[Insight-users] Level set segmentation parameters to anisotropic images
Luis Ibanez
luis.ibanez at kitware.com
Wed May 14 10:01:32 EDT 2008
Hi Loic,
Yes,
the initial level set should be in the same format.
The LevelSet format must be consistent because it is common
to take the output of one type of level set filter and pass
it as input to a more sophisticated level set filter.
Regards,
Luis
-----------------------
BOURGEOIS Loic wrote:
> Hi Luis,
>
> Yes sorry I have read the ITK Software Guide but I inverted my thought in this mail... So, the initial level to set to the filter must be in this form, isn't it?
>
> Loic
>
> -----Message d'origine-----
> De : Luis Ibanez [mailto:luis.ibanez at kitware.com]
> Envoyé : mercredi 14 mai 2008 15:42
> À : BOURGEOIS Loic
> Cc : Insight Users
> Objet : Re: Level set segmentation parameters to anisotropic images
>
>
>
>
> Hi Loic,
>
>
> You may find useful to read the ITK Software Guide
>
>
> http://www.itk.org/ItkSoftwareGuide.pdf
>
>
> in particular, you should read section 9.3 "Level Set Segmentation"
> in pdf-page 563.
>
>
> As you will see in Figure 9.13 in page 563,
> the Level Set is defined as:
>
>
> a) f(x,y,z) > 0 is inside
> a) f(x,y,z) = 0 is the shape (zero set)
> a) f(x,y,z) < 0 is outside
>
>
> Regards,
>
>
> Luis
>
>
> ---------------------
> BOURGEOIS Loic wrote:
>
>>Hi,
>>
>>Thank you for your very quick reply.
>>
>>But I think I put my initial level set in a wrong form because with the same parameters and the initial level set provided by the Fast-Marching filter, the Geodesic filter works (the contour has correctly evolved).
>>
>>So I have a simple question : what is exactly the form of the initial level set? (Is it a function f(x,y,z)<0 if (x,y,z) corresponding voxel is inside the object, else f(x,y,z)>0 and f(x,y,z)=0 on the contour? like a signed distance map for example)
>>
>>Thanks in advance,
>>
>>Loic
>>
>>-----Message d'origine-----
>>De : Luis Ibanez [mailto:luis.ibanez at kitware.com]
>>Envoyé : mardi 13 mai 2008 18:42
>>À : BOURGEOIS Loic
>>Cc : Insight Users
>>Objet : Re: Level set segmentation parameters to anisotropic images
>>
>>
>>
>>
>>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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>>
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>>
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> __________________________
>
> Ce message (et toutes ses pièces jointes éventuelles) est confidentiel et établi à l'intention exclusive de ses destinataires. Toute utilisation de ce message non conforme à sa destination, toute diffusion ou toute publication, totale ou partielle, est interdite, sauf autorisation expresse. L'IFP décline toute responsabilité au titre de ce message.
>
> This message and any attachments (the message) are confidential and intended solely for the addressees. Any unauthorised use or dissemination is prohibited. IFP should not be liable for this message.
>
> Visitez notre site Web / Visit our web site : http://www.ifp.fr
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