table of contents
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 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. 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 WollnyCOPYRIGHT¶
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'.v2.4.3 | USER COMMANDS |