---
name: "mia-3disosurface-from-volume"
section: "1"
platform: "linux"
package: "mia-tools"
version: "2.4.7-11+b1"
release: "Debian 12 (Bookworm)"
platforms: ["linux"]
url: "https://new.carta.tech/mia-3disosurface-from-volume"
---

# mia-3disosurface-from-volume(1)

Extract an ist-surface froma a 3D image.

## 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=(required, input); io

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

- \-o --out-file=(required, output); 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'.