Provided by: mia-tools_2.4.6-5build3_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:
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'.