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

NAME

       ('mia\-3dmotioncompica\-nonrigid',) - Non-linear registration of a series of 3D images.

SYNOPSIS

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

DESCRIPTION

       mia-3dmotioncompica-nonrigid   This   program  implements  a  3D  version  of  the  motion
       compensation algorithm described in Wollny G, Kellman P, Santos  A,  Ledesma-Carbayo  M-J,
       "Automatic  Motion  Compensation  of  Free Breathing acquired Myocardial Perfusion Data by
       using    Independent    Component    Analysis",    Medical    Image    Analysis,     2012,
       DOI:10.1016/j.media.2012.02.004.

OPTIONS

   File-IO
              -i --in-file=(input, required); io
                     input images of consecutively numbered filed (nameXXXX.ext)
                      For supported file types see PLUGINS:3dimage/io

              -o --out-file=(output, required); io
                     output  image  name  (as C format string including a %04d in order to define
                     the file numbering)
                      For supported file types see PLUGINS:3dimage/io

                 --save-refs=
                     save reference images, the given string is  used  as  file  name  base,  the
                     number  pattern  follows  the  input images, and the output format is always
                     'vista'

                 --save-regs=
                     save intermediate registered images, the given string is used as  file  name
                     base,  the number pattern follows the input images, and the output format is
                     always 'vista'

                 --save-coeffs=
                     save mixing matrix to a text file

                 --save-features=
                     save feature images as PNG

   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
                 --fastica=internal
                     FastICA implementationto be used
                      For supported plugins see PLUGINS:fastica/implementation

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

                 --no-normalize
                     don't normalized ICs

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

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

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

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

              -a --start-c-rate=32
                     start coefficinet rate in spines,  gets  divided  by  --c-rate-divider  with
                     every pass

                 --c-rate-divider=4
                     cofficient rate divider for each pass

              -d --start-divcurl=20
                     start divcurl weight, gets divided by --divcurl-divider with every pass

                 --divcurl-divider=4
                     divcurl weight scaling with each new pass

              -w --imagecost=image:weight=1,cost=ssd,
                     image cost

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

              -P --passes=3
                     registration passes

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: fastica/implementation

       internal  This is the MIA implementation of the FastICA algorithm.

                     (no parameters)

       itpp      This is the IT++ implementation of the FastICA algorithm.

                     (no parameters)

EXAMPLE

       Register  the  perfusion  series  given  in  images  imagesXXXX.v  by  using  4-class  ICA
       estimation. Skip two images at the beginning, use at most 4 registration threads, a  nlopt
       based   optimizer  and  otherwiese  use  the  default  parameters.  Store  the  result  in
       registeredXXXX.v

       mia-3dmotioncompica-nonrigid -i images0000.v -o  registered%04d.v  -k  2  -C  4  -t  4  -O
              nlopt:opt=ld-var1,xtola=0.001,ftolr=0.001,maxiter=300

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'.