[Insight-users] How to use Watershed segmentation in 3D.
Luis Ibanez
luis.ibanez at kitware.com
Mon Aug 25 11:06:29 EDT 2008
Hi Wassim,
The command line should be:
Watershed3D.exe Patient01.mhd Watershed.mhd 0.001 0.1
That is:
The "threshold" should be in the order of 0.001,
you may want to raise if your image is noisy.
The "level" should be in the range 0.0 -> 0.2
and usually 0.1 shows you prominet features of the image.
raising the value shows you larger regions,
lowering the value shows you smaller regions.
Please run it first with the data from
http://public.kitware.com/pub/itk/Data/LiverTumor
before you experiment with your own data.
Regards,
Luis
--------------------------------
wassim_belhadj at topnet.tn wrote:
> Hi
> I tried the code that you have join to Sara but I was one exception:
> "list iteraror not dereferencable"
>
>
> Can we list the parameters to pass as arguments
> inputImage Patient01.mhd
> outputImage = res.mhd
> lowerThreshold =?
> outputScaleLevel =?
>
> Thanks in advance
>
> On Fri, 22 Aug 2008 12:59:06 -0400, "Luis Ibanez" <luis.ibanez at kitware.com>
> wrote:
>
>>Hi Sara,
>>
>>Thanks for your detailed question regarding Watersheds.
>>
>>
>>Please take a look at the attached code.
>>
>>It process the image "Patient01" from
>>
>> http://public.kitware.com/pub/itk/Data/LiverTumor/.
>>
>>in a time of
>>
>> 4 minutes 38 seconds.
>>
>>This was profiled in an QuadCore Intel Xeon 2.66 Ghz. (with 16Gb RAM).
>>(although the process uses only one of the cores)
>>
>>Note that the process peaks 1Gb of memory allocation when it is running.
>>
>>Depending on the configuration of your system, it may be that the program
>>started swapping memory at some point.
>>
>>Please give a try at the attached code and let us know what you find.
>>
>>
>> Regards,
>>
>>
>> Luis
>>
>>
>>
>
> -----------------------------------------------------------------------------------------------------------------------------------
>
>>On Fri, Aug 22, 2008 at 11:19 AM, sara meghellati
>><sara_meghellati at yahoo.fr>wrote:
>>
>>
>>>I'm sending again my questions as nobody have answered me.
>>>
>>>--- En date de : *Ven 22.8.08, sara meghellati
>>
>><sara_meghellati at yahoo.fr>*a écrit :
>>
>>>De: sara meghellati <sara_meghellati at yahoo.fr>
>>>Objet: [Insight-users] Please help:problem with wathershed segmentation
>>>applied to 3D grayscale Image
>>>À: "insight itk" <insight-users at itk.org>
>>>Date: Vendredi 22 Août 2008, 13h48
>>>
>>> Dear itk experts,
>>>
>>>I'm segmenting a volume (3D grayscale image) using watershed method
>>
>>inspired from the WatershedSegmentation1
>>
>>>(2D RGB image as input)example provided within itk.
>>>
>>>My code is well working for 2D grayscale images but when I change
>>>
>>>the dimension to 3, the code
>>> still running as it get stuck in a
>>>
>>>loop!! I wait for more than 18min but no results!! Is it normal
>>>
>>>that this kind of segmentation takes age to give the result in 3d
>>>
>>>image or there is some thing wrong with my code? Please could you help
>>
>>me on that? Also, how can I follow the progress of the code?
>>
>>>I pass my code bellow. In this example I used the 3D data provided
>>>
>>>in /.
>>>
>>>#include <iostream>
>>>
>>>#include "itkImage.h"
>>>
>>>#include "itkGradientAnisotropicDiffusionImageFilter.h"
>>>
>>>#include "itkGradientMagnitudeImageFilter.h"
>>>
>>>#include "itkWatershedImageFilter.h"
>>>
>>>#include "itkImageFileReader.h"
>>>
>>>#include "itkImageFileWriter.h"
>>>
>>>#include "itkVectorCastImageFilter.h"
>>>
>>>#include "itkUnaryFunctorImageFilter.h"
>>>
>>>#include "itkScalarToRGBPixelFunctor.h"
>>>
>>>
>>>
>>>#include "itkVTKImageExport.h"
>>>
>>>#include "itkVTKImageImport.h"
>>>
>>>
>>>
>>>#include "vtkImageData.h"
>>>
>>>#include "vtkImageImport.h"
>>>
>>>#include "vtkImageExport.h"
>>>
>>>#include "vtkImageActor.h"
>>>
>>>#include "vtkRenderer.h"
>>>
>>>#include "vtkRenderWindow.h"
>>>
>>>#include "vtkRenderWindowInteractor.h"
>>>
>>>#include "vtkInteractorStyleTrackballCamera.h"
>>>
>>>#include "vtkImageShiftScale.h"
>>>
>>>
>>>
>>>// This function will connect the given itk::VTKImageExport filter to
>>
>>the
>>
>>>given vtkImageImport filter.
