[Insight-users] Segmentation of noisy images

[ml sc]

Dear Jon,

Thank you. This was already helpful.

Best regards,
Claudia


2011/12/7 Jon Haitz Legarreta <jhlegarreta at vicomtech.org>

> Dear Claudia,
> as for the dimensions, since ITK image types are templated over the
> dimensionality, ITK will perform segmentation over 2D or 3D images without
> any further consideration
> .
> As for the noise, you can try any edge preserving smothing filter ITK
> offers (depending on the input images and requirements you have). You will
> get rid of the noise and the sharp boundaries of your structures of
> interest will be hopefully preserved, since you will need them afterwards
> to perform the segmentation.
> If you didn't have a look at it yet, the ITK Software Guide may give you
> some hints on this.
>
> In order to fill the holes, since you will apply the filter to an already
> binarized image you may want to use the use the
> BinaryMorphologicalClosingImageFilter. It works quite well.
>
> So far, I've only used VTK for visualization purposes, so I am not aware
> of the image processing filters it may have.
>
> Hope this helps.
>
> Kind regards,
> JON HAITZ
>
>
>
>
>
> On 6 December 2011 16:42, mlsc 310 <mlsc310 at gmail.com> wrote:
>
>> Hi,
>>
>> I would like to do 3D segmentation on noisy medical images. The aim is to
>> obtain at the end a binarized image volume where voxels that correspond to
>> tissue are set to 1 and the background voxels are set to 0. I can consider
>> that the object is uniform, but I have to eliminate the noisy voxels on the
>> background and after segmentation I need to fill the holes on the object
>> that I'll get during the segmentation process.
>> As I'm using C++, I think that I can find on ITK and VTK some of the
>> tools I need, but it is not clear for me which tools are more appropriate
>> and when shall I use ITK or VTK for some of the steps.
>> So far, I'm trying to find out if ConnectedThresholdImageFilter (ITK),
>> FillHolesFilter (VTK) and PolyDataToImageData (VTK) are of any use on this.
>> I appreciate any help.
>>
>> Regards,
>> Claudia
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