NAME

       mia-2dseries2sets - Combine images of a series to sets.

SYNOPSIS

       mia-2dseries2sets -o <out-directory> [options] <PLUGINS:2dimage/io>

DESCRIPTION

       mia-2dseries2sets  This program takes all image files that are given as free parameters on
       the command line and creates segmentation sets based on information found in  the  images.
       Used  information  is  the z-location of the slice and the acquisition number. The code is
       taylored to used the according descriptors defined in the DICOM standard. All images  with
       the  same  slice  location  will  be  grouped together in one segmentation set and ordered
       according to their acquisition  number.  Slice  locations  are  rounded  to  three  digits
       accuracy to make proper comparison of floating point values feasible.

OPTIONS

              -o --out-directory=(required, output); string
                     output directory (needs to exist and be writable)

                 --no-copy
                     don't copy image files to output directory

   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).

PLUGINS: 2dimage/io

       bmp       BMP 2D-image input/output support. The plug-in supports reading and  writing  of
                 binary  images  and  8-bit  gray scale images. read-only support is provided for
                 4-bit gray scale images. The color table is ignored and  the  pixel  values  are
                 taken as literal gray scale values.

                     Recognized file extensions:  .BMP, .bmp

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

       Create  the  segmentation  sets  from  a  series of DICOM images and copy the files to the
       output directory (copying is the default).

       mia-2dseries2sets -o /home/user/series /net/dicoms/patient1/series1/*.dcm

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'.