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

[Leila Baghdadi]

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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