If you are using Avizo, volume mesh can be generated with the "generate tetragrid" function. However, you have to have surfacic meshes that are closed and have no intersections.

You can read the Avizo's manual and try the example for more informations: all steps are described.

For information, Abaqus INP files can be directly generated from some versions of Avizo.

"How can I convert directly from image (tiff/jpeg) into 3D mesh" : That is not possible yet.

You have to :

-binarize your images

-generate surfacic meshes

-simplify (reduce the number of element) and improve these meshes

-generate the volume mesh with tetrahedra

I'm currently working on the same problem.

I was (partly) successful for a moderately complex part using

ImageJ/Fiji to binarize the image stack

3Dslicer to create an stl

Meshlab to reduce the number of triangles (use quadratic edge decimation)

Meshmixer to repair the part (necessary because meshlab may create holes)

Salome or Freecad to convert to step/iges (you should not have more than about 20000 triangles, otehrwise it will take very long to do this)

Problem in my case is that Abaqus can not mesh the resulting IGES because of too badly formed triangles; an alternative might be using netgen.

can you uppload a Picture of the geometry which you want to mesh in 3D? 

i have some experince in working with Delamination shape from D-scan. Maybe i can give an advice.

You could also try iso2mesh, which is a free plugin for matlab/octave.

It depends of the part of the image you want. You can also try ITKsnap http://www.itksnap.org/pmwiki/pmwiki.php.

It alows you to use 4 modes of segmentation and th chance to export it as a mesh file.

http://www.itksnap.org/pmwiki/pmwiki.php?n=Documentation.TutorialSectionAutoSegmentation

Martin Baeker: I also tried what you did previously but to no avail. As for meshlab, it crashed like a lot during processing and the result was not satisfactory. I try not to use stl>iges method since lots of problems and need to modified manually later on. I just realized that in Abaqus 6.14, there's a plug-in to import/export stl into/from Abaqus but I don't explore it much since I just upgraded from 6.9 a couple of weeks ago.

Tamar Qaimari: Below is the sample of the geometry that I want to mesh in 3D (natural fibre).

Raúl Rodríguez-Cruces: I looked in their website so correct me if I'm wrong but seems that it only do surface meshing?

Hi Ahmad - you may want to take a look at my company Simpleware's software for these type of problems - please see http://simpleware.com/ for more information, where you can get a free trial.

Philippe

If you are using Avizo, volume mesh can be generated with the "generate tetragrid" function. However, you have to have surfacic meshes that are closed and have no intersections.

You can read the Avizo's manual and try the example for more informations: all steps are described.

For information, Abaqus INP files can be directly generated from some versions of Avizo.

"How can I convert directly from image (tiff/jpeg) into 3D mesh" : That is not possible yet.

You have to :

-binarize your images

-generate surfacic meshes

-simplify (reduce the number of element) and improve these meshes

-generate the volume mesh with tetrahedra

I faced the same problem that is happened with Ahmad Tarmezee. for exmaple I have some spherse and I treid to generate a volume mesh in AVIZO but after the segmentation I could not find a way to do it. can anyone kindly explain how to use Avizo to get a volume mesh?

@Ibrahim, in Avizo under Help>User Guide, look up the following tutorials. It is two steps:

Surface Reconstruction from 3D Images

Creating a Tetrahedral Grid from a Triangular Surface

Hope this helps.

Hello,

You can generate a mesh in AVIZO and save it as .inp. But the way AVIZO writes the set of nodes and elements is not readable by ABAQUS. So you need to open your .inp file, generated from AVIZO and rewrite the nodes and elements in the form that is readable by ABAQUS. Dont forget to separate your set of elements using as a header for XXX type of elements (depends on what you choose):

*Element, type=XXX, elset=Elements

Otherwise you can save your surface aa an .obj or .stl file and move to MeshLab for generating your mesh, and then using AUTOCAD 3D generate an .iges file which can be imported to ABAQUS as a part. Hope this helps.

One way of creating 3D volume mesh from 3D not clean surface mesh obtained from Avizo is-

first export not cleaned surface file in .stl format from Avizo.

Now import it in meshlab and apply filters to remove open surfaces and other filters if desired (like smoothing filter and re meshing filters). All clean up process must be done here using various filters. then export this surface file again in .stl format

Now import it in Gmsh and use these steps to convert 3D surface geometry to 3D volume geometry-

. File -> Merge -> “filename.stl”

. Geometry -> Elementary entities -> Add -> New -> Volume, click on the surface to build the volume

. Mesh -> 3D

Thank you for the top'c

I recently found the software graphite which internally uses tetgen to mesh stls but which is rather good in repairing the stl if tetgen finds problems. Did not work always, but in many cases.

