NAME

       ('mia\-2dsegmentcropbox',) - Evaluate a crop-box around a manual segmentation.

SYNOPSIS

       mia-2dsegmentcropbox -i <in-file> -o <out-file> [options]

DESCRIPTION

       mia-2dsegmentcropbox  This  program  is  used  on  a  segmentation  set and evaluates a bounding box that
       encloses the segmentation in all slices. This bounding box is then used  to  crop  the  original  images,
       correct  the  segmentation  and  store a new segmentation set with the cropped images. The cropped images
       will be of the same type as the original images. If no segmentation is given in the set,  the  result  is
       undefined.

OPTIONS

              -i --in-file=(input, required); string
                     input segmentation set

              -p --override-imagepath
                     Instead  of  using the path of the image files as given in the segmentation set, assume the
                     files are located in the current directory

              -o --out-file=(output, required); string
                     output segmentation set

              -c --cropped-base=crop
                     Base name for the cropped image files, the file type and numbering will  be  based  on  the
                     input image file type and numbering.

              -e --enlarge=5
                     Enlarge  the  area  around  the  obtained  sbounding  box  by this number of pixels in each
                     direction

   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
                        trace ‐ Function call trace
                        fail ‐ Report test failures
                        warning ‐ Warnings
                        error ‐ Report errors
                        debug ‐ Debug output
                        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).

EXAMPLE

       Evaluate the optimal cropping for a segmentation set segment.set and enlarge it by 3  pixels.  Store  the
       resulting set in the file cropped.set.

       mia-2dsegmentcropbox -i segment.set -o cropped.set -e 3

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                                        v2.4.6                              mia-2dsegmentcropbox(1)