[Insight-users] [Question] 3D Fill

[Luis Ibanez]

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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