[Insight-users] [Question] 3D Fill

[Luis Ibanez]

Hi Maximilien,


Please read the documentation of the filters.

For example, in:
http://public.kitware.com/Insight/Doxygen/html/classitk_1_1MaskImageFilter.html

The method call:

                               maskFilter->SetOutsideValue( 40000 );

http://public.kitware.com/Insight/Doxygen/html/classitk_1_1MaskImageFilter.html/O//

Seems to be what you are looking for.


The same method is available in the MaskNegatedImageFilter.

http://public.kitware.com/Insight/Doxygen/html/classitk_1_1MaskNegatedImageFilter.html


      Regards,


              Luis


-------------------------------------------------------------------------
On Thu, Jul 30, 2009 at 5:21 AM, Maximilien Renard<iixamaxii at gmail.com> wrote:
> Hi Luis,
>
> Thank you for your answer!
>
> I've taken a look to the MaskImageFilter and the
> MaskNegatedImageFilter. If I'm right, the MaskNegatedImageFilter would
> be what I want to do BUT it replaces the pixels of the MaskImage with
> a value != 0 by a 0 pixel in the output image. I could not figure out
> if it possible to change that behaviour and make the filter replace
> those pixels by another value (like 4000 for example).
> Is this possible ?
>
> Thank you very much,
>
> Best regards,
>
>
> Maximilien Renard
>
> 2009/7/28 Luis Ibanez <luis.ibanez at kitware.com>:
>> Hi Maximilien,
>>
>> A) For pasting the values back in to the image,
>>      you may want to use the MaskImageFilter or
>>      the NegatedMaskImageFilter.
>>
>>
>> B) Most ITK filters are N-Dimensional.
>>      The region growing filters will work fine in
>>      2D, 3D, 4D....
>>
>> C) You may start by debugging your process of
>>      copying images in and out of ITK. It doesn't
>>      seem that your problem is related to the
>>      region growing itself.
>>
>>
>>   Regards,
>>
>>
>>         Luis
>>
>>
>> ------------------------------------------------
>> On Sat, Jul 25, 2009 at 6:17 AM, Maximilien Renard <iixamaxii at gmail.com>
>> wrote:
>>>
>>> Hi there,
>>>
>>> I'm trying to realize a function (Fill3D) that uses the connected
>>> threshold filter to fill a region of a 3D image with another value
>>> based on a threshold.
>>>
>>> This is the function I'm using now :
>>>
>>> void CVolumeData::Fill3D(int X, int Y, int Z, unsigned short
>>> LowThreshold, unsigned short HighThreshold, unsigned short
>>> ReplacementValue) {
>>>        typedef itk::ConnectedThresholdImageFilter < ITK3DImageType,
>>> ITK3DImageType> FilterType;
>>>        FilterType::Pointer filter = FilterType::New();
>>>        ITK3DImageType::IndexType seed;
>>>        seed[0] = X;
>>>        seed[1] = Y;
>>>        seed[2] = Z;
>>>        CVolumeData *pResultImage;
>>>        int DimX, DimY, DimZ, x, y, z;
>>>
>>>        filter->SetSeed(seed);
>>>        filter->SetLower(LowThreshold);
>>>        filter->SetUpper(HighThreshold);
>>>        filter->SetReplaceValue(4000);
>>>
>>>        filter->SetInput(GetITK3DImage());
>>>        filter->Update();
>>>        pResultImage = new CVolumeData(m_MainView);
>>>        pResultImage->SetITK3DImage(filter->GetOutput());
>>>
>>>        GetDimensions(DimX, DimY, DimZ);
>>>
>>>        for (z = 0; z < DimZ; z++)
>>>                for (y = 0; y < DimY; y++)
>>>                        for (x = 0; x < DimX; x++) {
>>>                                if (pResultImage->GetVoxel(x, y, z) >=
>>> 4000) {
>>>                                        SetVoxel(x, y, z,
>>> ReplacementValue);
>>>                                }
>>>                        }
>>>
>>>        delete(pResultImage);
>>> }
>>>
>>> The last 3 for (DimZ, DimY and DimX) are necessary to replace the
>>> filled zone in the original image without replacing the zone of the
>>> original image which lies outside the threshold values. Sadly it takes
>>> lots of time. Is there a better way to do this ?
>>>
>>> Next question, I need to do a Fill2D function too. Here again I have a
>>> problem. I use the extract image filter to extract the slice I need,
>>> then I apply the Fill3D filter on the image (Fill3D that doesn't work
>>> properly now) and what I wanted to do is use the PasteImageFilter to
>>> paste the result of the Fill3D (which has only one slice) back into
>>> the original 3D Image.
>>>
>>> But once again it doesn't work. The result is that the new slice is
>>> entirely black...
>>>
>>> void CVolumeData::Fill2D(int X, int Y, int Z, unsigned short
>>> LowThreshold, unsigned short HighThreshold, unsigned short
>>> ReplacementValue, int SubView) {
>>>        int DimX, DimY, DimZ;
>>>        int x, y, z;
>>>
>>>        GetDimensions(DimX, DimY, DimZ);
>>>
>>>        typedef itk::ExtractImageFilter< ITK3DImageType, ITK3DImageType >
>>> FilterType;
>>>        FilterType::Pointer filter = FilterType::New();
>>>
>>>        ITK3DImageType::RegionType inputRegion =
>>> GetITK3DImage()->GetLargestPossibleRegion();
>>>
>>>        if (SubView == CMainView::MODE_XY) {
>>>                CVolumeData SliceVolume(m_MainView);
>>>
>>>                SliceVolume.CreateVolume(DimX, DimY, 1, 1.0f, 1.0f, 1.0f,
>>> 0, false);
>>>
>>>                ITK3DImageType::SizeType size = inputRegion.GetSize();
>>>                size[2] = 1;
>>>                ITK3DImageType::IndexType start = inputRegion.GetIndex();
>>>                start[2] = Z;
>>>                ITK3DImageType::RegionType desiredRegion;
>>>                desiredRegion.SetSize(size);
>>>                desiredRegion.SetIndex(start);
>>>
>>>                filter->SetExtractionRegion(desiredRegion);
>>>
>>>                filter->SetInput(GetITK3DImage());
>>>
>>>                filter->Update();
>>>
>>>                SliceVolume.SetITK3DImage(filter->GetOutput());
>>>
>>>                SliceVolume.Fill3D(X, Y, 0, LowThreshold, HighThreshold,
>>> ReplacementValue);
>>>
>>>                typedef itk::PasteImageFilter< ITK3DImageType,
>>> ITK3DImageType,
>>> ITK3DImageType > ImageReplacementFilterType;
>>>                ImageReplacementFilterType::Pointer ImageReplacementFilter
>>> =
>>> ImageReplacementFilterType::New();
>>>
>>>
>>>  ImageReplacementFilter->SetSourceImage(SliceVolume.GetITK3DImage());
>>>
>>>  ImageReplacementFilter->SetSourceRegion(SliceVolume.GetITK3DImage()->GetLargestPossibleRegion());
>>>
>>>
>>>  ImageReplacementFilter->SetDestinationImage(GetITK3DImage());
>>>                ImageReplacementFilter->SetDestinationIndex(start);
>>>
>>>                ImageReplacementFilter->Update();
>>>                SetITK3DImage(ImageReplacementFilter->GetOutput());
>>>        }
>>> }
>>>
>>> I'd enjoy any kind of help !
>>>
>>> Thank you very much,
>>>
>>> Best regards,
>>>
>>>
>>> Maximilien Renard
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>>
>>
>