The collapse of the dimension using extractFilter does not make sense

Dear all,

I want to do 3d segmentation of an especific vessel but i am having a lot of problems with memory with the 3d filters as this vessels has no contrast at all and i do not have any prior info only intensities and I have decided to do it in 2d. I read a series of dicoms and I am trying to collapse the x dimension because it is the view where i can see much better the vessel. I check the dimensions and they are correct [numberslice,589,180] and i copy the result in a 2d dicom and I see that the result doesn´t show what it is expect. It is as if the image was twisted when it reads the series and then when i read the matrix (volume) through x, the results does not have anything to do with the view i want to see.

Any help?. Thanks

//  Find input image size
	InputImageType::RegionType inputRegion =
	InputImageType::SizeType size = inputRegion.GetSize();
	const unsigned int collapseDim = 0;
	InputImageType::SizeType::SizeValueType numSlices = size[collapseDim];
	size[collapseDim] = 0;   // collapse dimension ( 3D->2D )

							 //  Set region for 2D extraction
	InputImageType::IndexType start = inputRegion.GetIndex();
	InputImageType::RegionType desiredRegion;

//  Extract 2D slices, perform processing
	for (unsigned int sliceNumber = 0; sliceNumber<numSlices; sliceNumber++)
		start[collapseDim] = sliceNumber;


		using PixelType = short;
		constexpr unsigned int Dimension = 2;
		using ImageType = itk::Image< PixelType, Dimension >;

		using WriterType = itk::ImageFileWriter< ImageType >;

		WriterType::Pointer writer = WriterType::New();

		std::string index = std::to_string(sliceNumber);
		std::string  fileoutput = "results" + index + ".dcm";


		catch (itk::ExceptionObject & err)
			std::cerr << "ExceptionObject caught !" << std::endl;
			std::cerr << err << std::endl;
			return EXIT_FAILURE;



The question is not entirely clear to me. Can you provide some images/screenshots?

Not tested but:

size[collapseDim] = 0; 

Try with 1:

size[collapseDim] = 1; 

And let us know!

Hello, i think the collapseDim is correct because i want the sagital view but it is the result what i find weird. I realized that the slice was upside down because i created a dicom for each slice to see the result, and it is not

the same as the sagittal view of the 3d slicer when i load the dicom series and it is there where i can see much better the vessels. And the slices i extract are upside down.

Thank you