[Insight-users] Selecting the sigma for the vesselness

[Chris McIntosh]

rashedk wrote:
> However, I dont understand one thing: Why did the author of the Manniseng
> VED's ITK implementation compare the VED filter responses to that of the
> multiscale vesselness response in his ITK journal paper? Link here:
> http://insight-journal.org/dspace/bitstream/1926/558/5/VEDArticle2.pdf
>   

I can't speak for the authors, but I believe its because the VED filter was
originally presented as an improvement over the original frangi filter.

> Dont they do different things? VED enhances vessels whereas multiscale
> vesselness detects vessels? 
> What I am trying to get at is, if VED does a better job than the standard
> vesselness filter, then how can we use it to detect vessels only. 
>   

Can you define more explicitly what you mean by detect? Do you want the 
vessel radius for each vessel,
or a binary segmentation of the image into vessel and non-vessel, or an 
image showing just the vessels (
the result of masking the image with a binary segmentation).

Thanks,

Chris

> Thanks
> Rashed karim 
>
>
>
> Chris McIntosh-2 wrote:
>   
>> Hello Rashed,
>>
>> It appears I misunderstood your goal. It seems you are trying to 
>> determine the vessel radius
>> at each voxel, and not filter the image. Or perhaps segment the entire 
>> vessel...
>>
>> Yes your interpretation of the VED filter is correct. As is your 
>> interpretation of Frangi's approach.
>> I thought there was a multi-scale version of that filter in ITK already, 
>> but perhaps I was wrong.
>>
>> The Hessian3DToVesselnessMeasuerImageFilter, however, is not Frangi's 
>> filter.
>> http://www.itk.org/Doxygen34/html/classitk_1_1Hessian3DToVesselnessMeasureImageFilter.html
>>
>> "3D Multi-scale line filter for segmentation and visualization of 
>> curvilinear structures in medical images", Yoshinobu Sato, Shin 
>> Nakajima, Hideki Atsumi, Thomas Koller, Guido Gerig, Shigeyuki Yoshida, 
>> Ron Kikinis.
>>
>> is the filter that is used there.
>>
>> Cheers,
>>
>> Chris
>>
>>
>>
>> rashedk wrote:
>>     
>>> Hi Chris, 
>>>
>>> Doesn't Manniseng's VED filter *enhance* the vessels rather than
>>> detecting
>>> them? It does do multi-scale analysis, but goes one step further by
>>> applying
>>> the appropriate diffusion (iso- or aniso-) process. So the output of the
>>> VED
>>> filter should be the same image with the vessels enhanced and not the
>>> vesselness. Please, correct me if I am wrong. 
>>>
>>> What I also don't understand is why
>>> Hessian3DToVesselnessMeasureImageFilter
>>> does not implement a multiscale approach? If it is Frangi's vesselness
>>> which
>>> is implemented here, then his paper did suggest returning the highest
>>> response by varying the sigma. 
>>>
>>> Regards, 
>>> Rashed
>>>
>>>
>>>
>>> Chris McIntosh-2 wrote:
>>>   
>>>       
>>>> Hello,
>>>>
>>>> I'm not sure if this helps, but just in case.
>>>>
>>>> In general, using a constant sigma for an image is troublesome because 
>>>> the ideal scale for each vessel
>>>> is the actual radius of that vessel (in voxels). So you need a different 
>>>> scale at each voxel.
>>>>
>>>> I would suggest looking at:
>>>> http://hdl.handle.net/1926/558
>>>>
>>>> They implement a powerful multi-scale technique for vessel filtering, 
>>>> where each pixel's response
>>>> is tested under a range of scales and the maximal response is taken.
>>>>
>>>>
>>>> Cheers,
>>>>
>>>> Chris
>>>>
>>>> rashedk wrote:
>>>>     
>>>>         
>>>>> Hi everyone, 
>>>>>
>>>>> I am currently using the vesselness filters to detect vessels. I use a
>>>>> pipeline with HessianRecursiveGaussianImageFilter and
>>>>> Hessian3DToVesselnessMeasureImageFilter filters which works fine.
>>>>> However, I
>>>>> am using a trial and error approach for selecting the sigma. In a
>>>>> previous
>>>>> post I came across an approach whereby sigma selection can be done
>>>>> effectively by observing the responses of a single pixel that is known
>>>>> to
>>>>> be
>>>>> part of a vessel (a.k.a multi-scale analysis). How do I constraint the
>>>>> above
>>>>> filters to only process a single pixel and not the entire image? 
>>>>>
>>>>> Thanks, 
>>>>>
>>>>> Rashed Karim
>>>>>   
>>>>>       
>>>>>           
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>>>>
>>>>
>>>>     
>>>>         
>>>   
>>>       
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>>     
>
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