NAME

       mia-2dmyocard-ica - Run an ICA analysis on a series of 2D images

SYNOPSIS

       mia-2dmyocard-ica -i <in-base> [options]

DESCRIPTION

       mia-2dmyocard-ica  This  program  is used to run a ICA on a series of myocardial perfusion
       images to create sythetic references that can be  used  for  motion  correction  by  image
       registration.  If the aim is to run a full motion compensation then it is better to create
       a segmentation set and use mia-2dmyoica-nonrigid. If the input data is given by means of a
       segmentation  set,  then  on  can  also  use  mia-2dmyocard-icaseries.   This  program  is
       essentially used to test different options on  how  to  run  the  ICA  forreference  image
       creation.

OPTIONS

              -i --in-base=(required)
                     input file name ofolloing pattern nameXXXX.ext X=numbers  For supported file
                     types see PLUGINS:2dimage/io

                 --coefs=
                     output mixing coefficients to this file

              -o --out-base=ref
                     output file name base

              -t --type=exr
                     output file type

              -k --skip=2
                     skip images at beginning of series

              -e --end=60
                     last image in series

              -C --components=0
                     nr. of components, 0=estimate automatically

              -m --strip-mean
                     strip mean image from series

              -f --save-features=
                     save feature image

              -p --strip-periodic
                     strip only periodic component

              -x --max-ica-iterations=0
                     max ICA solver iterations

              -n --ica-normalize
                     ica_normalize feature images

                 --all-features=
                     save all feature images to

              -L --LV-crop-amp=0
                     LV crop mask amplification, 0.0 = don't crop

              -a --auto-components
                     automatic esitmation of number of components based on  correlation.  Implies
                     -m and -n (Experimental)

   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: 2dimage/io

       bmp       BMP 2D-image input/output support

                     Recognized file extensions:  .BMP, .bmp

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

EXAMPLE

       Evaluate the synthetic references from images imageXXXX.exr and save them  to  refXXXX.exr
       by using five independend components, mean stripping, normalizing, and skipping 2 images.

       mia-2dmyocard-ica -i imageXXXX.exr -o ref -k 2 -C 5 -m -n

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'.