mia-3disosurface-from-volume

NAME

mia-3disosurface-from-volume - Extract an ist-surface froma a 3D image.

SYNOPSIS

mia-3disosurface-from-volume -i <in-file> -o <out-file> [options]

DESCRIPTION

mia-3disosurface-from-volume This program is used to extract an iso-surface from the input gray scale image by using marching thetrahedra.

OPTIONS

File-IO

-i --in-file=(required, input); io

input image
For supported file types see PLUGINS:3dimage/io

-o --out-file=(required, output); io

output mesh
For supported file types see PLUGINS:mesh/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

Image options

-s --iso-value=128

iso-value of iso surface to be extracted

-b --bordered

put an empty border around the image to ensure a closed surface

Mesh options

-f --max-faces=-1

maximum number of Faces,

-e --max-edges=-1

maximum number of Edges

-c --max-cost=0.1

maximum cost for edge collaps

-r --ratio=4

ratio of faces(edges) to target number, at which the optimization changes from edge-length to volume-optimized

-w --reverse-winding

reverse the winding of the triangles in order to make normals point away from the high intensity area

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:

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

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. Supported is only the ASCII format 3D meshes with normales and per-vertex RGB colors. Alpha values and texture coordinates, as well as per face properties are ignored. Polygons are read and triangulated.

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

Extract the surface corresponding to the value 30 and stop optimizing when the mesh consists of less than 100000 triangles.

mia-3disosurface-from-volume -i image.v -o mesh.vmesh -s 30 -f 100000

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’.