mia-3disosurface-from-volume(1) 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=(input, required); io
input image For supported file types see PLUGINS:3dimage/io
-o --out-file=(output, required); 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:
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

Image options

-s --iso-value=128
iso-value of iso surface to be extractediso-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,maximum number of Faces,
-e --max-edges=-1
maximum number of Edgesmaximum number of Edges
-c --max-cost=0.1
maximum cost for edge collapsmaximum cost for edge collaps
-r --ratio=4
ratio of faces(edges) to target number, at which the optimization changes from edge-length to volume-optimizedratio 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).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: [email protected]

 
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: [email protected]

 
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

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'.