[Insight-users] Anisotropic Diffusion filtering

[rashedk]

Hi Luis, 

Thanks for your reply. I am working with GIPL images, and so after you asked
me to test the anisotropic filter with a single slice of my image, I started
trying to use the ExtractImageFilter to extract a slice. So to read and
write GIPL images by setting ImageIO explicitly: 

typedef itk::GiplImageIO ImageIOType; 
ImageIOType::Pointer giplIO = ImageIOType::New(); 
reader->SetImageIO(giplIO); 
writer->SetImageIO(giplIO); 

I am not able to extract a slice of my image (after adding these lines to
the example code of ExtractImageFilter). Now I am getting the feeling that
perhaps there are some issues with GIPL Input/Output in ITK?? 

However, i have tested flushing a GIPL reader's output to a GIPL writer's
input without a filter in between, and that works perfectly fine. 





Luis Ibanez wrote:
> 
> 
> Hi Rashed,
> 
> 
> 
>   1) Could you post somewhere in a public web site
>      a slice of one of your 3D images ?
> 
> 
>   2) The numerical values recommended for the parameters
>      of this filter, are for a typical MRI image.
> 
>      If your images happen to have a very different
>      appearance then you need to explore different settings
>      for the parameters.
> 
>      I would strongly suggest you to do this first in a single
>      slice of the 3D image (use the ExtractImageFilter), since
>      it will be a lot faster to try many different combinations
>      of the filter parameters.
> 
> 
>   3) 50 iterations, should be more than enough for producing
>      a visible effect in the images... unless your images are
>      very particular,
> 
>      What is the modality of your images ? (CT? MRI? Ultrasound ?)
>      What is the content of the image ? brain?, liver?
> 
> 
>   4) The time step should be small. The critical values are in the
>      order of 0.625. Whenever you go higher than that the filter
>      becomes numerically unstable. You should probably stay below
>      half that value, just to be safe.
> 
>      Note however, that there is a relationship between the time
>      step and the number of iterations. After all, this filter is
>      simulating the melting of the material in your image as if it
>      were a physical problem. This is a discretization of a continuous
>      physical model. If you use half of the time steps, you will need
>      double the iterations in order to cover the same process.
> 
>      That being said, this is just a simile, there is no real melting
>      happening here, so you simply use the physical model as an analogy
>      for smoothing the image.
> 
> 
>   5) A Gaussian smoothing of 20-30 is *HUGE*.
> 
>      What specific filter did you use for the smoothing ?
>      What is the pixel spacing of your images ?
> 
> 
> 
>   Please give us more information,
> 
> 
>      Thanks
> 
> 
>         Luis
> 
> 
> ---------------------
> rashed karim wrote:
>> Hi everyone,
>>  
>> I am trying to use the itkGradientAnisotropicDiffusionImageFilter class 
>> for smoothing my MRI images. To my dismay, my images are not responding 
>> to the filter even when I run 50 or so iterations with a conductance of 
>> about 3.0 (i.e. output image is the same as the input image with no 
>> visible difference). An earlier forum post had suggested to use a 3.0 
>> conductance level, but such a high conductance rate makes the 
>> output image unrecognizable (lots of salt-pepper noise).
>>  
>> So has anyone used this filter before, and if so, what sort of 
>> parameter values (number of iterations, conductance and time step) 
>> should I be looking to use. Although I know that these values depend 
>> on the type of my images I am working with, but any suggestions will be 
>> very useful.
>>  
>> Also in the documentation it says somewhere that the time step parameter 
>> is similar to the width of the gaussian kernel. I have tried values of 
>> 20.0 - 30.0. However, I get a warning message telling me that this sort 
>> of value is an "unstable time step" for my images. The message also 
>> suggests a timestep which is usually a very small value (~ 0.05). What i 
>> dont understand, is that I had no problems (isotropic) 
>> Gaussian smoothing my images with widths ranging from 20.0 - 30.0, then 
>> why does the anisotropic filter complain for such widths?
>>  
>> Here is part of my code if it helps:
>>  
>>  typedef itk::Image< PixelType, 3 > InputImageType;
>>  typedef itk::Image< PixelType, 3 > OutputImageType;
>>  typedef itk::ImageFileReader< InputImageType > ReaderType;
>>  typedef itk::ImageFileWriter< OutputImageType >  WriterType;
>>  typedef itk::GiplImageIO ImageIOType;
>>  typedef itk::GradientAnisotropicDiffusionImageFilter<InputImageType, 
>> OutputImageType > FilterType;
>>  
>> 
>>  ReaderType::Pointer reader = ReaderType::New();
>>  WriterType::Pointer writer = WriterType::New();
>>  ImageIOType::Pointer giplIO = ImageIOType::New();
>>  FilterType::Pointer filter = FilterType::New();
>> 
>>  reader->SetFileName( argv[1] );
>>  writer->SetFileName( argv[2] );
>>  
>>  
>>  // for GIPL files
>>  reader->SetImageIO(giplIO);
>>  writer->SetImageIO(giplIO);
>>  
>>  //reader->Update();
>>  
>>  writer->SetInput(filter->GetOutput());
>>  filter->SetInput(reader->GetOutput());
>>  filter->SetNumberOfIterations( numberOfIterations );
>>  filter->SetTimeStep( timeStep );
>>  filter->SetConductanceParameter( conductance );
>>  writer->Update();
>> 
>> Thanks for any suggestions,
>> 
>>  
>> 
>> Regards,
>> 
>> Rashed Karim.
>> 
>> 
>> ------------------------------------------------------------------------
>> 
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