Provided by: mia-tools_2.4.7-13_amd64 bug

NAME

       mia-2dmyoset-all2one-nonrigid - Non-linear registration of a series of 2D images.

SYNOPSIS

       mia-2dmyoset-all2one-nonrigid      -i      <in-file>      -o      <out-file>     [options]
       <PLUGINS:2dimage/fullcost>

DESCRIPTION

       mia-2dmyoset-all2one-nonrigid This program runs non-rigid  registration  of  a  series  of
       images  given  in  an  image  set. All images are registered to one user defined reference
       image.

OPTIONS

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

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

                 --out-filebase=reg
                     file name basae for registered files, file type is deducted from  the  image
                     file type in the input data set.

   Registration
              -k --skip=0
                     Skip images at the beginning of the series

              -O --optimizer=gsl:opt=gd,step=0.1
                     Optimizer used for minimization

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

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

              -r --ref=-1
                     reference frame (-1 == use image in the middle)

   Help & Info
              -V --verbose=warning
                     verbosity  of  output,  print messages of given level and higher priorities.
                     Supported priorities starting at lowest level are:

                        trace ‐ Function call trace
                        debug ‐ Debug output
                        info ‐ Low level messages
                        message ‐ Normal messages
                        warning ‐ Warnings
                        fail ‐ Report test failures
                        error ‐ Report errors
                        fatal ‐ Report only fatal errors

                 --copyright
                     print copyright information

              -h --help
                     print this help

              -? --usage
                     print a short help

                 --version
                     print the version number and exit

   Processing
                 --threads=-1
                     Maxiumum number of threads to use for processing,This number should be lower
                     or  equal  to  the  number  of  logical processor cores in the machine. (-1:
                     automatic estimation).

PLUGINS: 1d/splinebc

       mirror    Spline interpolation boundary conditions that mirror on the boundary

                     (no parameters)

       repeat    Spline interpolation boundary conditions that repeats the value at the boundary

                     (no parameters)

       zero      Spline interpolation boundary conditions that assumes zero for values outside

                     (no parameters)

PLUGINS: 1d/splinekernel

       bspline   B-spline kernel creation , supported parameters are:

                     d = 3; int in [0, 5]
                       Spline degree.

       omoms     OMoms-spline kernel creation, supported parameters are:

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

PLUGINS: 2dimage/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.

       lsd       Least-Squares Distance measure

                     (no parameters)

       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. Various evaluation kernels are available., supported parameters are:

                     eval = ds; dict
                       plugin subtype.  Supported values are:
                           sq ‐ square of difference
                           ds ‐ square of scaled difference
                           dot ‐ scalar product kernel
                           cross ‐ cross product kernel

       ssd       2D imaga 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
                 2D  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: 2dimage/fullcost

       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; factory
                       Cost function kernel.  For supported plug-ins see PLUGINS:2dimage/cost

                     debug = 0; bool
                       Save intermediate resuts for debugging.

                     ref =(input, io)
                       Reference image.  For supported file types see PLUGINS:2dimage/io

                     src =(input, io)
                       Study image.  For supported file types see PLUGINS:2dimage/io

                     weight = 1; float
                       weight of cost function.

       labelimage
                 Similarity cost function that maps labels  of  two  images  and  handles  label-
                 preserving multi-resolution processing., supported parameters are:

                     debug = 0; int in [0, 1]
                       write the distance transforms to a 3D image.

                     maxlabel = 256; int in [2, 32000]
                       maximum number of labels to consider.

                     ref =(input, io)
                       Reference image.  For supported file types see PLUGINS:2dimage/io

                     src =(input, io)
                       Study image.  For supported file types see PLUGINS:2dimage/io

                     weight = 1; float
                       weight of cost function.

       maskedimage
                 Generalized  masked  image  similarity  cost  function  that also handles multi-
                 resolution processing. The provided masks should be  densly  filled  regions  in
                 multi-resolution  procesing  because otherwise the mask information may get lost
                 when downscaling the image. The reference mask and the transformed mask  of  the
                 study  image  are combined by binary AND. The actual similarity measure is given
                 es extra parameter., supported parameters are:

                     cost = ssd; factory
                       Cost     function     kernel.      For     supported     plug-ins      see
                       PLUGINS:2dimage/maskedcost

                     ref =(input, io)
                       Reference image.  For supported file types see PLUGINS:2dimage/io

                     ref-mask =(input, io)
                       Reference   image   mask    (binary).    For   supported  file  types  see
                       PLUGINS:2dimage/io

                     src =(input, io)
                       Study image.  For supported file types see PLUGINS:2dimage/io

                     src-mask =(input, io)
                       Study   image   mask   (binary).    For   supported   file    types    see
                       PLUGINS:2dimage/io

                     weight = 1; float
                       weight of cost function.

PLUGINS: 2dimage/io

       bmp       BMP  2D-image  input/output support. The plug-in supports reading and writing of
                 binary images and 8-bit gray scale images. read-only  support  is  provided  for
                 4-bit  gray  scale  images.  The color table is ignored and the pixel values are
                 taken as literal gray scale values.

                     Recognized file extensions:  .BMP, .bmp

                     Supported element types:
                       binary data, unsigned 8 bit

       datapool  Virtual IO to and from the internal data pool

                     Recognized file extensions:  .@

       dicom     2D image io for DICOM

                     Recognized file extensions:  .DCM, .dcm

                     Supported element types:
                       signed 16 bit, unsigned 16 bit

       exr       a 2dimage io plugin for OpenEXR images

                     Recognized file extensions:  .EXR, .exr

                     Supported element types:
                       unsigned 32 bit, floating point 32 bit

       jpg       a 2dimage io plugin for jpeg gray scale images

                     Recognized file extensions:  .JPEG, .JPG, .jpeg, .jpg

                     Supported element types:
                       unsigned 8 bit

       png       a 2dimage io plugin for png images

                     Recognized file extensions:  .PNG, .png

                     Supported element types:
                       binary data, unsigned 8 bit, unsigned 16 bit

       raw       RAW 2D-image output support

                     Recognized file extensions:  .RAW, .raw

                     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

       tif       TIFF 2D-image input/output support

                     Recognized file extensions:  .TIF, .TIFF, .tif, .tiff

                     Supported element types:
                       binary data, unsigned 8 bit, unsigned 16 bit, unsigned 32 bit

       vista     a 2dimage io plugin for vista images

                     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

PLUGINS: 2dimage/maskedcost

       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 with masking., 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 with masking support.

                     (no parameters)

       ssd       Sum of squared differences with masking.

                     (no parameters)

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.

EXAMPLE

       Register  the  perfusion  series  given  in  segment.set  by  optimizing  a  spline  based
       transformation  with  a coefficient rate of 16 pixel using Mutual Information and penalize
       the transformation by using divcurl with aweight of 2.0.

       mia-2dmyoset-all2one-nonrigid -i segment.set -o registered.set
                  -f spline:rate=16,penalty=[divcurl:weight=2.0] image:cost=mi,weight=2.0

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'.