Provided by: mia-tools_2.4.6-4ubuntu2_amd64 bug

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:

                        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 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:
                           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'.