<div>Anja,</div>
<div> </div>
<div>there's also another tool you might want to have a look at for generating tetrahedral meshes. It's called "Voxelizer" by Dan Morris, you can get it here: <a href="http://techhouse.brown.edu/~dmorris/projects/voxelizer/">http://techhouse.brown.edu/~dmorris/projects/voxelizer/</a> </div>
<div> </div>
<div>I have used it in the past to generate volumetric meshes from a surface representation in a virtual surgical training simulator a while ago.</div>
<div> </div>
<div>Good luck with your work!</div>
<div> </div>
<div>Stefan<br><br></div>
<div class="gmail_quote">On Thu, Dec 3, 2009 at 12:45 PM, Anja Ende <span dir="ltr"><<a href="mailto:anja.ende@googlemail.com">anja.ende@googlemail.com</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">Thank you all for your reply. I will try the iso2Mesh tool and will<br>let the list know about my experience.<br>
<br>Cheers,<br>Anja<br><br>2009/12/3 Andriy Fedorov <<a href="mailto:fedorov@bwh.harvard.edu">fedorov@bwh.harvard.edu</a>>:<br>
<div>
<div></div>
<div class="h5">> Anja,<br>><br>> Here's a package that you might find helpful:<br>><br>> <a href="http://iso2mesh.sourceforge.net/" target="_blank">http://iso2mesh.sourceforge.net/</a><br>><br>> I personally never used it, but I did have good experience with Tetgen<br>
> and CGAL for the tasks similar to what you want to accomplish. From<br>> the first look, iso2mesh appears to be a wrapper around several lower<br>> level meshing tools (including Tetgen and some algorithms from CGAL).<br>
><br>> You can use CGAL+Tetgen directly to construct a tetrahedral mesh from<br>> segmentation, but this will require some time to understand formats,<br>> parameters, and write some extra code. It looks like iso2mesh does<br>
> this transparently from the user, but I have not tried it myself to<br>> confirm this.<br>><br>> If you do use this iso2mesh tool, please update the list with your experience.<br>><br>> Andriy Fedorov<br>
><br>><br>><br>><br>>> Date: Wed, 2 Dec 2009 18:46:25 -0500<br>>> From: Luis Ibanez <<a href="mailto:luis.ibanez@kitware.com">luis.ibanez@kitware.com</a>><br>>> Subject: Re: [Insight-users] Using the meshing classes in ITK<br>
>> To: Anja Ende <<a href="mailto:anja.ende@googlemail.com">anja.ende@googlemail.com</a>><br>>> Cc: <a href="mailto:insight-users@itk.org">insight-users@itk.org</a><br>>> Message-ID:<br>>> <<a href="mailto:f7abd23c0912021546y796561f2y93d4dedc095761af@mail.gmail.com">f7abd23c0912021546y796561f2y93d4dedc095761af@mail.gmail.com</a>><br>
>> Content-Type: text/plain; charset=ISO-8859-1<br>>><br>>> Hi Anja,<br>>><br>>> Welcome to ITK !<br>>><br>>> Your question is a very interesting one.<br>>><br>
>><br>>> And to put it shortly:<br>>><br>>> It is one for which we don't have<br>>> a full answer involving only ITK methods.<br>>><br>>><br>>> There are two major pieces to what you are<br>
>> trying to do:<br>>><br>>> 1) Segmenting brain structures from MR and CT brain data.<br>>><br>>> 2) Generating tetrahedral meshes from the segmented<br>>> regions<br>>><br>
>><br>>><br>>> For (1), ITK provides a very rich set of methods.<br>>><br>>><br>>> For (2), you will have to use additional tools.<br>>><br>>><br>>> Regarding (1), the type of segmentation methods that you<br>
>> need to use is closely related to the specific brain structure<br>>> that you want to segment.<br>>><br>>> Popular methods are:<br>>><br>>> * Region growing<br>>> * Level Sets<br>
>> * Statistical Classification<br>>> * Atlas-based segmentation<br>>><br>>> and combinations of them, for example<br>>><br>>> * EM segmentation.<br>>><br>>> You will find an introduction to (some of the)<br>
>> segmentation methods in ITK, in the<br>>> Software Guide:<br>>><br>>> <a href="http://www.itk.org/ItkSoftwareGuide.pdf" target="_blank">http://www.itk.org/ItkSoftwareGuide.pdf</a><br>>><br>
>><br>>> You will also find a good deal of Brain segmentation<br>>> tools at NAMIC:<br>>> <a href="http://www.na-mic.org/Wiki/index.php/Main_Page" target="_blank">http://www.na-mic.org/Wiki/index.php/Main_Page</a><br>
>><br>>> and<br>>><br>>> NITRC:<br>>> <a href="http://www.nitrc.org/" target="_blank">http://www.nitrc.org/</a><br>>><br>>><br>>> Many of them, based on ITK.<br>>><br>
>><br>>><br>>> Regarding the tetrahedral mesh generation:<br>>> ITK itself does not provide that functionality.<br>>><br>>> The tool that you should try is:<br>>> <a href="http://www.ccad.uiowa.edu/mimx/IA-FEMesh/" target="_blank">http://www.ccad.uiowa.edu/mimx/IA-FEMesh/</a><br>
