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Re: [SCIRUN-USERS] Biomesh3D resulting mesh shifted

Chronological Thread 
  • From: Brett Burton <>
  • To: Jess Tate <>
  • Cc: Hon Fai Choi <>,
  • Subject: Re: [SCIRUN-USERS] Biomesh3D resulting mesh shifted
  • Date: Thu, 29 May 2014 12:51:00 -0600

Like Jess implied, Biomesh transforms the original segmentation into a
different coordinate space in order to generate the original mesh. during
this first transformation, it creates a transformation file
([FileName] It uses this transform to shift the heart
back, but as you may notice by the name of the .tf file, Biomesh also pads
your data. If you are finding that this shift is very slight, it is probably
due to the padding. Jess's approach will work, in both cases, to get you
aligned again.

Let us know if you have further questions


On May 29, 2014, at 12:38 PM, Jess Tate <> wrote:

> 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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