NAME

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

SYNOPSIS

       mia-2dmyocard-icaseries -i <in-file> [options]

DESCRIPTION

       mia-2dmyocard-icaseries  This  program  is  used  to  run  a ICA on a series of myocardial
       perfusion images given in a segmentation set in order 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 run mia-2dmyoica-nonrigid,  since  this  program  is
       essentially the same without the registration bits.

OPTIONS

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

              -r --references=(output); string
                     File name base for the reference images. Image type and numbering scheme are
                     taken from the input images.

              -c --save-cropped=(output); string
                     save cropped set of the original set to this file, the image files will  use
                     the stem of the name as file name base

                 --save-feature=(output); string
                     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:

                        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

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

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

                 --normalize
                     normalized ICs

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

              -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-feature ‐ difference of the feature images
                        delta-peak ‐ difference of the peak enhancement images
                        features ‐ 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).

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

       Evaluate  the  synthetic  references  from set segment.set and save them to refXXXX.??? by
       using five independend components, and skipping 2  images.  Per  default  a  bounding  box
       around  the LV will be segmented and scaled by 1.4 and the cropped images will be saved to
       cropXXXX.??? and a segmentation set cropped.set  is created. The image file  type  ???  is
       deducted from the input images in segment.set.

       mia-2dmyocard-icaseries -i segment.set -r ref -o ref -k 2 -C 5

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'.