krm15 / acme Goto Github PK

The first one (S2.3 Running the software on a 2D intersecting circle voting example) generates black images ... and the second one (S2.4 Running the code on somite data) generates a black image on the step 11 (Apply the planarity detection filter - The source code for this filter is located at MR-Source/Examples/MultiscalePlateMeasureImageFilter.cxx) here is the code that isn't working for me ...

// Declare the type of multiscale vesselness filter
typedef itk::MultiscaleStructMeasureImageFilter<
InputImageType, OutputImageType> MultiscalePlateFilterType;

// Create a vesselness Filter
MultiscalePlateFilterType::Pointer MultiscalePlateFilter =
MultiscalePlateFilterType::New();
MultiscalePlateFilter->SetInput( reader->GetOutput() );
MultiscalePlateFilter->SetObjectType( 0 );
MultiscalePlateFilter->SetSigmaMin( atof(argv[4]) );
MultiscalePlateFilter->SetSigmaMax( atof(argv[4]) );
MultiscalePlateFilter->SetNumberOfSigmaSteps( 1 );

try
{
MultiscalePlateFilter->Update();
}
catch( itk::ExceptionObject & err )
{
std::cerr << "Exception caught: " << err << std::endl;
return EXIT_FAILURE;
}

std::cout << "Writing out the enhanced image to " << argv[2]
<< std::endl;

ImageWriterType::Pointer writer = ImageWriterType::New();
writer->SetFileName( argv[2] );
writer->SetInput ( MultiscalePlateFilter->GetOutput() );

try
{
writer->Update();
}
catch( itk::ExceptionObject & err )
{
std::cerr << "Exception caught: " << err << std::endl;
return EXIT_FAILURE;
}

reader->GetOutput() contains the preprocessed image and its good i already verified it. The problem is when i do "writer->SetInput ( MultiscalePlateFilter->GetOutput() );" ... that is a black image ... whats the problem?

It seems all the code is written for 3d images. Is there any way that I can apply the tensor voting code to 2d images?

In file included from /lustre/home/acct-bmelgn/bmelgn-5/panweihao/ACME/Code/Examples/MembraneOrientationBasedHessianCalculator.cxx:45:0:
/lustre/home/acct-bmelgn/bmelgn-5/panweihao/ACME/Code/PlanarityFilter/itkMembraneScaleSelectionImageFilter.h: At global scope:
/lustre/home/acct-bmelgn/bmelgn-5/panweihao/ACME/Code/PlanarityFilter/itkMembraneScaleSelectionImageFilter.h:120:37: error: ‘ThreadIdType’ has not been declared
ThreadIdType threadId);
^
In file included from /lustre/home/acct-bmelgn/bmelgn-5/panweihao/ACME/Code/PlanarityFilter/itkMembraneScaleSelectionImageFilter.h:137:0,
from /lustre/home/acct-bmelgn/bmelgn-5/panweihao/ACME/Code/Examples/MembraneOrientationBasedHessianCalculator.cxx:45:
/lustre/home/acct-bmelgn/bmelgn-5/panweihao/ACME/Code/PlanarityFilter/itkMembraneScaleSelectionImageFilter.txx:106:56: error: ‘ThreadIdType’ has not been declared
::ThreadedGenerateData(const RegionType& windowRegion, ThreadIdType threadId)
^
In file included from /lustre/home/acct-bmelgn/bmelgn-5/panweihao/ACME/Code/Examples/MembraneOrientationBasedHessianCalculator.cxx:52:0:
/lustre/home/acct-bmelgn/bmelgn-5/panweihao/ACME/Code/PlanarityFilter/itkStructMeasureImageFilter.h:154:37: error: ‘ThreadIdType’ has not been declared
ThreadIdType threadId);
^
In file included from /lustre/home/acct-bmelgn/bmelgn-5/panweihao/ACME/Code/PlanarityFilter/itkStructMeasureImageFilter.h:187:0,
from /lustre/home/acct-bmelgn/bmelgn-5/panweihao/ACME/Code/Examples/MembraneOrientationBasedHessianCalculator.cxx:52:
/lustre/home/acct-bmelgn/bmelgn-5/panweihao/ACME/Code/PlanarityFilter/itkStructMeasureImageFilter.txx:223:67: error: ‘ThreadIdType’ has not been declared
::ThreadedGenerateData(const OutputImageRegionType& windowRegion, ThreadIdType threadId)
^
make[2]: *** [Examples/CMakeFiles/membraneOrientationBasedHessianCalculator.dir/MembraneOrientationBasedHessianCalculator.o] Error 1
make[1]: *** [Examples/CMakeFiles/membraneOrientationBasedHessianCalculator.dir/all] Error 2
make: *** [all] Error 2

I got a 403 forbidden error when accessing https://wiki.med.harvard.edu/pub/SysBio/Megason/ACME/

Is there any other download link for the example data?