I use GeoDict from Math2Market to solve the same problem. They have dedicated modules to import CT images and export them for analysis in ABAQUS. It is a commercial software but they do have academic versions for research purposes.

I am a contributor of Horos and HorliX (Horos-based DICOM viewer).

We have developed HorliX as a kind of a DICOM-based simulation platform.

In the simulation process you could get 3D-meshed dataset. You should modify them as you want.

If you are interested in electronical treatment, you should read this case report: Article Long Brief Pulse Method for Pulse-wave modified Electroconvu...

Although we didn't describe the reason why the 'long' brief pulse was used in the report, we determined it by the result of the simulation in fact.

It's a computer-assisted-treatment.

Hi Ahmad, hope you 'd already found a solution, though in any case that someone else is facing the same problem, I have a procedure to propose:

If you managed to convert ct scan images to *.stl files (with ImagJ, avizo, 3d slicer, Invesalious or whatevr). {edited 4 months after initial post--- software Seg3d from university of UTAH seems to create easily ISOsurfaces that you can later export as *.vtk ascii (*.pts, *val or *.fac etc) ascii binary *.stl, or ascii *.STL this last one works best as import mesh file for Rhino }.

then you can use Rhinoceros (RHINO) software and a dedicated plugin from ITASCA called GRINDLE, that converts 3d Mesh (outer cell mesh ) to Volume mesh compatible to ITasca software (eg FLAC3D and 3DEC) but also ANSYS and ABAQUS. Grindle has great tools for Re-Meshing prior to production of Volume mesh (optimization of mesh surface, mesh dimensions, aspect ratio and many other..).

Ofcourse Rhino and Grindle are comercial products that costs some money , though it will be easy to find someone in this community (Research gate) to perform this task for you in case you/your institution faces fund shortages! if you get what i mean! ;-)

HorliX ver1.0.3 is now available at MacAppStore:

https://itunes.apple.com/us/app/horlix/id1389724182

contact my collegue Jan-Marcel Hausherr [email protected] at the Fraunhofer HTL ww.htl.fraunhofer.de ... perhaps he can help you.

I explained my methodology in more detail: https://github.com/horosproject/horos/issues/385#issuecomment-418318093

For Avizo/Amira there exists the extension XWind, which allows the creation of tetrahedra meshes directly from the segmented data.

So you just import your voxel data-set, segment your data (using thresholding, watershed, or whatever), and mesh the resulting label-field.

You can control tetrahedra properties (size, facet angles, ...), also separately for the different materials, and at the material boundaries the tetrahedra will match perfectly.

There is no need to take the tedious way via first creating a surface and then meshing the enclosed volume.

Export is possible to the formats of most often used FE programs (e.g. Abaqus, Ansys, COMSOL, ...)

Hi, Andreas.

You recommend some proprietary FE programs.

I think we need to create a brand-new Finite Element Equation when the model to be analyzed does NOT obey ordinary equations, for example: ∇^2Φ=0 .

These soft can analyze that kind of equations?

No answer?

I think that it is better to modify Open-Source FEM programs in this case.

By the way,

What is the best Open-Source FEM soft?

I have modified and used certain FEM soft with its source code so far.

But it is written in VisualBasic.

It is impossible to link it with HorliX on OS X or to embed it in HorliX directly.

I am not so familiar with FEM.

Please teach me the Open-Source FEM soft you recommend.

If you still have the problem, you may try to finance the Avizo extension XWind or test it as a trial version first. I know that my colleagues were successful using the generated tetrahed meshes for further analysis. If in case you got other financial support by now you may try GeoDict (which was already recommended earlier) which i can highly recommened as it is a perfect tool for analyzing materials of all kinds.

Dear friend it is so very easy to convert CT scan images in to volume mesh. Only you need to use Mimics software. https://www.materialise.com/en/medical/mimics-innovation-suite

@ Ankit Nayak, the mesh quality of mimics is not very well.

Have you found the solution to this problem?

@Yu Guoji yes

@Ankit Nayak Can you share the steps? I have not find the method, in addition, Abaqus can import stl format file, and it can generate tetrahedral mesh.

Yu Guoji Please check your message box