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Re: [SCIRUN-USERS] Biomesh3D resulting mesh shifted

Chronological Thread 
  • From: Hon Fai Choi <>
  • To: Brett Burton <>
  • Cc: Jess Tate <>,
  • Subject: Re: [SCIRUN-USERS] Biomesh3D resulting mesh shifted
  • Date: Fri, 30 May 2014 10:19:25 +0200

Hi Jess and Brett,

thank you very much for the suggestions. The shift that I have is
quite large, I have attached a picture as illustration. Could you also
tell me how I can read the .tf file? I tried to open it with Wordpad,
but it seems to be a binary file.

I have also an additional question regarding BioMesh3D. Is there a way
that I can put a threshold on the minimal size of the mesh elements? I
have followed the user documentation and the input parameter for the
element size seems to only limit the maximal size of the elements.

Hon Fai

On Thu, May 29, 2014 at 8:51 PM, Brett Burton <> wrote:
> 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
> Brett
> 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

Attachment: shifted_mesh.png
Description: PNG image

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