NAME

       mia-3dcrispsegment - Label segmentation according to probabilities.

SYNOPSIS

       mia-3dcrispsegment -i <in-file> -o <out-file> [options]

DESCRIPTION

       mia-3dcrispsegment  This program creates a label image from a fuzzy segmentation. or each pixel the label
       is set to the class with the higest probability plus a given offset

OPTIONS

              -i --in-file=(required)
                     input class file, should contain multiple  images  with  tissue  class  probabilities   For
                     supported file types see PLUGINS:3dimage/io

              -o --out-file=(required)
                     output class label image  For supported file types see PLUGINS:3dimage/io

              -l --label-offset=1
                     label offset

   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
                        warning ‐ Warnings
                        error ‐ Report errors
                        fail ‐ Report test failures
                        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).

PLUGINS: 3dimage/io

       analyze   Analyze 7.5 image

                     Recognized file extensions:  .HDR, .hdr

                     Supported element types:
                       unsigned  8  bit,  signed 16 bit, signed 32 bit, floating point 32 bit, floating point 64
                       bit

       datapool  Virtual IO to and from the internal data pool

                     Recognized file extensions:  .@

       dicom     Dicom image series as 3D

                     Recognized file extensions:  .DCM, .dcm

                     Supported element types:
                       unsigned 16 bit

       inria     INRIA image

                     Recognized file extensions:  .INR, .inr

                     Supported element types:
                       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

       mhd       MetaIO 3D image IO using the VTK implementation (experimental).

                     Recognized file extensions:  .MHA, .MHD, .mha, .mhd

                     Supported element types:
                       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

       vff       VFF Sun raster format

                     Recognized file extensions:  .VFF, .vff

                     Supported element types:
                       unsigned 8 bit, signed 16 bit

       vista     Vista 3D

                     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

       vti       3D image VTK-XML in- and output (experimental).

                     Recognized file extensions:  .VTI, .vti

                     Supported element types:
                       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

       vtk       3D VTK image legacy in- and output (experimental).

                     Recognized file extensions:  .VTK, .VTKIMAGE, .vtk, .vtkimage

                     Supported element types:
                       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

       Set the labels based on the input class probability file cls.v adding the offset 2 to each label and save
       the result to labeled.v.

       mia-3dcrispsegment -i cls.v -o labeled.v -l 2

AUTHOR(s)

       Gert Wollny

COPYRIGHT

       This software is Copyright (c) 1999‐2013 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'.

2.0.10                                           25 January 2014                           mia-3dcrispsegment(1)