[Insight-users] Re: ITK Filters to generte Speed Image (Other than Sigmoid)

[Luis Ibanez]

Hi Conn,

You may want to try:

EdgePotential
http://www.itk.org/Insight/Doxygen/html/classitk_1_1EdgePotentialImageFilter.html

and he ExpNegativeImageFilter
http://www.itk.org/Insight/Doxygen/html/classitk_1_1ExpNegativeImageFilter.html


The first compute the gradient of the image and then pass it through an
exponential. The second only do the exponential. The advangate of the 
second is that you can select your own gradient-magnitude-like filter.
The disadvantage is that you use two filters.


Note... however that the reason why we moved into using the Sigmoid for
constructing speed images was that the traditional methods (edge 
potential) do not offer enough flexibility for controlling the creation
of the speed image.


I would suggest you to reconsider the way you are using the Sigmoid
filter...  you probably just need to find better values for Alpha
and Beta.


Note also that if the gradient magnitude image have gaps in the contours
there is not much that you can improve over that when computing the
speed image. Probably the only thing that can help you there is to
increase the CurvatureScaling of the level set...

Presence of gaps in the gradient magnitude simply means that the
intensities of the object that you are trying to segment are too
close to some neighbor anatomical structure.

If you want to be pragmatic you could also consider the use of
"stoppers" as they are implemented in the SNAP application in
InsightApplications.



    Regards,


       Luis



---------------------
conn sullivan wrote:

> Hello Luis,
>  
> What are the ITK filters other than Sigmoid that can be used to generate 
> speed images?
> In some cases, gradient magnitude + sidmoid filter is not helping me due 
> to gaps produced on boundaries of gradient magnitude.  This leads to 
> leackage in the final output.
>  
> Thanks,
> Conn
>  
> 
> 
> */Luis Ibanez <luis.ibanez at kitware.com>/* wrote:
> 
> 
> 
>     Hi Conn,
> 
> 
>     The speed image computation starts in :
> 
>     Insight/Code/Algorithms/
>     itkSegmentationLevelSetimageFilter.txx
> 
>     The computation is delegated to the SegmentationFunction
>     by invoking its method:
> 
>     CalculateSpeedImage();
> 
>     This method is implemented in the file
> 
>     Insight/Code/Algorithms/
>     itkCannySegmentationLevelSetFunction.txx
> 
>     in lines 30-38.
> 
> 
>     The speed image is computed as a distance map to the Canny
>     edges in the method CalculateDistanceimage() in lines 81-102
>     of the same file.
> 
> 
> 
> 
>     Regards,
> 
> 
> 
>     Luis
> 
> 
> 
>     -----------------------------------------------------------------------------
>     conn sullivan wrote:
> 
>      > Hello Luiz,
>      >
>      > I appreciate your reply. I get the speed image now. I have one more
>      > question. Are speed values taken directly ! from these speed
>     image. Also,
>      > what is z(x) computed for canny edge filter. What part of code from
>      > .cxx file performs this calculation?
>      >
>      > Thanks,
>      > Conn.
>      >
>      > */Luis Ibanez /* wrote:
>      >
>      >
>      > Hi Conn,
>      >
>      >
>      > Thanks for posting the output of the two readers.
>      >
>      > We tracked this problem down and found that what you are missing is
>      > to invoke the "GenerateSpeedImage()" method in the Canny level set
>      > filter before you invoke GetSpeedImage().
>      >
>      > Note that the GenerateSpeedImage() method must be called after
>      > runninig the filter with Update().
>      >
>      >
>      > For your convinience we added this code to the example in
>      >
>      > Insight/Examples/Segmentation/
>      > CannySegmentationLevelSetImageFilter.cxx
>      >
>      >
>      >
>      > In order to get the new version simply update your CVS checkout
>     of ITK,
>     ! > or go to the CVS-Web portal and download the new version of this
>     file:
>      >
>      >
>     http://www.itk.org/cgi-bin/viewcvs.cgi/Examples/Segmentation/CannySegmentationLevelSetImageFilter.cxx?rev=1.27&root=Insight&view=log
>      >
>      >
>      >
>      >
>      > Regards,
>      >
>      >
>      >
>      > Luis
>      >
>      >
> 
> 
> 
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