Provided by: mia-tools_2.0.13-1_amd64 bug

NAME

       mia-3dprealign-nonrigid - Registration of a series of 3D images.

SYNOPSIS

       mia-3dprealign-nonrigid -i <in-file> -o <out-file> [options]

DESCRIPTION

       mia-3dprealign-nonrigid This program runs the non-rigid registration of an image series by
       first registering an already aligned subset of the images to one reference,  and  then  by
       registering  the remaining images by using synthetic references. The is a 3D version of G.
       Wollny, M-J Ledesma-Cabryo,  P.Kellman,  and  A.Santos,  "Exploiting  Quasiperiodicity  in
       Motion Correction of Free-Breathing," IEEE Transactions on Medical Imaging, 29(8), 2010.

OPTIONS

   File-IO
              -i --in-file=(required)
                     input  images  following the naming pattern nameXXXX.ext  For supported file
                     types see PLUGINS:3dimage/io

              -o --out-file=(required)
                     file name base for registered files given as C-format string  For  supported
                     file types see PLUGINS:3dimage/io

                 --save-references
                     Save synthetic references to files refXXXX.v

   Preconditions & Preprocessing
              -k --skip=0
                     Skip images at the begin of the series

                 --preskip=20
                     Skip  images  at  the  beginning+skip  of the series when searching for high
                     contrats image

                 --postskip=2
                     Skip images at the end of the series when searching for high contrats image

                 --max-candidates=20
                     maximum number of candidates for global reference image

              -S --cost-series=image:cost=[ngf:eval=ds]
                     Const function to use for the analysis of the series  For supported  plugins
                     see PLUGINS:3dimage/fullcost

                 --ref-idx=
                     save reference index number to this file

   Registration
              -O --optimizer=gsl:opt=gd,step=0.01
                     Optimizer    used    for    minimization     For   supported   plugins   see
                     PLUGINS:minimizer/singlecost

              -l --mr-levels=3
                     multi-resolution levels

              -f --transForm=spline
                     transformation type  For supported plugins see PLUGINS:3dimage/transform

              -1 --cost-subset=image:cost=[ngf:eval=ds]
                     Cost function for registration during the subset registration  For supported
                     plugins see PLUGINS:3dimage/fullcost

              -2 --cost-final=image:cost=ssd
                     Cost  function for registration during the final registration  For supported
                     plugins see PLUGINS:3dimage/fullcost

   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
                        warning ‐ Warnings
                        error ‐ Report errors
                        fail ‐ Report test failures
                        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/fullcost

       divcurl   divcurl penalty cost function, 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]

                     weight = 1 (float)
                       weight of cost function.  in [-1e+10, 1e+10]

       image     Generalized  image  similarity  cost function that also handles multi-resolution
                 processing.  The  actual  similarity  measure  is  given  es  extra  parameter.,
                 supported parameters are:

                     cost = ssd (string)
                       Cost function kernel.

                     debug = 0 (bool)
                       Save intermediate resuts for debugging.

                     ref = ref.@ (io)
                       Reference image.  For supported file types see PLUGINS:3dimage/io

                     src = src.@ (io)
                       Study image.  For supported file types see PLUGINS:3dimage/io

                     weight = 1 (float)
                       weight of cost function.  in [-1e+10, 1e+10]

       taggedssd Evaluates  the  Sum  of  Squared  Differences  similarity measure by using three
                 tagged image pairs. The cost function value is  evaluated  based  on  all  image
                 pairs,  but the gradient is composed by composing its component based on the tag
                 direction., supported parameters are:

                     refx = (required, io)
                       Reference image  X-tag.  For supported file types see PLUGINS:3dimage/io

                     refy = (required, io)
                       Reference image  Y-tag.  For supported file types see PLUGINS:3dimage/io

                     refz = (required, io)
                       Reference image  Z-tag.  For supported file types see PLUGINS:3dimage/io

                     srcx = (required, io)
                       Study image X-tag.  For supported file types see PLUGINS:3dimage/io

                     srcy = (required, io)
                       Study image Y-tag.  For supported file types see PLUGINS:3dimage/io

                     srcz = (required, io)
                       Study image Z-tag.  For supported file types see PLUGINS:3dimage/io

                     weight = 1 (float)
                       weight of cost function.  in [-1e+10, 1e+10]

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:
                       unsigned 16 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

       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

       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

                     rot-center = [[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

                     rot-center = [[0,0,0]] (streamable)
                       Relative rotation center, i.e.  <0.5,0.5,0.5> corresponds to the center of
                       the volume.

       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/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]

                     weight = 1 (float)
                       weight of penalty energy.  in [0, 3.40282e+38]

PLUGINS: minimizer/singlecost

       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 the image series given  by  images  imageXXXX.v  by  optimizing  a  spline  based
       transformation  with  a coefficient rate of 16 pixel, skipping two images at the beginning
       and using normalized gradient fields as initial cost measure and  SSD  as  final  measure.
       Penalize  the  transformation  by using divcurl with aweight of 2.0. As optimizer an nlopt
       based newton method is used.

       mia-3dprealign-nonrigid mia-3dprealign-nonrigid  -i imageXXXX.v -o registered -t vista  -k
              2-F   spline:rate=16,penalty=[divcurl:weight=2]   -1   image:cost=[ngf:eval=ds]  -2
              image:cost=ssd -O nlopt:opt=ld-var1,xtola=0.001,ftolr=0.001,maxiter=300

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'.