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=(required, input); 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'.

USER COMMANDS                                        v2.4.7                           mia-2dmyocard-icaseries(1)