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

NAME

       mia-2dmyomilles - Run a registration of a series of 2D images.

SYNOPSIS

       mia-2dmyomilles -i <in-file> -o <out-file> [options]

DESCRIPTION

       mia-2dmyomilles  This  program  is  use  to  run  a  modified  version  of  the  ICA based
       registration approach described in Milles et al. 'Fully  Automated  Motion  Correction  in
       First-Pass  Myocardial  Perfusion  MR  Image  Sequences',  Trans.  Med.  Imaging., 27(11),
       1611-1621, 2008. Changes include the extraction of the  quasi-periodic  movement  in  free
       breathingly  acquired data sets and the option to run affine or rigid registration instead
       of the optimization of translations only.

OPTIONS

   File-IO
              -i --in-file=(required)
                     input perfusion data set

              -o --out-file=(required)
                     output perfusion data set

              -r --registered=reg
                     file name base for registered files

                 --save-references=
                     save synthetic reference images to this file base

                 --save-cropped=
                     save cropped image set to this file

                 --save-feature=
                     save the features images resulting from the ICA and some intermediate images
                     used  for the RV-LV segmentation with the given file name base to PNG files.
                     Also save the coefficients of the initial  best  and  the  final  IC  mixing
                     matrix.

   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

   ICA
              -C --components=0
                     ICA components 0 = automatic estimation

                 --normalize
                     normalized ICs

                 --no-meanstrip
                     don't strip the mean from the mixing curves

              -g --guess
                     use initial guess for myocardial perfusion

              -s --segscale=1.4
                     segment and scale the crop box around the LV (0=no segmentation)

              -k --skip=0
                     skip images at the beginning of the series as they are of other modalities

              -m --max-ica-iter=400
                     maximum number of iterations in ICA

              -E --segmethod=features
                     Segmentation method
                        delta-peak ‐ difference of the peak enhancement images
                        features ‐ feature images
                        delta-feature ‐ difference of the feature images

   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).

   Registration
              -c --cost=ssd
                     registration criterion

              -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:2dimage/transform

              -l --mg-levels=3
                     multi-resolution levels

              -P --passes=2
                     registration passes

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: 2dimage/transform

       affine    Affine transformation (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

       rigid     Rigid   transformations   (i.e.  rotation  and  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

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

       rotation  Rotation  transformations  (i.e.  rotation  about  a given center, one degree 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]] (streamable)
                       Relative rotation center, i.e.  <0.5,0.5> corresponds to the center of the
                       support rectangle.

       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]] (2dfvector)
                       anisotropic  coefficient  rate  in  pixels,  nonpositive  values  will  be
                       overwritten by the 'rate' value..

                     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    term.     For    supported    plug-ins    see
                       PLUGINS:2dtransform/splinepenalty

                     rate = 10 (float)
                       isotropic coefficient rate in pixels.  in [1, 3.40282e+38]

       translate Translation only (two 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: 2dtransform/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  perfusion  series given in 'segment.set' by using automatic ICA estimation.
       Skip two images at the beginning and otherwiese use  the  default  parameters.  Store  the
       result in 'registered.set'.

       mia-2dmyomilles   -i segment.set -o registered.set -k 2

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'.