xenial (1) mia-2dmyomilles.1.gz

Provided by: mia-tools_2.2.7-3_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=(input, required); string
                     input perfusion data set

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

              -r --registered=
                     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
                        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

   ICA
              -C --components=0
                     ICA components 0 = automatic estimationICA 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)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 modalitiesskip images at
                     the beginning of the series as they are of other modalities

              -m --max-ica-iter=400
                     maximum number of iterations in ICAmaximum 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).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 minimizationOptimizer used for minimization  For supported plugins see
                     PLUGINS:minimizer/singlecost

              -f --transForm=rigid
                     transformation typetransformation type  For supported plugins see PLUGINS:2dimage/transform

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

              -R --reference=-1
                     Global reference all image should be aligned to. If set to a non-negative value, the images
                     will be aligned to this references, and the cropped output image date will be injected into
                     the original images. Leave at -1 if you don't  care.  In  this  case  all  images  with  be
                     registered  to  a mean position of the movementGlobal reference all image should be aligned
                     to. If set to a non-negative value, the images will be aligned to this references, and  the
                     cropped  output  image  date  will be injected into the original images. Leave at -1 if you
                     don't care. In this case all images with be registered to a mean position of the movement

              -P --passes=2
                     registration passesregistration 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 in [0, 5]
                       Spline degree.

       omoms     OMoms-spline kernel creation, supported parameters are:

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

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]]; 2dfvector
                       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]]; 2dfvector
                       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 in [1, inf)
                       isotropic coefficient rate in pixels.

       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 in [0, inf)
                       penalty weight on curl.

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

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

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

PLUGINS: minimizer/singlecost

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

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

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

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

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

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

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

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

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

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

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

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

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

       gsl       optimizer  plugin  based  on  the  multimin  optimizers  ofthe  GNU  Scientific  Library  (GSL)
                 https://www.gnu.org/software/gsl/, supported parameters are:

                     eps = 0.01; double in (0, inf)
                       gradient  based  optimizers:  stop  when  |grad| < eps, simplex: stop when simplex size <
                       eps..

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

                     opt = gd; dict
                       Specific optimizer to be used..  Supported values are:
                           bfgs ‐ Broyden-Fletcher-Goldfarb-Shann
                           bfgs2 ‐ Broyden-Fletcher-Goldfarb-Shann (most efficient version)
                           cg-fr ‐ Flecher-Reeves conjugate gradient algorithm
                           gd ‐ Gradient descent.
                           simplex ‐ Simplex algorithm of Nelder and Mead
                           cg-pr ‐ Polak-Ribiere conjugate gradient algorithm

                     step = 0.001; double in (0, inf)
                       initial step size.

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

       nlopt     Minimizer algorithms using the NLOPT library, for a description of the  optimizers  please  see
                 'http://ab-initio.mit.edu/wiki/index.php/NLopt_Algorithms', supported parameters are:

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

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

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

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

                     lower = -inf; double
                       Lower boundary (equal for all parameters).

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

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

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

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

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

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

EXAMPLE

       Register  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

       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'.