NAME

       mia-raw2volume - Convert raw data into a 3D image

SYNOPSIS

       mia-raw2volume -i <in-file> -o <out-file> -s <size> [options]

DESCRIPTION

       mia-raw2volume  This  program  is  used to convert raw data into 3D images with apropriate
       metadata.

OPTIONS

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

              -o --out-file=(output, required); io
                     output file name  For supported file types see PLUGINS:3dimage/io

              -r --repn=ubyte
                     input pixel type
                        none ‐ no pixel type defined
                        float ‐ floating point 32 bit
                        sbyte ‐ signed 8 bit
                        ulong ‐ unsigned 64 bit
                        double ‐ floating point 64 bit
                        sint ‐ signed 32 bit
                        ushort ‐ unsigned 16 bit
                        sshort ‐ signed 16 bit
                        uint ‐ unsigned 32 bit
                        slong ‐ signed 64 bit
                        bit ‐ binary data
                        ubyte ‐ unsigned 8 bit

              -b --big-endian
                     input data is big endian

              -f --scale=[1,1,1]
                     scale of input voxels <FX,FY,FZ>scale of input voxels <FX,FY,FZ>

              -k --skip=0
                     skip number of bytes  from  beginning  of  fileskip  number  of  bytes  from
                     beginning of file

              -s --size=(required); 3dbounds
                     size of input <NX,NY,NZ>size of input <NX,NY,NZ>

   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).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:
                       signed 16 bit, unsigned 16 bit

       hdf5      HDF5 3D image IO

                     Recognized file extensions:  .H5, .h5

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

       nifti     NIFTI-1 3D image IO

                     Recognized file extensions:  .NII, .nii

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

       pixel size of <1.2, 2.3, 3.4> to an Analyze file image.hdr

       mia-raw2volume -i data.raw -o image.hdr -s "<10,20,30>" -k "<1.2,2.3,3.4>" -r ushort

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'.