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Re: [Seg3D] Seg3d


Chronological Thread 
  • From: Jess Tate <jess@sci.utah.edu>
  • To: Matthew Muntean <matthew@muntean.com>
  • Cc: Gregory Jones <greg@sci.utah.edu>, Elizaveta.Chabanova@regionh.dk, Corinne Garcia <cgarcia@sci.utah.edu>, SCI Webmaster <webmaster@sci.utah.edu>, seg3d@sci.utah.edu
  • Subject: Re: [Seg3D] Seg3d
  • Date: Fri, 14 Oct 2016 21:41:23 -0600
Hi Matthew,

Seg3D is meant as a segmentation tool, and as such only allows for image data manipulation and segmentation.  Seg3D does output isosurfaces of the segmentation volumes, so there is one thing you can try in Seg3D to generate a triangle surface of lower resolution.  The resolution of the isosurface is dependent on the resolution of the segmentation, therefore, you can use the resample tool to downsample the image, then generate the isosurface and save it out.  One of the advantages of this method is that it allows for processing of the segmentation in the reduced resolution,  which can allow for greater control of the final mesh than sampling the polygon mesh.  

We have other software specifically for mesh generation from segmentation: Cleaver and Biomesh3D.  Both of these have control of the final resolution of the mesh, though cleaver has more transparent controls.  These are also both volume mesh generators, which you can use to get a surface mesh using SCIRun.  

SCIRun is a modular problem solving environment that has a number of mesh manipulation options.  mesh decimation is a little tricky in general, and takes a little work in SCIRun, but it is flexible enough that it can be done.  

Another software that you can take a look at is Meshlab.  I know it has mesh decimation tools that you can use on the isosurface generated from Seg3D.  Preview is another software that has similar tools that may help you.  

cheers,
Jess






On Oct 14, 2016, at 5:50 PM, Matthew Muntean <matthew@muntean.com> wrote:

Hi, just jumping in here on a tangential note. I've used both Slicer and Seg3D for awhile, lately for 3d printing.

I have found Slicer has some very useable poly reduction tools - is there a recommended pipeline for polygon reduction from Seg3D, that generates watertight reduced models?

Thanks.

On 10/15/2016 4:17 AM, Jess Tate wrote:
Hi Elizaveta,

You can use Seg3D to segment the volume that you are interested in studying and find the volume of that segmentation.  Slicer probably allows for something similar. The segmentation process can be easy or challenging depending on the scan quality and type and your results specifications.  The volume calculation is quick after that.  Please see the seg3d tutorial for more information about segmentation (seg3d.org).  You can also use this email list (seg3d@sci.utah.edu) to ask questions.

cheers,
Jess


On Oct 14, 2016, at 5:35 AM, Gregory Jones <greg@sci.utah.edu> wrote:

Hello Elizaveta,

Your question is probably best answered by the group working on seg3d. Thus, I have copied the seg3d team with this email. If you don’t hear from them soon, please let me know.

Cheers,
Greg

Elizaveta Chabanova <Elizaveta.Chabanova@regionh.dk>

Affiliation: Copenhagen University Hospital Herlev, Department of Diagnostic Radiology X, Denmark 

Re Software: {Software:value}

Subject: Volume measurments

Message: Hi, I have to measure fat volumes based on MRI data. Is ti possible to measure the volumes from DICOM data using one of the SW - Seg3D or 3DSlicer ? 

Best regard

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