DOKK / manpages / debian 10 / mia-tools / mia-3disosurface-from-volume.1.en
mia-3disosurface-from-volume(1) General Commands Manual mia-3disosurface-from-volume(1)

('mia\-3disosurface\-from\-volume',) - Extract an ist-surface froma a 3D image.

mia-3disosurface-from-volume -i <in-file> -o <out-file> [options]

mia-3disosurface-from-volume This program is used to extract an iso-surface from the input gray scale image by using marching thetrahedra.

input image
For supported file types see PLUGINS:3dimage/io
output mesh
For supported file types see PLUGINS:mesh/io

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
print copyright information

print this help

-? --usage
print a short help

print the version number and exit

iso-value of iso surface to be extracted

put an empty border around the image to ensure a closed surface

maximum number of Faces,

maximum number of Edges

maximum cost for edge collaps

ratio of faces(edges) to target number, at which the optimization changes from edge-length to volume-optimized

reverse the winding of the triangles in order to make normals point away from the high intensity area

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).

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

Virtual IO to and from the internal data pool

('Recognized file extensions: ', '.@')

Dicom image series as 3D

('Recognized file extensions: ', '.DCM, .dcm')

Supported element types:
signed 16 bit, unsigned 16 bit

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 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

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-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 Sun raster format

('Recognized file extensions: ', '.VFF, .vff')

Supported element types:
unsigned 8 bit, signed 16 bit

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

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

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

Virtual IO to and from the internal data pool

('Recognized file extensions: ', '.@')

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 triangle mesh input/output support

('Recognized file extensions: ', '.PLY, .ply')

STL mesh io plugin

('Recognized file extensions: ', '.STL, .stl')

Vista/Simbio triangle mesh input/output support

('Recognized file extensions: ', '.-, .V, .VMESH, .v, .vmesh')

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')

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

Gert Wollny

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