Provided by: mia-tools_2.4.6-1_amd64 
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:
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. 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'.