Hello, I was able to reproduced a truncated volume with clang on OSX. This looks like a 32-bit truncation issue.
I also created the following pipeline: ImageFilterReader->StreamingImageFilter->ImageFileWriter I set the NumberofStreamDivisions to 20 on the StreamingImageFIlter, to make the reader stream, but I didn't use streaming in the writer. The volume still appears truncated. This narrows the problem to the Nifti reading. Hopefully, there is a problem in the itk ImageIO[1], and not in the Nifti library. Contributions to fix the problem are welcome. Brad [1] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx On Sep 21, 2015, at 6:32 PM, Maryana <nexn...@gmail.com> wrote: > > > > Hi! > > If anyone would like to repeat the test, this is my test file: > https://www.dropbox.com/s/7hpen46znk1h58l/brain_8bit.nii?dl=0 > If I convert that file to MetaIO without streams, and use ExtractImageFilter > to read one file perpendicular to Y (as in the code I'm sending bellow) it > works fine. However if I convert it to MetaIO using streams and use the same > code to read the same slice, I end up with a truncated image. I have the same > result when I use Paraview for visualization. By the way, for what I've read > from ITK documentation NIfti supposedly supports streamed reading. So I'm > guessing that using Nifti in this case would be ok. Is this correct? Would > anyone have an idea on what's wrong? > > Thank you! > > > > Code for reading slice: > > > > #include "itkImageFileReader.h" > #include "itkImageFileWriter.h" > #include "itkExtractImageFilter.h" > #include "itkImage.h" > > > int main( int argc, char ** argv ) > { > > typedef unsigned char InputPixelType; > typedef unsigned char OutputPixelType; > > typedef itk::Image< InputPixelType, 3 > InputImageType; > typedef itk::Image< OutputPixelType, 2 > OutputImageType; > > typedef itk::ImageFileReader< InputImageType > ReaderType; > typedef itk::ImageFileWriter< OutputImageType > WriterType; > > std::string fileIn = "mri2_stream.mha"; > std::string fileOut = "slice.tif"; > const char * inputFilename = fileIn.c_str(); > const char * outputFilename = fileOut.c_str(); > > ReaderType::Pointer reader = ReaderType::New(); > WriterType::Pointer writer = WriterType::New(); > > reader->SetFileName( inputFilename ); > writer->SetFileName( outputFilename ); > > typedef itk::ExtractImageFilter< InputImageType, OutputImageType > > FilterType; > FilterType::Pointer filter = FilterType::New(); > filter->InPlaceOn(); > filter->SetDirectionCollapseToSubmatrix(); > > reader->UpdateOutputInformation(); > InputImageType::RegionType inputRegion = > reader->GetOutput()->GetLargestPossibleRegion(); > > InputImageType::SizeType size = inputRegion.GetSize(); > > std::cout << "Size: " << std::endl; > std::cout << size[0] << std::endl; > std::cout << size[1] << std::endl; > std::cout << size[2] << std::endl; > > > InputImageType::IndexType start = inputRegion.GetIndex(); > const unsigned int sliceNumber = 800; > > std::cout << "Start: " << std::endl; > std::cout << start[0] << std::endl; > std::cout << start[1] << std::endl; > std::cout << start[2] << std::endl; > > size[1] = 0; > start[1] = sliceNumber; > > InputImageType::RegionType desiredRegion; > desiredRegion.SetSize( size ); > desiredRegion.SetIndex( start ); > > filter->SetExtractionRegion( desiredRegion ); > > filter->SetInput( reader->GetOutput() ); > writer->SetInput( filter->GetOutput() ); > > try > { > writer->Update(); > } > catch( itk::ExceptionObject & err ) > { > std::cerr << "ExceptionObject caught !" << std::endl; > std::cerr << err << std::endl; > return EXIT_FAILURE; > } > > > return EXIT_SUCCESS; > } > > > > On Mon, Sep 21, 2015 at 12:07 PM, Maryana <nexn...@gmail.com> wrote: > Hi, > > I use Linux Mint 64bits, GCC 4.8, Cmake 2.8. I'm compiling to this platform. > > Thank you! > > On Mon, Sep 21, 2015 at 11:55 AM, Bradley Lowekamp <blowek...@mail.nih.gov> > wrote: > Hello Maryana, > > What compiler, platform and architecture are you compiling for? > > Brad > > On Sep 21, 2015, at 2:54 PM, Maryana <nexn...@gmail.com> wrote: > > > > > Hi ITK Users/Devs, > > > > I'm new to ITK and I need to write a small program to convert Nifti images > > to MetaIO. However, I need to use the streamed reader/writer because my > > image volumes can have several gigabytes. I was doing some tests with the > > following code but I've realized that whenever I use the stream I end up > > with a truncated volume. I'm using ITK 4.8. I'm sure my volume is of > > unsigned char type. Also, when I comment out the > > writer->SetNumberOfStreamDivisions(20); line I works fine. Does anyone > > knows what is wrong? > > > > Thank you! > > > > #include <cstdlib> > > #include <string> > > #include <iostream> > > > > #include "itkImage.h" > > #include "itkImageFileReader.h" > > #include "itkImageFileWriter.h" > > #include "itkImageRegionIterator.h" > > #include "itkNiftiImageIO.h" > > #include "itkMetaImageIO.h" > > > > > > int main(int argc, char const *argv[]){ > > > > std::string fileIn = "brain_8bit.nii"; > > std::string fileOut = "mri2_stream.mha"; > > > > typedef itk::Image<unsigned char,3> Image3D; > > > > //Reader > > typedef itk::ImageFileReader<Image3D> ReaderType; > > ReaderType::Pointer reader = ReaderType::New(); > > reader->SetFileName(fileIn); > > > > //Writer > > typedef itk::ImageFileWriter<Image3D> WriterType; > > WriterType::Pointer writer = WriterType::New(); > > writer->SetFileName(fileOut); > > writer->SetNumberOfStreamDivisions(20); > > writer->SetInput(reader->GetOutput()); > > > > > > std::cout << "Input: " << fileIn << std::endl; > > std::cout << "Output: " << fileOut << std::endl; > > > > std::cout << "Writing..." << std::endl; > > try > > { > > writer->Update(); > > } > > catch( itk::ExceptionObject & err ) > > { > > std::cerr << "ExceptionObject caught !" << std::endl; > > std::cerr << err << std::endl; > > return EXIT_FAILURE; > > } > > std::cout << "Finished." << std::endl; > > > > > > return EXIT_SUCCESS; > > } > > > > > > > > > > > > -- > > "Tudo no mundo começou com um sim. Uma molécula disse sim a outra molécula > > e nasceu a vida" - Clarice Lispector > > _______________________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-developers > > > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users
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