncc
local normalized cross correlation with masking support., supported parameters are:

w = 5; uint in [1, 256]
half width of the window used for evaluating the localized cross correlation.

mi
Spline parzen based mutual information., supported parameters are:

cut = 0; float in [0, 40]
Percentage of pixels to cut at high and low intensities to remove outliers.

mbins = 64; uint in [1, 256]
Number of histogram bins used for the moving image.

mkernel = [bspline:d=3]; factory
Spline kernel for moving image parzen hinstogram. For supported plug-ins see PLUGINS:1d/splinekernel

rbins = 64; uint in [1, 256]
Number of histogram bins used for the reference image.

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 in [0, 1000]
Use automatic masking of the moving image by only takeing intensity values into accound that are larger than the given threshold.

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.

sthresh = 0; double
Threshold intensity value for source image.

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: [email protected]

 
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]]; 3dfvector
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]]; 3dfvector
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

norot = 0; bool
Don't optimize the rotation.

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 in [1, inf)
isotropic coefficient rate in pixels.

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: [email protected]

 
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 in [0, inf)
penalty weight on curl.

div = 1; float in [0, inf)
penalty weight on divergence.

norm = 0; bool
Set to 1 if the penalty should be normalized with respect to the image size.

weight = 1; float in (0, inf)
weight of penalty energy.

PLUGINS: minimizer/singlecost

gdas
Gradient descent with automatic step size correction., supported parameters are:

ftolr = 0; double in [0, inf)
Stop if the relative change of the criterion is below..

max-step = 2; double in (0, inf)
Maximal absolute step size.

maxiter = 200; uint in [1, inf)
Stopping criterion: the maximum number of iterations.

min-step = 0.1; double in (0, inf)
Minimal absolute step size.

xtola = 0.01; double in [0, inf)
Stop if the inf-norm of the change applied to x is below this value..

gdsq
Gradient descent with quadratic step estimation, supported parameters are:

ftolr = 0; double in [0, inf)
Stop if the relative change of the criterion is below..

gtola = 0; double in [0, inf)
Stop if the inf-norm of the gradient is below this value..

maxiter = 100; uint in [1, inf)
Stopping criterion: the maximum number of iterations.

scale = 2; double in (1, inf)
Fallback fixed step size scaling.

step = 0.1; double in (0, inf)
Initial step size.

xtola = 0; double in [0, inf)
Stop if the inf-norm of x-update is below this value..

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 in (0, inf)
gradient based optimizers: stop when |grad| < eps, simplex: stop when simplex size < eps..

iter = 100; uint in [1, inf)
maximum number of iterations.

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 in (0, inf)
initial step size.

tol = 0.1; double in (0, inf)
some tolerance parameter.

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 in [0, inf)
Stopping criterion: the absolute change of the objective value is below this value.

ftolr = 0; double in [0, inf)
Stopping criterion: the relative change of the objective value is below this value.

higher = inf; double
Higher boundary (equal for all parameters).

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).

maxiter = 100; int in [1, inf)
Stopping criterion: the maximum number of iterations.

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 in [0, inf)
Initial step size for gradient free methods.

stop = -inf; double
Stopping criterion: function value falls below this value.

xtola = 0; double in [0, inf)
Stopping criterion: the absolute change of all x-values is below this value.

xtolr = 0; double in [0, inf)
Stopping criterion: the relative change of all x-values is below this value.

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) 1999-2015 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'.