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

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'.