[Insight-users] Level set segmentation parameters to anisotropic images

[Luis Ibanez]

Hi Loic,

It will be very hard to track the problem if you just look at
the full pipeline.

The best way is to verify every one of the intermediate stages
of the process.

A level set segmentation involves a large number of parameters
and it is hard to figure out which one of them is not set up
correctly. In general several of them will need to be adjusted.


Could you please start by connecting an Observer to the filter
and printing out the iteration events ?

Also, at the end of execution of the filter you could print
out the number of iterations that it took to run.

This will help to determine how much work the filter is
actually doing.

E.g. it may be that you are not running enough iterations,
or it may be that your RMS error tolerance is set too high
and the filter terminates prematurely...



You may want to consider playing with SNAP before you continue
the path of writing your own code. In this way you will learn
faster about how to fine tune the segmentation parameters.



     Regards,



         Luis



---------------------
BOURGEOIS Loic wrote:
> Hi Luis,
> 
> Thanks for your suggestion, I have decided to use "GeoInterp: Contour Interpolation with Geodesic Snakes
> http://www.insight-journal.org/midas/view_item.php?itemid=512" adapted to my problem. I put the distance map (Danielsson) of my pre-segmented object instead of Fast-Marching as the initial level set but the output level set of the geodesic filter is the same of the input.
> Am I missing something?
> 
> Regards,
> 
> Loic
> 
> -----Message d'origine-----
> De : Luis Ibanez [mailto:luis.ibanez at kitware.com]
> Envoyé : lundi 12 mai 2008 18:43
> À : BOURGEOIS Loic; Insight Users
> Objet : Re: Level set segmentation parameters to anisotropic images
> 
> 
> 
> Hi Loic,
> 
>                     Welcome to ITK !
> 
> It is hard to tell if the anisotropy of your MET images
> would prevent LevelSet methods from running well.
> 
> 
> I would expect that an anisotropy larger than 1:5
> will make hard for level sets to behave properly.
> However... this also depends on the actual content
> of your image...
> 
> 
> ---
> 
> What I would suggest is for you to try the SNAP application.
> 
>    You can download binaries from http://www.itksnap.org/
> 
> or build it from the version in InsightApplications.
> 
> SNAP is build on top of ITK and provides a nice interface
> for using LevelSets.
> 
> Another application that may be useful is Slicer:
> 
>      http://www.na-mic.org/Slicer/Download/Snapshots/
> 
> 
> ---
> 
> By testing your images with these applications will get
> a feeling of whether the anisotropy is too large for the
> LevelSets to work properly.
> 
> Please note that ITK LevelSet can be run by turning the
> consideration of the spacing ON and OFF.
> 
> You may want to use them with using the spacing ON.
> 
> Also, a quick experiment that will help you see the
> influence of anisotropy is to run the GradientMagnitude
> RecursiveGaussianImagefilter in your image, and then
> visualizing the image with slice orthogonal to the
> plan of acquisition.
> 
> E.g. using a plane XZ, where Z is the direction with
> the largest spacing. In this way you should see
> rectangular pixels, and how they may have affected
> the gradients of the image.
> 
> 
> Please let us know what you find,
> 
> 
> 
>      Thanks
> 
> 
>         Luis
> 
> 
> ----------------------
> BOURGEOIS Loic wrote:
> 
>>Hello Mr. Ibanez,
>>
>>I am new in this mailing list. I have to segment MET 3D (Microscopy 
>>Electron Tomography) images which are very anisotropic : contrast is 
>>quite good along x and y axis but is very low along z axis. So the issue 
>>is to tune different parameters to the level set (geodesic) between x 
>>and y axis, and z axis. Is there possible?
>>
>>Regards,
>>
>>Loic Bourgeois
>>
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