NAME

       mia-2dsegseriesstats - Evaluate time-intensity curves in masked regions of image series.

SYNOPSIS

       mia-2dsegseriesstats -o <original> -g <registered> [options]

DESCRIPTION

       mia-2dsegseriesstats  This  program  is used evaluate various time-intensity curves over a
       series of images given by a segmentation set. Specifically, the  program  is  taylored  to
       evaluate average intensities and variations of sections the left ventricle myocardium. The
       segmentation set must contain the segmentations for  all  slices  that  will  be  accessed
       during evaluation.

OPTIONS

              -o --original=(input, required); string
                     original segmentation set

              -g --registered=(input, required); string
                     registered segmentation set

              -k --skip=2
                     images  to  skip  at  the begin of the series, if (k < 0) use RV peak of the
                     registered set if set

              -r --reference=-1
                     reference frame for automatic curve extraction. Negative values can be  used
                     to indicate specific values (if given in the segmentation set):
                        -3: Middle of the series
                        -2: prefererred reference
                        -1: LV peak
                        if  any  of the above is not available or the value is < -3, use the last
                     frame of the series.

              -c --curves=(output); string
                     region average value curves, The output files  each  comprises  a  table  in
                     plain-text  format  that  contains  three columns for each section of the LV
                     myocardium: The first column contains  the  values  obtained  by  using  the
                     original segmentation of the reference on all images of the original series,
                     the  second  column  contains  the  values  obtained   by   the   registered
                     segmentation  of  the  reference on all images of the registered series, and
                     the third column contains the values obtained by using the segmentations  of
                     each slice on the original images.

              -v --varcurves=(output); string
                     region variation values, same formt as described above.

              -n --nsections=0
                     number  of  sections to use, 0=use as segmented, otherwise Otherwise, the LV
                     myocardium is divided into n sections that enclose equal angles starting  at
                     the right ventricle insertion point moving clock-wise using the LV center as
                     angular point.

   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).

EXAMPLE

       Evaluate  the  two curve typed for 12 sections from segemntation sets orig.set and reg.set
       skipping the first 2 frames. The output will be written to  curves.txt  and  varcurves.txt
       respectively.

       mia-2dsegseriesstats -i org.set -g reg.set -c curves.txt -v varcurves.txt -n 12 -k 2

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'.