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Name:Andrea Ferrero
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Institution:University of California, Davis
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Hi Qianqian,

thanks for the heads up. My problem is how to export those surfaces, after I computed them, into a format readable by a 3D design software like AutoDesk. I computed the surfaces and they look like what I wanted, but now I need to export it from Matlaband this is the step I am still missing. I couldn't find any reference in the documentation that addressed it, though I believe it must be trivial.

Thanks for the quick reply.

Andrea


Time:: Wed Oct 20 2010 20:50:58 GMT-0700 (PST)</timestamp>

Name:Qianqian Fang
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hi Andrea

yes, iso2mesh does produce surfaces. Please check out the Doc/Workflow page to find out the general workflow. Typically, you should use v2s to extract surfaces from a volumetric image. Sometimes, you can also use v2m to produce surfaces too. Please also read my slides to find out other utilities, including surface smoothing, upsampling/downsampling etc.

Qianqian


Time:: Mon Oct 18 2010 21:45:55 GMT-0400 (EST)</timestamp>

Name:Andrea Ferrero
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Institution:University of California, Davis
Message:
HI guys,

I just discovered iso2mesh today and it looks a great tool for a research project I am working on, where I need to take a 3D CT image and convert it into a solid mold with AutoDesk. It is not clear to me though how I save the mesh after I run the vol2mesh script on my 3D image data. I am interested into the surface only of my object, to create a mold that is empty inside and full outside. Do I save the face variable? if so how?

Thank you very much for the attention,

Andrea


Time:: Mon Oct 18 2010 17:24:37 GMT-0700 (PST)</timestamp>

Name:Qianqian Fang
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Institution:
Message:
hi Sanket

For the maxvol parameter, please see this page for details. It simply sets the maximum volume of all the elements. All of your input surface nodes will be preserved in the final volumetric mesh. It will add new nodes on the surface or volume to ensure the quality constraint.

Qianqian


Time:: Tue Jul 27 2010 18:42:02 GMT-0400 (EST)</timestamp>

Name:Sanket Jain
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Institution:
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Thank you Dr. Fang for your reply. On looking again, I realised the fresurfer surface mesh are pretty dense. I might end up using only 30-40% of the total mesh points as you suggested. Instead of using the meshresample, I tried the surf2mesh command with keepratio of 0.3/0.4 and the mesh was successfully created. I believe this function calls the meshresample function. But still, I had one question about surf2mesh function.

As I decreased the maxvol parameter, I got mesh with smaller elements. Not really surprised with that but, is there any units associated with that parameter? Is there any way to calculate the optimum maxvol based on the size of the geometry to be meshed?

Also, I will revisit meshing after I complete my current projects. I was looking for a meshing tools for future use and I think I found one :) Thank You for all your inputs.


Time:: Tue Jul 27 2010 15:47:59 GMT-0500 (CST)</timestamp>

Name:Qianqian Fang
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Message:
hi Sanket

do a "help remeshsurf" see the possible options. For simplicity, you can set opt as a scalar, which will be the desired maximum element diameter of the resulting mesh; in that case, the grid-size will be set to opt/4 automatically.

Please do a meshresample first to reduce the mesh density and then do a remeshsurf; this can save a lot of memory for you.

By the way, do you have to keep the original surface more than 50%? FreeSurfer produces very dense surface mesh, for me, I usually keep only 5~10% of the elements. If you have a very dense surface mesh, tetgen will take a long time to make tetrahedral mesh.

You can also try MeshLab to manually select and correct these bad elements in the original mesh, but generally speaking, this is pretty difficult. I've chatted with the FreeSurfer developers in our building, but at this point, there is nothing we can do about it.


Time:: Tue Jul 27 2010 13:03:21 GMT-0400 (EST)</timestamp>

Name:Sanket Jain
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Institution:
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What is the opt structure in remeshsurf function? I am not sure what the values for its opt.gridsize and others would be in my case. Is there any way I use the same gridsize and elemsize as my original surface mesh? or Does it nullify the whole objective of performing the resurfmehs.
Time:: Tue Jul 27 2010 10:45:21 GMT-0500 (Central Daylight Time)</timestamp>

Name:FangQ
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Institution:
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hi Sanket

this the most frequently encountered error with iso2mesh (or tetgen). It is very likely that your original mesh contains self-intersecting elements, and mesh simplification (decimation) usually won't fix it (If you are using FreeSurfer, the pial surface it produced usually have this type of issue).

There is a work-around, but you might have to play with the options to get it to work. Please look into the sample script sample/demo_remesh_surface.m. It calls a function named remeshsurf in the toolbox. What this function does is to first convert a closed surface into a binary image, and then re-extract a surface from the volume, and the extraction script guarantees that the produced mesh is self-intersection free.

If your mesh is complex, you may have to use a large volume to re-voxelize your surface. Give it a try and let me know if it works.

Qianqian


Time:: Mon Jul 26 2010 19:54:04 GMT-0400 (EST)</timestamp>

Name:Sanket Jain
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Institution:Medical College of Wisconsin
Message:
I used a cortical surface and created a volumetric mesh using the surf2mesh function. If I use the keepratio value <=0.5; the mesher works really well. But if I use the keepratio value>0.5, I get the following message.

Error: Invalid PLC.

  Two subfaces (17561, 18027, 83603) and (83474, 83572, 18027) 
  are found intersecting each other. 
  Hint:  Use -d switch to find all intersecting facets. 
volume mesh generation is complete

I am not sure the reason for this message and also if there is any potential work around it.

Thanks, Sanket


Time:: Mon Jul 26 2010 16:05:00 GMT-0500 (Central Daylight Time)</timestamp>

Name:Qianqian Fang
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Name:Edouard Oudet
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