mia-3drigidreg(1)

NAME
mia-3drigidreg - 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 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:

        trace - Function call trace
        debug - Debug output
        info - Low level messages
        message - Normal messages
        warning - Warnings
        fail - Report test failures
        error - Report errors
        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 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: .@

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. The orientation is transformed in the same way like it is done with 'dicomtonifti --no-reorder' from the vtk-dicom package.

    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:
        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 debugging 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: .@

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 of the 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:
            simplex - Simplex algorithm of Nelder and Mead
            cg-fr - Flecher-Reeves conjugate gradient algorithm
            cg-pr - Polak-Ribiere conjugate gradient algorithm
            bfgs - Broyden-Fletcher-Goldfarb-Shann
            bfgs2 - Broyden-Fletcher-Goldfarb-Shann (most efficient version)
            gd - Gradient descent.

    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-direct - Dividing Rectangles
            gn-direct-l - Dividing Rectangles (locally biased)
            gn-direct-l-rand - Dividing Rectangles (locally biased, randomized)
            gn-direct-noscal - Dividing Rectangles (unscaled)
            gn-direct-l-noscal - Dividing Rectangles (unscaled, locally biased)
            gn-direct-l-rand-noscale - Dividing Rectangles (unscaled, locally biased, randomized)
            gn-orig-direct - Dividing Rectangles (original implementation)
            gn-orig-direct-l - Dividing Rectangles (original implementation, locally biased)
            ld-lbfgs-nocedal - None
            ld-lbfgs - Low-storage BFGS
            ln-praxis - Gradient-free Local Optimization via the Principal-Axis Method
            ld-var1 - Shifted Limited-Memory Variable-Metric, Rank 1
            ld-var2 - Shifted Limited-Memory Variable-Metric, Rank 2
            ld-tnewton - Truncated Newton
            ld-tnewton-restart - Truncated Newton with steepest-descent restarting
            ld-tnewton-precond - Preconditioned Truncated Newton
            ld-tnewton-precond-restart - Preconditioned Truncated Newton with steepest-descent restarting
            gn-crs2-lm - Controlled Random Search with Local Mutation
            ld-mma - Method of Moving Asymptotes
            ln-cobyla - Constrained Optimization BY Linear Approximation
            ln-newuoa - Derivative-free Unconstrained Optimization by Iteratively Constructed Quadratic Approximation
            ln-newuoa-bound - Derivative-free Bound-constrained Optimization by Iteratively Constructed Quadratic Approximation
            ln-neldermead - Nelder-Mead simplex algorithm
            ln-sbplx - Subplex variant of Nelder-Mead
            ln-bobyqa - Derivative-free Bound-constrained Optimization
            gn-isres - Improved Stochastic Ranking Evolution Strategy
            none - don't specify algorithm

    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-direct - Dividing Rectangles
            gn-direct-l - Dividing Rectangles (locally biased)
            gn-direct-l-rand - Dividing Rectangles (locally biased, randomized)
            gn-direct-noscal - Dividing Rectangles (unscaled)
            gn-direct-l-noscal - Dividing Rectangles (unscaled, locally biased)
            gn-direct-l-rand-noscale - Dividing Rectangles (unscaled, locally biased, randomized)
            gn-orig-direct - Dividing Rectangles (original implementation)
            gn-orig-direct-l - Dividing Rectangles (original implementation, locally biased)
            ld-lbfgs-nocedal - None
            ld-lbfgs - Low-storage BFGS
            ln-praxis - Gradient-free Local Optimization via the Principal-Axis Method
            ld-var1 - Shifted Limited-Memory Variable-Metric, Rank 1
            ld-var2 - Shifted Limited-Memory Variable-Metric, Rank 2
            ld-tnewton - Truncated Newton
            ld-tnewton-restart - Truncated Newton with steepest-descent restarting
            ld-tnewton-precond - Preconditioned Truncated Newton
            ld-tnewton-precond-restart - Preconditioned Truncated Newton with steepest-descent restarting
            gn-crs2-lm - Controlled Random Search with Local Mutation
            ld-mma - Method of Moving Asymptotes
            ln-cobyla - Constrained Optimization BY Linear Approximation
            ln-newuoa - Derivative-free Unconstrained Optimization by Iteratively Constructed Quadratic Approximation
            ln-newuoa-bound - Derivative-free Bound-constrained Optimization by Iteratively Constructed Quadratic Approximation
            ln-neldermead - Nelder-Mead simplex algorithm
            ln-sbplx - Subplex variant of Nelder-Mead
            ln-bobyqa - Derivative-free Bound-constrained Optimization
            gn-isres - Improved Stochastic Ranking Evolution Strategy
            auglag - Augmented Lagrangian algorithm
            auglag-eq - Augmented Lagrangian algorithm with equality constraints only
            g-mlsl - Multi-Level Single-Linkage (require local optimization and bounds)
            g-mlsl-lds - Multi-Level Single-Linkage (low-discrepancy-sequence, require local gradient based optimization and bounds)
            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'.