[Insight-users] Fast Marching segmentation on 3D image: an empty result volume

[Leila Baghdadi]

Sara,

If you plan to use itk and related packages, I suggest spending sometime
and learning how to build and use all the packages. 
I normally run cmake in InsightApplications and then go to the directory
of the packages I want and run make in there, that way I do not have to
wait for everything to build before using one of them. If you manage to
build SNAP correctly, you should find the executable "InsightSNAP" in
your build directory. You just run that and take it from there. Keep in
mind that you can find alot more info at http://www.itksnap.org/

HTH

Leila

On Wed, 2008-27-08 at 15:25 +0000, sara meghellati wrote:
> Thank you leila for your suggestions.
> I have just build the Insight application, the configuration and the
> built are fine (102 projects) and now I want to run some of these
> apllications but I don't know how ? 
> SNAP exist in InsightApplications but I couldn't found it in
> InsightApplicationsBin or in the VC Solution explorer ? how can I use
> it ?
> Thanks
> Sara 
> 
> 
> --- En date de : Mer 27.8.08, Leila Baghdadi
> <baghdadi at phenogenomics.ca> a écrit :
> 
>         De: Leila Baghdadi <baghdadi at phenogenomics.ca>
>         Objet: Re: [Insight-users] Fast Marching segmentation on 3D
>         image: an empty result volume
>         À: sara_meghellati at yahoo.fr
>         Cc: "insight itk" <insight-users at itk.org>
>         Date: Mercredi 27 Août 2008, 16h11
>         
>         Sara,
>         
>         Here is some advice on segmentation. 
>         When you first start using an algorithm, the best way is to visualize
>         the algorithm in action. So you need to use a program that allows you to
>         do that. Once you have figured out all the parameters you can use
>         command line programs!
>         
>         I would suggest the SNAP program, it is part of InsightApplications and
>         it has a few version of level set implemented. You can open up your
>         image place your seed and see how it works. It has a few cool features
>         that allows you to preview the edge image and so on. (read the tutorial)
>         
>         good luck
>         
>         Leila
>         
>         On Wed, 2008-27-08 at 14:04 +0000, sara meghellati wrote:
>         > Hi,
>         > Sorry to ask again, I looked in the mailing list but I couldn't find
>         > an answer to my question.
>         > I'm now testing the level set segmentation code with 3D data. I have
>         > started with the fast marching based method. The code works well for
>         > 2D image but when I use 3D date (I use Patient1.mhd from
>         > http://public.kitware.com/pub/itk/Data/LiverTumor/) I get an empty
>         > volume as segmented image. I have checked the output of smoothing,
>         > gradient magnitude and the sigmoid and all are fine, just the output
>         > of the FastMarchingFilter is empty.
>         > To run this code I have used different seed points (for instance
>         > (160,200,6)) but the result still always empty.
>         > I used the same parameter as in page 539 of ItksoftwareGuide for left
>         > ventricle and I have used a stopping value of 100.
>         > Regarding the book, this code needs a good speed image to run well and
>         > the seed region should be near to the images edges. Perhaps the
>         > parameters I'm using are not suitable for this example so could you
>         > tell me the appropriate parameters That can be used to make this code
>         > running well for this example (Patient1.mhd)? or perhaps there
>         > is other thing wrong.
>         >  
>         > Thank you in advance.
>         > Regards
>         > Sara
>         >  
>         >  
>         >  
>         >  
>         > 
>         > 
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> 
> 
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