[Insight-users] Feature Image and Processing Time Geodesic Active Contours

[Ella Maria Kadas]

Hi,    I know I've know i already asked that, but i was wondering, better hoping that i am doing something wrong:   I am using a dicom Series of 25 slices of image t2 Head MRT 640x640    min gray value = -51   max gray value = 1359 I want to use the GeodesicActiveContourFilter, but i get only bad Segmentation results. So i tried to improve the Output of the Sigmoid, which is still partly to dark. I read what it does but still couldn't get good parameters so that the final segmentation is a good one.   A more important question is this normal that the computation of  the sigmoid output in the pipeline step for this filters takes around 3 minutes?  It is really important for me to know because i intend to use it on a dicom series of 160 slices.This is a part of my code If anyone has an idea why it is so slow please let me know:
Reading dicom series works just fine and fast

GradientFilterType::Pointer gradientMagnitude = GradientFilterType::New();  SigmoidFilterType::Pointer sigmoid = SigmoidFilterType::New();  sigmoid->SetOutputMinimum(0.0);  sigmoid->SetOutputMaximum(1.0);    smoothing->SetInput(reader->GetOutput());  gradientMagnitude->SetInput(smoothing->GetOutput());  sigmoid->SetInput(gradientMagnitude->GetOutput());
  smoothing->SetTimeStep(0.0625);  smoothing->SetNumberOfIterations(10);  smoothing->SetConductanceParameter(1.0);
  const double sigma = 1.0;  gradientMagnitude->SetSigma(sigma);
  sigmoid->SetAlpha(-6.0); sigmoid->SetBeta(30.0); std::cout  << "I start to do my Stuff " << std::endl << std::endl; CastFilterType::Pointer caster1 = CastFilterType::New(); ………. WriterTypeChar::Pointer writerfinal = WriterTypeChar::New();ImageType::Pointer localImage = reader->GetOutput();typedef itk::FastMarchingImageFilter<ImageType,ImageType > FastMarchingFilterType;		FastMarchingFilterType::Pointer fastMarching = FastMarchingFilterType::New();				typedef itk::GeodesicActiveContourLevelSetImageFilter< ImageType,ImageType > GeodesicActiveContourFilterType;		GeodesicActiveContourFilterType::Pointer geodesicActiveContour = GeodesicActiveContourFilterType::New();				const double propagationScaling = 10.0;						geodesicActiveContour->SetPropagationScaling(propagationScaling);		geodesicActiveContour->SetCurvatureScaling(1.0);		geodesicActiveContour->SetAdvectionScaling( 1.0 );		geodesicActiveContour->SetMaximumRMSError( 0.02 );	
	geodesicActiveContour->SetNumberOfIterations( 120 );				geodesicActiveContour->SetInput( fastMarching->GetOutput() );		geodesicActiveContour->SetFeatureImage( sigmoid->GetOutput() );				thresholder->SetInput( geodesicActiveContour->GetOutput() );						ImageType::IndexType index1;		index1[0] = 381;		index1[1] = 423;		index1[2] = 14;		ImageType::IndexType index2;		index2[0] = 260;		index2[1] = 413;		index2[2] = 14;				typedef FastMarchingFilterType::NodeContainer NodeContainer;		typedef FastMarchingFilterType::NodeType NodeType; 		NodeContainer::Pointer seeds = NodeContainer::New();		double initialDistance = 5.0;		double seedValue = -initialDistance;		NodeType node1;		node1.SetValue(seedValue);		node1.SetIndex(index1);		seeds->Initialize();		seeds->InsertElement(0,node1);		NodeType node2;		node2.SetValue(seedValue);		node2.SetIndex(index2);		seeds->InsertElement(1,node2);		fastMarching->SetTrialPoints(seeds);		fastMarching->SetSpeedConstant(1.0);	
	fastMarching->SetOutputSize(reader->GetOutput()->GetBufferedRegion().GetSize());				std::cout << "Fast Marching started " << std::endl << std::endl;		caster4->SetInput( fastMarching->GetOutput() );		writer4->SetInput( caster4->GetOutput() );		char *name4 = "/Users/ellaK/Documents/DicomRead/FFM.gipl";		writer4->SetFileName(name4);		caster4->SetOutputMinimum( 0 );		caster4->SetOutputMaximum( 255 );				try{			writer4->Update();		}		catch( itk::ExceptionObject & excep ){			std::cerr << "Exception caught at writer1!" << std::endl;			std::cerr << excep << std::endl;        }
		writerfinal->SetInput(thresholder->GetOutput());		char *name6 = "/Users/ellaK/Documents/DicomRead/Segmentation.gipl";		writerfinal->SetFileName(name6);
				try		{		writerfinal->Update();		}		catch( itk::ExceptionObject & excep )		{			std::cerr << "Exception caught at writerfinal!" << std::endl;			std::cerr << excep << std::endl;		} }
		

 

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