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PROGRAM:

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=(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: .@

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


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'.

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