[Insight-users] Output index of ExtractImageFilter

[Luis Ibanez]

Hi Jeroen,

You may want to use the itkRegionOfInterestImageFilter as an alternative
to the ExtractImageFilter.

These two filters have different policies on how they compute the image
Origin and the Starting index of their region.


ExtractImageFilter:

    * Preserves the Origin
    * Use as Starting index of the output image the
      starting index of the region to be extracted.


RegionOfInterestImageFilter:

    * Use zeros in the starting index of the output
      image region
    * Computes the Origin of the output image as

      InputImageOrigin  +  Spacing  x  StartingIndex


It seems that for your application you are expecting the
behavior of the RegionOfInterestImageFilter.


    Regards,


       Luis


---------------------------
J.S.Wijnhout at lumc.nl wrote:
> Hi,
> 
>  
> 
> It seems I’m a bit confused about the ExtractImageFilter. I’m trying to 
> use it to extract a slice from a 3D image, so far so good. However when 
> I use the extracted slice as input for ResampleImageFilter I seem to be 
> getting into trouble (that is: garbage output).
> 
>  
> 
> After some debugging I got confused about the following: the 
> ExtractImageFilter does not recomputed the origin (apparently this is 
> intended) and consequently the image index is set to the index 
> corresponding to the extraction region. So if I want to extract slice 10 
> and use index=(0,0,10) then the index of the regions of the output image 
> is (0,0,10) as well. However, and this is the confusing part for me, the 
> size of the output image will be (256,256,1). That is, the index extends 
> beyond the maximum allowed image. How should I deal with this?
> 
>  
> 
> Best,
> 
> Jeroen
> 
>  
> 
> This is a code snippet where I’m trying to extract a slice and then 
> super-sample it:
> 
>   void SlabExtractionFilter::GenerateData ()
> 
>   {
> 
>     const Image *inputImage = GetInput ();
> 
>  
> 
>     m_Extracter->SetInput ( inputImage );
> 
>     m_Extracter->SetExtractionRegion ( slabRegion ); // selects a slice 
> from the volume
> 
>    
> 
>     m_Resampler->SetOutputDirection ( inputImage->GetDirection () );
> 
>     m_Resampler->SetOutputOrigin ( outputOrigin ); // the origin 
> belonging to the extracted slice            
> 
>     m_Resampler->SetOutputSpacing ( outputSpacing ); // one-third of the 
> spacing in the z-dimension of the input image
> 
>     m_Resampler->SetSize ( outputSize ); // 256,256,3
> 
>     m_Resampler->SetInput ( m_Extracter->GetOutput () );
> 
>  
> 
>     //m_Resampler->GraftOutput ( this->GetOutput () );
> 
>     m_Resampler->Update ();
> 
>     GraftOutput ( m_Resampler->GetOutput () );
> 
>  }
> 
> 
> ------------------------------------------------------------------------
> 
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