xenial (1) mia-mesh-to-maskimage.1.gz

Provided by: mia-tools_2.2.7-3_amd64 bug

NAME

       mia-mesh-to-maskimage - Create a binary mask from the mesh surfac.

SYNOPSIS

       mia-mesh-to-maskimage -i <in-file> -o <out-file> [options]

DESCRIPTION

       mia-mesh-to-maskimage This program converts a 3D mesh into a binary mask comprising the mesh surface. The
       output image size is either given on the command line or deducted from the mesh dimensions.

OPTIONS

   File I/O
              -i --in-file=(input, required); io
                     input mesh to be adapted  For supported file types see PLUGINS:mesh/io

              -o --out-file=(output, required); io
                     output image containing the binary mask  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:
                        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).

   Properties
                 --origin=[0,0,0]
                     coordinate of pixel at index 0,0,0coordinate of pixel at index 0,0,0

                 --spacing=[1,1,1]
                     voxel spacing in the output image, all values must be positive.voxel spacing in the  output
                     image, all values must be positive.

                 --size=[0,0,0]
                     size of the output image (0,0,0 = deduct)size of the output image (0,0,0 = deduct)

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

PLUGINS: mesh/io

       datapool  Virtual IO to and from the internal data pool

                     Recognized file extensions:  .@

       off       plugin to load/store some Geomview OFF Files

                     Recognized file extensions:  .OFF, .off

       ply       Ply triangle mesh input/output support

                     Recognized file extensions:  .PLY, .ply

       stl       STL mesh io plugin

                     Recognized file extensions:  .STL, .stl

       vista     Vista/Simbio triangle mesh input/output support

                     Recognized file extensions:  .V, .VMESH, .v, .vmesh

       vtk       A subset of VTK mesh in-and output: Triangle  meshes  are  written,  and  triangle  meshes  and
                 triangle  strips  are read. Additional per-vertex attributes are supported: 'normals', 'colors'
                 for three component colors, and 'scale' for a scalar value attached to each vertex. The data is
                 written by the vtkPolyDataWriter in binary format.

                     Recognized file extensions:  .VTK, .VTKMESH, .vtk, .vtkmesh

EXAMPLE

       The  input  mesh  input.vmesh is converted into the binary mask mask.v. The image size is set to 50,50,50
       and the size is obtained automatically to include the whole mesh

       mia-mesh-to-maskimage -i input.vmesh -o mask.v --origin 0,0,0

AUTHOR(s)

       Gert Wollny

       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'.