[Insight-users] ConnectedThresholdImageFilter on one slice only ?

[Luis Ibanez]

Hi Maximilien,

Let's cut the problem in pieces...

    1) Have you managed to extract one 2D slice
       from the input 3D image, using the ExtractImageFilter ?

    2) Did you manage to run the ConnectedThreshold filter
       in the 2D slice ?

Please let us know,


     Thanks


        Luis


-------------------------
Maximilien Renard wrote:
> Hi there again,
> 
> Can't anybody please tell me how I can get this to work or what I'm
> doing wrong, I've tried several times to read the doc and I
> unfortunately still don't understand what I should do.
> 
> I would really appreciate any little help.
> 
> Thanks a lot,
> 
> Maximilien
> 
> P.S. Right before I wanted to send this e-mail, I've just noticed I
> would have sent this e-mail (like the other one just here below) to
> Luis Ibanez only. This was a mistake :)
> 
> 2008/12/26 Maximilien Renard <iixamaxii at gmail.com>:
> 
>>Hi Luis,
>>
>>Thank you for your answer, I was actually using a self-made method
>>that was using GetBufferPointer(). This method was called for each
>>voxel of the image which is probably why it was slow.
>>
>>Now, I'm trying to use the ImagePasteFilter but I must say, I couldn't
>>understand how it should be used. I've made following :
>>
>>SliceVolume.Fill3D(X, Y, 0, LowThreshold, HighThreshold,
>>ReplacementValue); // Which then contains the image with the selected
>>region filled
>>
>>typedef itk::PasteImageFilter< ITK3DImageType, ITK3DImageType,
>>ITK3DImageType > ImageReplacementFilterType;
>>ImageReplacementFilterType::Pointer ImageReplacementFilter =
>>ImageReplacementFilterType::New();
>>
>>ImageReplacementFilter->SetInput(SliceVolume.GetITK3DImage());
>>ImageReplacementFilter->SetSourceImage(SliceVolume.GetITK3DImage());
>>ImageReplacementFilter->SetDestinationImage(GetITK3DImage());
>>
>>ImageReplacementFilter->SetDestinationIndex(start);
>>ImageReplacementFilter->Update();
>>
>>If I try to use this, I'm getting this message :
>>
>>Qt has caught an exception thrown from an event handler. Throwing
>>exceptions from an event handler is not supported in Qt. You must
>>reimplement QApplication::notify() and catch all exceptions there.
>>
>>terminate called after throwing an instance of
>>'itk::InvalidRequestedRegionError'
>> what():  /home/ixm/InsightToolkit-3.8.0/Code/Common/itkDataObject.cxx:397:
>>Requested region is (at least partially) outside the largest possible region.
>>The program has unexpectedly finished.
>>
>>I've searched a little bit on the internet if I can found some example
>>of the use of this filter but I didn't find anything (maybe I'm
>>missing something that would make the doc cristal clear for me ?)
>>
>>Anyway I really appreciate your help,
>>
>>Thank you very much,
>>
>>Maximilien
>>
>>2008/12/25 Luis Ibanez <luis.ibanez at kitware.com>:
>>
>>>Hi Maximilien,
>>>
>>>The process you are describing seems to be a reasonable
>>>way of doing this.
>>>
>>>
>>>More specifically:
>>>
>>>  1) Extract the slice with the
>>>
>>>                   "ExtractImageFilter"
>>>
>>>  2) Run the connectedThresholdImageFilter
>>>     in 2D on the extracted slice
>>>
>>>
>>>  3) Copy the slice back to the image, using the
>>>
>>>             "PasteImageFilter"
>>>
>>>
>>>I'm surprised to hear that the last part takes a lot of
>>>time. It should take a couple of seconds at most.
>>>Were you doing this by using ImageIterators ?
>>>or were you using calls to SetPixel() and GetPixel() ?
>>>
>>>Please give it a try to the PasteImageFilter
>>>http://www.itk.org/Insight/Doxygen/html/classitk_1_1PasteImageFilter.html
>>>
>>>and let us know if you still experience any problems.
>>>
>>>
>>>   Regards,
>>>
>>>
>>>       Luis
>>>
>>>
>>>
>>>-------------------------
>>>Maximilien Renard wrote:
>>>
>>>>Hi there,
>>>>
>>>>I'm trying to use ConnectedThresholdImageFilter on one slice of an 3D
>>>>Image only (the result should be the original image exactly the same
>>>>except the specified slice where we put the seed).
>>>>Now I'm extracting the slice into a new 3D Image where it is alone,
>>>>then I apply the filter and finally I copy every voxel of the filtered
>>>>image one by one into the original one. But that takes a lot of time
>>>>(the last step is very long).
>>>>
>>>>Is there a better way to do that ? I'm new to ITK and I'm not
>>>>acknowledged with ITK Doxygen documentation which is quite hermetic
>>>>for me (I was used to read documentations such as the one of PHP or
>>>>Qt).
>>>>
>>>>Thanks for your future help,
>>>>
>>>>Best regards and merry christmas,
>>>>
>>>>Maximilien Renard
>>>>_______________________________________________
>>>>Insight-users mailing list
>>>>Insight-users at itk.org
>>>>http://www.itk.org/mailman/listinfo/insight-users
>>>>
>>>
>