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Re: [Cleaver] element reordering


Chronological Thread 
  • From: Jess <jess@sci.utah.edu>
  • To: Petar Petrov <pip010@gmail.com>
  • Cc: cleaver@sci.utah.edu
  • Subject: Re: [Cleaver] element reordering
  • Date: Mon, 2 Oct 2017 16:24:59 -0600
Changing the resolution of the segmentation requires more than changing the header.  there is a resample tool in Seg3D that will do it.  Increasing the resolution this way will also use more memory, but I’m not sure how it compares to changing the cleaver parameters.  

The RAM usage is unfortunately large, but there isn’t much that can be done to reduce it if you have thin regions.  If there are only two tissue interfaces (concentric) each layer can be meshed separately and combined in SCIRun.  

cheers,
Jess






On Oct 2, 2017, at 12:44 PM, Petar Petrov <pip010@gmail.com> wrote:

Hi Jess,

Do you mean header only or actually resize the image?
The second option I think is out of question for Cleaver2, cause it is quite mem hungry ( 32-64GB) :)

Cheers,
Petar

On Mon, Oct 2, 2017 at 7:21 PM, Jess <jess@sci.utah.edu> wrote:
Hi Petar,

It looks like you are trying to mesh a thin region of tissue. These kind of regions always cause trouble for meshing software.  You can improve the results by increasing the resolution of the background mesh.  You can try changing the scaling factor to do this, or you can resample the segmentation in Seg3D.

cheers,
Jess




> On Oct 2, 2017, at 3:02 AM, Petar Petrov <pip010@gmail.com> wrote:
>
>
> Hello all,
>
> when I generate a mesh using cleaver2 I get alot of errors of wrong tet element orientation. Those get fixed by cleaver when you pass the -j flag
>
> The mesh is generated and I can successfully load in scirun, however when using the getFieldBoundary/GetDomainBoundary the following surface mesh is produced with plenty of holes :(
>
> Any idea how I can fix that?
>
> <MyImage.jpg>




--
All the best,
Petar Petrov
http://ppetrov.net


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