Mesh export in ITK-Snap

[Frank Lindseth]

Dear ITK-Snap developers,

Thank you for a great segmentation tool.
I think that ITK-Snap would be even greater with the possibility to
export the generated triangle meshes (.stl, .....).
(exporting the segmented data as an binary image that is imported
into an application that has mesh
generating/exporting functionality does not seem to give the
"quality" experienced inside ITK-Snap, several tool have been tried).
Looking thorough the mailing lists it seems that this feature have
been requested by others before.
What is the status regarding the possibility to export meshes in ITK-
Snap?

Any input would be greatly appreciated.

Thank you.

Frank

[Paul Yushkevich]

Hi Frank,

Thanks for bringing this up. The functionality you and others have requested is coming in the next release of SNAP, which will be announced on the 'itksnap-announce' mailing list.

Paul.

Penn Image Computing and Science Laboratory (PICSL)
Department of Radiology,
University of Pennsylvania

[MarkusK]

Very nice! Any hints of which file format you are going to use?

On 8 Maj, 15:33, "Paul Yushkevich" <pyushkev...@gmail.com> wrote:
> Hi Frank,
>
> Thanks for bringing this up. The functionality you and others have requested
> is coming in the next release of SNAP, which will be announced on the
> 'itksnap-announce' mailing list.
>
> Paul.
>

> On 5/8/07, Frank Lindseth <Frank.Linds...@sintef.no> wrote:
>
>
>
>
>
> > Dear ITK-Snap developers,
>
> > Thank you for a great segmentation tool.
> > I think that ITK-Snap would be even greater with the possibility to
> > export the generated triangle meshes (.stl, .....).
> > (exporting the segmented data as an binary image that is imported
> > into an application that has mesh
> > generating/exporting functionality does not seem to give the
> > "quality" experienced inside ITK-Snap, several tool have been tried).
> > Looking thorough the mailing lists it seems that this feature have
> > been requested by others before.
> > What is the status regarding the possibility to export meshes in ITK-
> > Snap?
>
> > Any input would be greatly appreciated.
>
> > Thank you.
>
> > Frank
>

> --
> Paul A. Yushkevich, Ph.D.
> Research Assistant Professor

[Paul Yushkevich]

Mesh export is already in the sourceforge CVS repository, so feel free to try it out! There is support for VTK mesh format, as well as STL and BYU formats. For other formats, you can use Paraview to convert.

paul.

[MarkusK]

Sweet! Unfortunately, I'm not really familiar with cvs and cmake,
where can I find build instructions for Windows? Or, I would be happy
to download a nightly binary build if there exists one?

Regards,

Markus

On 1 Juni, 16:50, "Paul Yushkevich" <pyushkev...@gmail.com> wrote:
> Mesh export is already in the sourceforge CVS repository, so feel free to
> try it out! There is support for VTK mesh format, as well as STL and BYU
> formats. For other formats, you can use Paraview to convert.
>
> paul.
>

[MarkusK]

I've tested the latest build, but STL mesh export only produces a file
with the following two lines:

solid ascii
endsolid

Nothing else. The VTK export seems to work ok, though. The BYU export
does not even produce a file. Anybody else getting the same problems?

Regards,

Markus

[Paul Yushkevich]

Hi Markus,

I am aware of this bug. For now please use VTK mesh export. I believe you can use ParaView to convert to a number of formats.

Paul.

[MarkusK]

If anyone is interested, I've written VTK import scripts for Blender3d
and 3dsMax:

http://kawzon.se/import_vtk.py (Blender: Place in .blender/scripts
folder)

or

http://kawzon.se/Import_VTK_mesh.ms (3dsMax: Run from anywhere)

Regards,

Markus

On 7 Juni, 15:55, "Paul Yushkevich" <pyushkev...@gmail.com> wrote:
> Hi Markus,
>
> I am aware of this bug. For now please use VTK mesh export. I believe you
> can use ParaView to convert to a number of formats.
>
> Paul.
>

[Amir Hossein Saveh]

Hi

 

you can segment and export in a parasolid Binary format.

 

From: itksna...@googlegroups.com [mailto:itksna...@googlegroups.com] On Behalf Of Vinay Mamidala
Sent: Tuesday, March 19, 2013 3:03 PM
To: itksna...@googlegroups.com
Subject: [itksnap-users:1035] Re: Mesh export in ITK-Snap

 

Hello everyone. Thanks for the wonderful ITKSNAP tool. Im relatively new to this field. Im working on the construction and analysis of a 3d model of Human spinal column regions. I have the mri data which im able to segment in SNAP. I would further want to import the segmented part to ANSYS for analysis. I m facing a problem with the import formats. Any help/suggestion is greatly appreciated. Thank you .

