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Re: [SCIRUN-USERS] Biomesh3D resulting mesh shifted


Chronological Thread 
  • From: Jess Tate <jess@sci.utah.edu>
  • To: Hon Fai Choi <honfai.choi@gmail.com>
  • Cc: scirun-users@sci.utah.edu
  • Subject: Re: [SCIRUN-USERS] Biomesh3D resulting mesh shifted
  • Date: Thu, 29 May 2014 12:38:26 -0600
Hi,

BioMesh should transform the final mesh back into the original space. Look
for the particle-union.tets-labeled_transformed.fld file. If it is not
there, then the last step didn't finish. If the file is not there or is
still the wrong size or origin, you can fix it pretty easily in SCIRun. Load
in the mesh and original segmentation. extract the surface of one of the
regions in the segmentation (or all of them) with GetDomainBoundary. Then
use SplitFieldByConnectedRegion or SplitFieldByDomain to remove any excess
space around the tet mesh from BioMesh. Then use AlignMeshBoundingBox to
align the tet mesh to the segmentation surface. This module will also give
you the transformation used if need for other meshes.

cheers,
Jess




On May 29, 2014, at 2:55 AM, Hon Fai Choi wrote:

> Hi all,
>
> I have a question regarding Biomesh3D. I use Seg3D to create the
> segmentations and save them as .nrrd files as input to Biomesh3D. When
> I export the resulting mesh with SciRun as a .vtk file and compare it
> with the original image, then the mesh is not in the right location.
> It's somehow shifted relative to where it should be. Has anyone
> encountered the same problem and knows how to fix this?
>
> thanks,
> Hon Fai


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