>>>
>>>template <typename ITK_Exporter, typename VTK_Importer>
>>>
>>>void ConnectPipelines(ITK_Exporter exporter, VTK_Importer* importer)
>>>
>>>{
>>>
>>>
>>>
>>
> importer->SetUpdateInformationCallback(exporter->GetUpdateInformationCallback());
>
>>>
>>>
> importer->SetPipelineModifiedCallback(exporter->GetPipelineModifiedCallback());
>
>>> importer->SetWholeExtentCallback(exporter->GetWholeExtentCallback());
>>>
>>> importer->SetSpacingCallback(exporter->GetSpacingCallback());
>>>
>>> importer->SetOriginCallback(exporter->GetOriginCallback());
>>>
>>> importer->SetScalarTypeCallback(exporter->GetScalarTypeCallback());
>>>
>>>
>>>
>>
> importer->SetNumberOfComponentsCallback(exporter->GetNumberOfComponentsCallback());
>
>>>
>>>
> importer->SetPropagateUpdateExtentCallback(exporter->GetPropagateUpdateExtentCallback());
>
>>> importer->SetUpdateDataCallback(exporter->GetUpdateDataCallback());
>>>
>>> importer->SetDataExtentCallback(exporter->GetDataExtentCallback());
>>>
>>>
>>>
>>
>>importer->SetBufferPointerCallback(exporter->GetBufferPointerCallback());
>>
>>> importer->SetCallbackUserData(exporter->GetCallbackUserData());
>>>
>>>}
>>>
>>>
>>>
>>>int main( )
>>>
>>>{
>>>
>>> typedef itk::Image<float, 3> ImageType;
>>>
>>> typedef itk::Image<unsigned long, 3> LabeledImageType;
>>>
>>> typedef itk::Image<float, 3> ScalarImageType;
>>>
>>> // for visualization purposes
>>>
>>> typedef itk::RGBPixel<unsigned char> RGBPixelType;
>>>
>>> typedef itk::Image<RGBPixelType, 3> RGBImageType;
>>>
>>>
>>>
>>> typedef itk::ImageFileReader<ImageType> FileReaderType;
>>>
>>> typedef itk::GradientAnisotropicDiffusionImageFilter<ImageType,
>>>ImageType> DiffusionFilterType;
>>>
>>> typedef itk::GradientMagnitudeImageFilter<ImageType,ImageType>
>>
>>GradientMagnitudeFilterType;
>>
>>>
>>> typedef itk::WatershedImageFilter<ScalarImageType>
>>>WatershedFilterType;
>>>
>>> typedef itk::ImageFileWriter<RGBImageType> FileWriterType;
>>>
>>>
>>>
>>> FileReaderType::Pointer reader = FileReaderType::New
>>>
>>> reader->SetFileName( "c:/images/3DImages/Patient01.mhd" );
>>>
>>> //reader->SetFileName("c:/Images/BrainProtonDensitySlice.png");
>>>
>>>
>>>
>>> DiffusionFilterType::Pointer diffusion =
>>
>>DiffusionFilterType::New();
>>
>>> diffusion->SetNumberOfIterations( atoi("10") );
>>>
>>> diffusion->SetConductanceParameter( atof("2.0") );
>>>
>>> diffusion->SetTimeStep(0.0625);
>>>
>>>
>>>
>>> GradientMagnitudeFilterType::Pointer gradient =
>>>GradientMagnitudeFilterType::New();
>>>
>>>
>>>
>>> WatershedFilterType::Pointer watershed =
>>
>>WatershedFilterType::New();
>>
>>> watershed->SetLevel( atof("0.15") );
>>>
>>> watershed->SetThreshold( atof("0.001") );
>>>
>>> typedef itk::Functor::ScalarToRGBPixelFunctor<unsigned long>
>>>ColorMapFunctorType;
>>>
>>> typedef itk::UnaryFunctorImageFilter<LabeledImageType,
>>
>>RGBImageType,
>>
>>>ColorMapFunctorType> ColorMapFilterType;
>>>
>>> ColorMapFilterType::Pointer colormapper =
>>
>>ColorMapFilterType::New();
>>
>>>
>>>
>>> FileWriterType::Pointer writer = FileWriterType::New();
>>>
>>> writer->SetFileName("c:/Images/WatershedSegImg.mhd");
>>>
>>>
>>>
>>> diffusion->SetInput(reader->GetOutput());
>>>
>>> gradient->SetInput(diffusion->GetOutput());
>>>
>>> watershed->SetInput(gradient->GetOutput());
>>>
>>> colormapper->SetInput(watershed->GetOutput());
>>>
>>> writer->SetInput(colormapper->GetOutput());
>>>
>>> writer->Update();
>>>
>>>
>>>
>>>try
>>>
>>> {
>>>
>>> writer->Update();
>>>
>>> }
>>>
>>> catch (itk::ExceptionObject &e)
>>>
>>> {
>>>
>>> std::cerr << e << std::endl;
>>>
>>> }
>>>
>>>
>>>
>>> return 0;
>>>
>>>
>>>
>>>}
>>>
>>>Thanks
>>>
>>>Sara
>>>
>>>
>>>------------------------------
>>>Envoyé avec Yahoo!
>>
> Mail<http://us.rd.yahoo.com/mailuk/taglines/isp/control/*http://us.rd.yahoo.com/evt=52423/*http://fr.docs.yahoo.com/mail/overview/index.html>
>
>>>.
>>>Une boite mail plus intelligente.
>>>
>>>_______________________________________________
>>>Insight-users mailing
>>
> listInsight-users at itk.orghttp://www.itk.org/mailman/listinfo/insight-users
>
>>>
>>>------------------------------
>>>Envoyé avec Yahoo!
>>
> Mail<http://us.rd.yahoo.com/mailuk/taglines/isp/control/*http://us.rd.yahoo.com/evt=52423/*http://fr.docs.yahoo.com/mail/overview/index.html>
>
>>>.
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>>>
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>>>
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>
>
>
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