Mechanical Engineering Student

NIT Trichy

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[Sebastián Vanrell]

Hi Vinay,

ANSYS is a software based in fem, isn't it? What kind of analysis do you want it to do?

The way that the information is defined is a non trivial issue, regarding to import it on ANSYS. What kind of information can import it? Or, what kind of format it can handle?

From my experience working with this kind of "translation" you have two alternatives:

1 - You can export the segmented object (or there are objects?) in STL format. This format defines every object with a mesh of triangles. Then you can try to import the segmented object in your software. (not always work)

2 - You can export the segmented object in STL format. Then, using a soft like solidworks, geomagic or rapidform, you can try to make an inverse engineering  aproach to get a well defined object (with nurbs surfaces) in a way ANSYS can interpret it.

Hope that help (if not, ask again)

Sebastián

2013/3/19 Vinay Mamidala <mvkum...@gmail.com>

[Vinay Mamidala]

First of all, Thank you Mr.Sebastian Vanrell and Aamir Hossein for
your early replies.

Yes, ANSYS is a software based in FEM. I actually want to do a static
structural fem analysis on the lumbar unit of the human spine. The
following formats of geometric input are supported for import into
ANSYS: IGES, STEP, CATIA, SAT.
I tried importing both stl and vtk formats of the segment bone into
ANSYS and it didnt work. Will try asap to import them in Solidworks.
Thanks for the help again .. !!
Also, kindly let me know if there are any opensource fea packages or
3d modelling packages which can work on the output of ITKSNAP..
Thanks alot again.. Im much obliged ..
Vinay.

[Dianne Patterson]

Open source 3d modeling software: 

check out meshlab: http://meshlab.sourceforge.net/

and netfabb: http://www.netfabb.com/basic.php

I was able to export an stl file from itk-snap, 

open and view the stl mask of the brain in netfabb and alter its size.

meshlab could also open the stl file, and it provides some tools for cleaning up the image.

-Dianne

Dianne Patterson, Ph.D.

Research Scientist
d...@email.arizona.edu
University of Arizona
Speech and Hearing Science 314

1131 E 2nd Street, Building #71
(Just East of Harvill)

621-9877

==============

If you write me (expecting an answer) and I don't respond within a

day, then the email may have been lost.
You can always write me at dian...@gmail.com
==============

[Eduardo Soudah]

Hi,

You can use GiD to read STL and VTK format and then generate a volumetric
mesh for fem simulation.
I am use to do it. I use ITKSNAP for the segmentation part, GiD to generate
a Volume mesh and after fem.

Regards,
Eduardo Soudah

-----Mensaje original-----
De: itksna...@googlegroups.com [mailto:itksna...@googlegroups.com]
En nombre de Vinay Mamidala
Enviado el: martes, 19 de marzo de 2013 20:03
Para: itksna...@googlegroups.com
Asunto: Re: [itksnap-users:1039] Re: Mesh export in ITK-Snap

[Dianne Patterson]

What is GiD?

-Thanks,

Dianne

[Eduardo Soudah]

You can find more information at:

 

http://gid.cimne.upc.es/

 

Regards,

Edu

[Vinay Mamidala]

Hi Aamir Hossein Saveh,

Can you explain how you exported in parasolid binary format... i could export the mesh only as VTK, STL or BYU formats. and also let me know if Convert3D tool can be used to read the above formats and convert to iges or stp .. Thanks in advance. 

[Amir Hossein Saveh]

Can I ask what project do you have ?

 

Best.

 

Dr. Saveh.

On Wed, 05/15/2013 10:42 PM, Mahsa Shk <mshak...@gmail.com> wrote:

Hello everyone,

 I need to export mesh as BYU format, so I used Segmentation>Export as surface mesh and saved my file in BYU format, but it adds the ".g" extention to my file. I mean the resulting file would be "filename.g" instead of "filename.byu" 

Am I doing something wrong?

Thanks for your help,

Mahsa

--

[M.Shakeri]

I am working on a Hippocampus segmentation method. I need to extract this structure and do a comparison with manual segmentation.

For exporting Hippocampus I am using itksnap and for the comparison I am going to use Meshvalmet.

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