Nima,

Surfaces are generated, but BioMesh transforms the images into a different coordinate space during its initial stage.  It is not transformed back until the final stage.  So, pulling files like particle-union.ts.fld or the tissue1.tight.fld, which are surface meshes, will ultimately be in the wrong space, but (like Jess said) they can be transformed back in SCIRun.  

I have also altered the original python scripts to give the transformed "tight" files if you would like to have those files automatically generated.  I have not created the python scripts for the particle-union files, though it wouldn't take much time to do so if you need them.  I can check those changes in, or send you the scripts that you can use to replace your old python scripts.

Brett

On Jun 9, 2015, at 12:00 PM, Nima Maftoon <n_maftoon@yahoo.com> wrote:

Thanks Jess!

About Question #3: shell elements are essentially surface elements. I am wondering why this should be difficult? I thought in one of the intermediate stages surface elements are generated.

Nima

---

From: Jess Tate <jess@sci.utah.edu>
To:
Cc: scirun-users@sci.utah.edu; Nima_Maftoon@MEEI.HARVARD.EDU; n_maftoon@yahoo.com
Sent: Tuesday, June 9, 2015 1:52 PM
Subject: Re: [SCIRUN-USERS] Questions about BioMesh3D

Hi Nima,

here are some answers to your question:

1)  The output of BioMesh3D is a scirun field file (.fld)  This is the native format for SCIRun, with which Biomesh is distributed.  You can use SCIRun to convert the fld file into other formats.  vtk and stl formats are supported as are several others.  Please refer to the SCIRun website (scirun.org) and documentation for more information.  

2)  There are several intermediate steps that save out files.  These are left so that you can rerun BioMesh from later stages if desired.  Also, you can use them to take advantage of the interactive mode  and visualize the results of the various stages.  The surface file is saved out as particle-union.ts.fld.  You will need to transform it back into the original coordinate system (can be done is scirun).  You can also use SCIRun to extract the surfaces from the tet mesh.    

3) This is not supported.

4) You can set the max volume of the tet elements with the tetgen flags in the model_config.py file (see http://wias-berlin.de/software/tetgen/).  You can also play with the sizing field variables in the config file.  

Hope that helps,

Jess

On Jun 9, 2015, at 11:26 AM, Elizabeth Jurrus <liz@sci.utah.edu> wrote:

A few questions for the mailing list...
- liz

-------- Forwarded Message --------

Subject:	Questions about BioMesh3D
Date:	Tue, 9 Jun 2015 15:58:08 +0000
From:	Maftoon, Nima <Nima_Maftoon@MEEI.HARVARD.EDU>
To:	liz@sci.utah.edu <liz@sci.utah.edu>

I have few quick questions. I played with the Mickey example and I think I got the ideas to some degree. What I don't understand yet are the followings:

1) Is the final mesh file, the binary .fld file in the "junctions" directory? What kind of format does it have? Which software reads this mesh format? Is it possible to have the mesh in a more general format like .unv, vtk or even stl format to be more accessible? med is a good new format as well (http://www.salome-platform.org/user-section/about/med).

2) I see that some intermediate node, face, ele and pts files are generated. What are these? If I just need the surface mesh information which files can give me that? A user may prefer to generate my volume elements myself in another meshing software.

3) It is said that 3D tetrahedral elements are generated. Is it also possible to generate 3D shell or plate elements for thin structures like membranes?

4) Is it possible to control the element size in the mesher?

I really appreciate your answers to these questions.

Nima Maftoon, PhD

Massachusetts Eye and Ear Infirmary
Harvard Medical School
243 Charles St
Boston, MA 02114
617 981 2638