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mia-3disosurface-from-volume(1) General Commands Manual mia-3disosurface-from-volume(1)

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 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'.
v2.4.6 USER COMMANDS