>><br>>> (which is also used by several groups at NAMIC):<br>>> <a href="http://www.na-mic.org/Wiki/index.php/NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development" target="_blank">http://www.na-mic.org/Wiki/index.php/NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development</a><br>
>><br>>><br>>> This tool needs as input a surface.<br>>> (a 2D manifold embedded in a 3D space)<br>>><br>>> You can generate such surface by taking the<br>>> segmentation (typically a binary image) of the<br>
>> brain structures of your interests and extracting<br>>> its Iso-surface with VTK (typically with the<br>>> vtkContourFilter) or with a ready-to-use tool<br>>> like ParaView <a href="http://www.paraview.org/" target="_blank">http://www.paraview.org</a>).<br>
>> (which is based on VTK).<br>>><br>>><br>>><br>>> Please take a look at these resources<br>>> and let us know if you have further<br>>> questions,<br>>><br>>><br>
>> Thanks<br>>><br>>><br>>> Luis<br>>><br>>><br>>><br>>> -------------------------------------------------------------------------------------<br>
>> On Wed, Dec 2, 2009 at 6:56 AM, Anja Ende <<a href="mailto:anja.ende@googlemail.com">anja.ende@googlemail.com</a>> wrote:<br>>>> Hello everyone,<br>>>><br>>>> This is more of a general question. I would like to know more about<br>
>>> generating meshes from MR and CT data. So, I have a brain image and I<br>>>> would like to generate a tetrahedral based mesh from it and then use<br>>>> it further for some FEM processing. I am a newbie to this field and<br>
>>> would like to ask a couple of questions and would be very grateful if<br>>>> someone can take the time to answer them:<br>>>><br>>>> - What pre-processing do I need to do to the itk image so that I can<br>
>>> feed it to a mesh generator? Would I first need to segment the bit<br>>>> that I am interested in? So, would I need to segment the background<br>>>> out of the image.<br>>>> - I am guessing the mesh generators would need some point set as their<br>
>>> input. How could I generate a point set from an itk image?<br>>>><br>>>> I am quite new to this area and am a bit lost as to how to start.<br>>>> Would really appreciate your help.<br>
>>><br>>>> Cheers,<br>>>><br>>>> Anja<br>>>> _____________________________________<br>>>> Powered by <a href="http://www.kitware.com/" target="_blank">www.kitware.com</a><br>
>>><br>>>> Visit other Kitware open-source projects at<br>>>> <a href="http://www.kitware.com/opensource/opensource.html" target="_blank">http://www.kitware.com/opensource/opensource.html</a><br>
>>><br>>>> Kitware offers ITK Training Courses, for more information visit:<br>>>> <a href="http://www.kitware.com/products/protraining.html" target="_blank">http://www.kitware.com/products/protraining.html</a><br>
>>><br>>>> Please keep messages on-topic and check the ITK FAQ at:<br>>>> <a href="http://www.itk.org/Wiki/ITK_FAQ" target="_blank">http://www.itk.org/Wiki/ITK_FAQ</a><br>>>><br>>>> Follow this link to subscribe/unsubscribe:<br>
>>> <a href="http://www.itk.org/mailman/listinfo/insight-users" target="_blank">http://www.itk.org/mailman/listinfo/insight-users</a><br>>>><br>><br><br><br><br></div></div>--<br>
<div>
<div></div>
<div class="h5">Cheers,<br><br>Anja<br>_____________________________________<br>Powered by <a href="http://www.kitware.com/" target="_blank">www.kitware.com</a><br><br>Visit other Kitware open-source projects at<br><a href="http://www.kitware.com/opensource/opensource.html" target="_blank">http://www.kitware.com/opensource/opensource.html</a><br>
<br>Kitware offers ITK Training Courses, for more information visit:<br><a href="http://www.kitware.com/products/protraining.html" target="_blank">http://www.kitware.com/products/protraining.html</a><br><br>Please keep messages on-topic and check the ITK FAQ at:<br>
<a href="http://www.itk.org/Wiki/ITK_FAQ" target="_blank">http://www.itk.org/Wiki/ITK_FAQ</a><br><br>Follow this link to subscribe/unsubscribe:<br><a href="http://www.itk.org/mailman/listinfo/insight-users" target="_blank">http://www.itk.org/mailman/listinfo/insight-users</a><br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>--<br>Stefan Daenzer <br>Körnerplatz 8<br>04107 Leipzig<br><br>Tel.: +49-176-61157550<br><br>"Work like you don't need the money, love like you've never been hurt and dance like no one is watching." - Randall G Leighton<br>