[Insight-users] vessel enhancing diffusion filter (release 200)

[Oleksandr Dzyubak]

Hi Frederico,

In 2-D case the Hessian matrix has 4 components.
If we are talking about 3-D, then it should be 9.
In general case it has to be 2^d, where d is your dimension.

I cropped and downsapmled my image just for the computation time saving 
sake.
In reality, my images would be much larger.
And as Luis mentioned in some of his emails a while ago,
there should be way/room for memory distributed calculations.
That is especially important for the cases like this one.

BTW, what was the pixel size of your image?

Thanks,

Alex


fjlb at duke.edu wrote:
> Oleksandr,
>
> I believe that the 6 in the formula is due to the fact that the 
> Hessian matrix
> contains six different partial derivatives, hence it needs to store 6 
> copies of
> your volume in memory. I have used the filter and I had to crop and 
> downsample
> my volumes for it to work. Try downsampling your volumes and it should 
> not be a
> problem.
>
>
> Federico
>
> Quoting Oleksandr Dzyubak <adzyubak at gmail.com>:
>
>> Hi Luis,
>>
>> First of all many thanks all of you for such a good filter, "Vessel 
>> enhancing diffusion filter".
>> With great pleasure I read the article from the the IJ distribution 
>> and the references therein.
>>
>> Since I am working on vessels, of course, I was tempted to give that 
>> filter a try. So I did.
>> As well as Laura, I got the same error message and following your advice
>> and formula, I calculated the memory request.
>>
>> I tested the filter using an image 565x440x100 pixels.
>> BTW, why 6 in your formula "sizeof(double) x 6 bytes per pixel"?
>> Do you store some intermediate results all the time?
>> Lets calculate memory. In my case sizeof(double)=8.
>>
>> octave:2> 8*6*(565*440*100)
>> ans = 1193280000
>>
>> OK. Filter + ImageItself = 1.19 +  0.0497 ~ 1.2397 GB
>>
>> I have 2 GB + 2 GB (swap). As you say, I almost hit the limit but 
>> some piece is still left.
>> Does a swap part count? I cropped the original image (which is 100 
>> times larger then the one I used)
>> down to 47MB just to test the filter and even with such a small image 
>> size the filter fails to allocate memory?
>>
>> Does it mean that this filter has no use for boxes with limited 
>> resources?
>>
>> BTW, the only 
>> "itkAnisotropicDiffusionVesselEnhancementImageFilterTest" fails.
>> The other one, 
>> "itkMultiScaleHessianSmoothed3DToVesselnessMeasureImageFilterTest" 
>> works fine.
>>
>> Just by luck or you implemented another memory model?
>>
>> Thanks,
>>
>> Alex
>>
>> Luis Ibanez wrote:
>>>
>>> Hi Laura,
>>>
>>> This is annoying, but normal.
>>>
>>> This code computes Hessians of images, which in 3D requires
>>> the allocation of sizeof(double) x 6 bytes per pixel.
>>>
>>> That is, you will need 48 bytes per pixel of your image
>>> in order to store the resulting Hessian alone. There will be
>>> of course additional intermediate allocations.
>>>
>>> If you need to process large images you may need a 64bits
>>> machine with a larger memory...
>>>
>>> What is the actual size (in pixels) of the image that
>>> you are processing ?
>>>
>>> Can you process selected regions of the image ?
>>>
>>> Usually there is a lot of empty (or at least, non interesting)
>>> space in medical images. You could use the RegionOfInterest
>>> filter to reduce the vessel enhancing processing to smaller
>>> section of the image.
>>>
>>>
>>> Please let us know,
>>>
>>>
>>>     Thanks
>>>
>>>
>>>        Luis
>>>
>>>
>>>
>>>
>>>
>>> ---------------------------------
>>> Laura Fernandez de Manuel wrote:
>>>> Hi all,
>>>>  We have been checking the implementation of the "Vessel Enhancing 
>>>> Diffusion Filter" depicted here:
>>>>  http://insight-journal.org/midas/handle.php?handle=1926/558
>>>>  although it works properly with the example 3D images provided 
>>>> (ranging from around 30 to 250 KB) we didn't succeed to make it 
>>>> work in images any larger (5MB images failed already for instance). 
>>>> We work in a system with 4GB RAM so we don't know which can be the 
>>>> source of the "Failed to allocate memory for image" errors that we 
>>>> get. Here, I attach the error message we get:
>>>>  
>>>> ------------------------------------------------------------------------------------------------------ 
>>>> ./itkAnisotropicDiffusionVesselEnhancementImageFilterTest.exe 
>>>> image00_2.mhd image_2Enhanced.mhd
>>>> Reading input image : image00_2.mhd
>>>> Enhancing vessels.........: image00_2.mhd
>>>> Iteration:      0
>>>> Computing vesselness for scale with sigma= 0.2
>>>> Exception caught:
>>>> itk::ExceptionObject (0138FB20)
>>>> Location: "class itk::SymmetricSecondRankTensor<double,3> 
>>>> *__thiscall itk::ImportImageContainer<unsigned long,class 
>>>> itk::SymmetricSecondRankTensor<double,3> >:: AllocateElements 
>>>> (unsigned long) const"
>>>> File: itk3.6.0\code\common\itkImportImageContainer.txx
>>>> Line: 193
>>>> Description: Failed to allocate memory for image.
>>>> ------------------------------------------------------------------------------------------------------  
>>>> Thanks a lot!
>>>>  carlos & laura
>>>>
>>>>   
>>>> ------------------------------------------------------------------------ 
>>>>
>>>>
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