Provided by: mia-tools_2.4.7-8ubuntu1_amd64 bug

NAME

       mia-2dto3dimage - Combine a series of 2D images to a volume.

SYNOPSIS

       mia-2dto3dimage -i <in-file> -o <out-file> [options]

DESCRIPTION

       mia-2dto3dimage  This  program  is used to combine a series of 2D images of equal size and
       type images following a certain numbering scheme to a 3D image.

OPTIONS

              -i --in-file=(input, required); io
                     input image(s) to be combined
                      For supported file types see PLUGINS:2dimage/io

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

   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

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. The orientation is transformed in the same way like it is
                 done with 'dicomtonifti --no-reorder' from the vtk-dicom package.

                     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:
                       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

       Convert a series of images imageXXXX.png to a 3D image 3d.v

       mia-2dto3dimage -i imageXXXX.png -o 3d.v

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'.