[COMSOL_Users] Complex geometries in COMSOL

[downy_squirrel]

Dear Colleagues,

could you be so kind to help me with the following issue, please?

I am trying to develop a quite simple, but realistic human head 3D model based on MR and CT images and use it as geometry in COMSOL Multiphysics.

My workflow is following: MRI/CT data --> segmentation through Simpleware/Amira/SPM --> STL-file --> COMSOL.

I have googled a lot, tried different settings while exporting to STL and then another different settings while importing in COMSOL, different settings of mesh -- everything is useless, still I have such issues as:
1.) Errors in rendering the geometry.
2.) Errors while meshing. Here [1] is an example of used model of white matter in STL format -- it seems to be good (MeshLab), what is wrong then, why I cannot create the mesh?
3.) Troubles segmenting the CSF.
4.) My current experiments involving only one tissue at a time, but which would be the best way to create a geometry consisting of all the subdomains at one time? I mean skin, skull, brain (or WM+GM) and CSF together as different subdomains in geometry.

Please, advise me in which direction I have to start digging. Could you share with me some information regarding which method, technology and software to do such a thing described above which you are using in your work?

I would very appreciate any of your help, thank you in advance.

Have a nice day.

With best wishes,
Dmitry

[1] http://www.rapidshare.com/files/243014428/wm.stl

P. S. Is it the only place for COMSOL users, whom/where is it possible to ask elsewhere?

[Daniel Smith]

Simpleware should be able to output a COMSOL mesh file, either .mphtxt or
.mphbin. You can then import the mesh into COMSOL which should work
perfectly (File>Import mesh). You can't make changes to the geometry once it
is in COMSOL. STL is not a good CAD or mesh file sharing format at all. You
could also get a human head object by requesting this model from your COMSOL
sales representitive:

http://www.comsol.com/showroom/gallery/2190/

/ Dan

Post by downy_squirrel
Dear Colleagues,
could you be so kind to help me with the following issue, please?
I am trying to develop a quite simple, but realistic human head 3D model
based on MR and CT images and use it as geometry in COMSOL Multiphysics.
My workflow is following: MRI/CT data --> segmentation through
Simpleware/Amira/SPM --> STL-file --> COMSOL.
I have googled a lot, tried different settings while exporting to STL and
then another different settings while importing in COMSOL, different
1.) Errors in rendering the geometry.
2.) Errors while meshing. Here [1] is an example of used model of white
matter in STL format -- it seems to be good (MeshLab), what is wrong then,
why I cannot create the mesh?
3.) Troubles segmenting the CSF.
4.) My current experiments involving only one tissue at a time, but which
would be the best way to create a geometry consisting of all the subdomains
at one time? I mean skin, skull, brain (or WM+GM) and CSF together as
different subdomains in geometry.
Please, advise me in which direction I have to start digging. Could you
share with me some information regarding which method, technology and
software to do such a thing described above which you are using in your
work?
I would very appreciate any of your help, thank you in advance.
Have a nice day.
With best wishes,
Dmitry
[1] http://www.rapidshare.com/files/243014428/wm.stl
P. S. Is it the only place for COMSOL users, whom/where is it possible to ask elsewhere?

[downy_squirrel]

Dear Daniel,

thank you for your advises!

So you are telling that I have to import in COMSOL not geometries, but meshes? Then my work should be also connected with the meshes only and not the geometries? But in that case how it is possible to create a different tissue, i. e. subdomains with different electromagnetic properties?

By the way, what is wrong with the STL format?

Once again, thank you very much, have a nice day.

Bye,
Dmitry

[amralabed]

ahhh the pain of working with complex geometries in Comsol....

I am working on a very similar problem to yours - but using heart. As Daniel suggested it is much easier to import the mesh into Comsol and then convert it back to a draw object in COmsol.

Post by downy_squirrel
1.) Errors in rendering the geometry.

This is realllly annoying and time-consuming to resolve. You have to play around with the import options in Comsol. In particular
-max angle between boundary elements (70 is a good start)
-max angle between neighbouring boundary elements (5-10)
-and remove small faces 0.01-0.04
by trying out different combinations of these , eventually, you will be able to import the mesh and create a draw object without any rendereing issues.

Post by downy_squirrel
4.) My current experiments involving only one tissue at a time,
but which would be the best way to create a geometry consisting of >> all the subdomains at one time?

Simpleware allows you to simultaneously mesh a number of masks at the same time. You can then import the mesh, made up of the differnt tissue masks, into comsol. If import is successful Comsol will treat each mask as a seperate subdomain. Because Simpleware takes care of contacts between different masks I found this a much better approach than importing each mask individually into comsol - sometimes u'll have gaps between subdomains which are difficult to find.

final tip.. make sure your segmented masks are at least 2 voxels wide in any direction (x,y,z,oblique). this helps reeduce the rendering errors u get in Comsol.

[downy_squirrel]

Dear Sir or Madam,

I thank you for your help and your wish to share you knowledge with a stranger like me! :)

Hm, I like COMSOL, I have had a look at ANSYS and Maxwell but did not like it... Why you have chosen COMSOL for your work if it has issues while working with complex geometries and is there are better software? Anyway, actually I would like to find some elegant solution to such a problem and stay with COMSOL...

Okey, I will try to import layered mesh into COMSOL instead of geometry. And thanks for advice about "max angle between..." -- I have never thought it would play such a big role. By the way maybe it would be also helpful to use filters or something like it in ScanIP in order to get more smooth segmented data for better meshing and import/rendering, how do you think?

Good luck to your research, have a nice day.

Bye,
Dmitry