[Insight-users] NoiseImageFilter for 3D images

[Bill Lorensen]

CT data is usually signed. Try short instead of unsigned short.


On Fri, Aug 16, 2013 at 9:19 AM, Bradley Lowekamp <blowekamp at mail.nih.gov>wrote:

> Hello Micro,
>
> I don't regularly work with CT, so I don't know for certain. What is the
> pixel type in your file?
>
> http://www.itk.org/Wiki/ITK/Examples/IO/ReadUnknownImageType
>
> Also why do you say you image is all zeros? Did you inspect it in am image
> viewer? Perhaps all the values were just too low to be seen?
>
> It may be best to have the output of the filter be at least of float,
> since its computing the standard deviation will be low in homogeneous
> regions which may be causing you to thing it's zero.
>
> You are correct that in 3d a radius of 2 aka [2,2,2] will yield a
> neighborhood with a size of [5,5,5].  This has to do with how the
> Neighborhood operators and iterator work. You can find some example which
> may help you understand the behavior better here:
>
> http://www.itk.org/Doxygen/html/examples.html
> http://www.itk.org/Wiki/ITK/Examples
>
> Brad
>
>
> On Aug 16, 2013, at 9:02 AM, Mirco Serra <mirco9091 at hotmail.it> wrote:
>
> Hello,
>
> Thanks for your answer!
>
> I am using unsigned short as image type both for the input and the output
> image. Is this the correct type for 3D CT images? Also, would you mind
> explaining me the way the radius for the local region is selected for 3D
> images? In 2D I know that a radius value of 1 corresponds to a 3x3 region,
> a radius of 2 is a 5x5 region and so on. Is it the same in 3D, i.e. a value
> of 1 is a region of 3x3x3?
>
> Many thanks,
>
> Mirco
>
> ------------------------------
> Subject: Re: [Insight-users] NoiseImageFilter for 3D images
> From: blowekamp at mail.nih.gov
> Date: Fri, 16 Aug 2013 08:48:56 -0400
> CC: insight-users at itk.org
> To: mirco9091 at hotmail.it
>
> Hello,
>
> What are your template parameters to the filter i.e. the image types used?
>
> I just tried this filter in SimpleITK with a couple different images and
> it seems to work fine.
>
> Thanks,
> Brad
>
> On Aug 16, 2013, at 5:05 AM, Mirco Serra <mirco9091 at hotmail.it> wrote:
>
> Hi guys,
>
> I am trying to use the NoiseImageFilter class in order to get the local
> standard deviation of a 3D DICOM/nrrd dataset. The filter works nicely with
> 2D images, but when I try to use for 3D datasets it does not work properly
> and it returns an image with only zeros as intensity values. Do you have
> any idea why this could happen? I struggled with it a lot but I could not
> find a solution! Is the filter for 3D images too?
>
> All the best and thank you very much,
>
> Mirco
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