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[SCIRUN-USERS] Fwd: Re: Biomesh3d client

Chronological Thread 
  • From: Elizabeth Jurrus <>
  • To:, "" <>, Sergei Turovets <>,, Moritz Dannhauer <>, Dana Brooks <>, Rob MacLeod <>
  • Subject: [SCIRUN-USERS] Fwd: Re: Biomesh3d client
  • Date: Thu, 17 Mar 2016 15:07:24 -0600

Hi everyone,

I'm adding cleaver to this mailing list to help with the windows crash in 3, below, and the sizing field parameters.

And I'm adding the scirun-users mailing list to help with sizing fields in SCIRun.

- liz

-------- Forwarded Message -------- Subject: Re: Biomesh3d client Date: Thu, 17 Mar 2016 15:44:05 -0300 From: Mariano Fernandez <> To: Moritz Dannhauer <> CC: Sergei Turovets <>, Dana Brooks <>, Rob MacLeod <>, Elizabeth Jurrus <>

Dear Moritz and Rob,

Thanks for your help. I found your tutorial "Meshing methods and instructions" were instructive.
This what I've tried until now (also for your records / debug):

1) The tetgen implementation in SCIRun 5 provided by Moriz runs with no errors. The resulting surfaces of the mesh are rather "voxelized" (not smooth, see attached). I tried to include smoothing (as described in the tutorial file in point 2.5) but the tetgen fails because of self intersecting facets, which is expected as described in your help ( That's a known limitation of tetgen.

2) Biomesh alone (third method) is too slow (still running).

3) Cleaver + biomesh seems to be the best world (method number 4) in terms of quality elements, smooth surfaces and speed. I created the Sizing fileds using biomesh3d with the -s1:4 switch (as described in the tutorial). However, I couldn't make cleaver run in windows: in the verbose mode, and after "Creating Octree Mesh ..." the program terminates with no reason and no output.
So, I installed and compiled cleaver in a Virtual Machine with ubuntu 64 bits. I generated the sizing field with the Cleaver-gui and exported it as nrrd file. Then, in SCIRun I changed it by adding 1, 2, 3, 4, 5, and 10 units (as described in point 4.7.c). It works with plus3, plus4, plus5, and plus10. When adding one or 2, or even using the original unmodified Volume-sizing-field, cleaver crashes (just a "Killed" mesage on prompt) I assume it is because of memory requirements.

So, a couple of questions:

a) In point 4.4.b it says that "more info available if needed" in order to combine sizing fields. I would like to know how to combine the individual tissue sizing fields in SciRun to control them independently. So far, I've been only changing the full already combined and cleaver generated "volume sizing field".

b) The gray matter surfaces are still not as smooth as I would like (see "dents" in attached figures) and there is not much variation between "volume sizing field +5" and "volume sizing field +3" (see attached). Are these two effects expected? With lower sizing fields, is it expected that the GM surface gets smoother? Or is it already determined by the segmentation?

Thanks again,

Best regards,


2016-03-14 13:23 GMT-03:00 Moritz Dannhauer <>:
Hi Mariano, I will let you know once they bug-fixed it.
Find attached also some responses from another SCI user regarding your cleaver2 error messages and a short tutorial.


On Mar 14, 2016, at 9:40 AM, Mariano Fernandez wrote:

> Thanks Moritz,
> Actually, tetgen is what I use (within the iso2mesh Matlab toolbox), but I will try your SCIRun 5 implementation. Please, let me know when you consider Cleaver 2 is ready.
> Bests,
> Mariano.

> It seems like this user is thinking that a coarse mesh would be more likely to complete.  That doesn't seem to be the case given the "default binary_dir = Model configuration file Files\SCIRun does not exist." line in his error message.  Besides, his computer would crash long (from memory hogging) before a week was up if Cleaver was working.
> In any case, here's a write-up of meshing steps that can be used, though I admit…I don't know much about using it on a windows machine.  This should still be up to date.


> Also…does he have the Cleaver documentation?  That would be able to explain the flags that he was asking about, but he should be aware that you can't define how many elements the mesher produces.  You have to set scaling parameters such that they create a coarser mesh, but you don't have direct control over the total number of elements, or the dimensions of them.

Attachment: Plus5.png
Description: PNG image

Attachment: tetgen_in_SCIRun.png
Description: PNG image

Attachment: Plus3.png
Description: PNG image

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