[ITK] Read raw image and save as nii

[Dženan Zukić]

Can you try endian: big?

On Fri, May 20, 2016 at 2:18 PM, Paulo Guilherme Freire <
pauloguilhermefreire at gmail.com> wrote:

> Hi, Matt.
>
> Thank you for your answer! I tried different kinds of image pixel type
> (short, unsigned short, int, unsigned char, double) but to no avail. I
> really don't know what's wrong.
>
> An example of a .nhdr file I'm using is the following:
>
> NRRD0004
> # Complete NRRD file format specification at:
> # http://teem.sourceforge.net/nrrd/format.html
> type: short
> dimension: 3
> space: left-posterior-superior
> sizes: 512 512 512
> space directions: (0.5,0,0) (0,0.5,0) (0,0,0.5)
> kinds: domain domain domain
> endian: little
> encoding: raw
> space origin: (0,0,0)
> data file: CHB_train_Case01_FLAIR.raw
>
> Best,
> Paulo
>
> Matt McCormick <matt.mccormick at kitware.com> schrieb am Fr., 20. Mai 2016,
> 15:03:
>
>> Hi Paulo,
>>
>> Your code looks good. Is the image pixel type correct for the input data?
>>
>> HTH,
>> Matt
>>
>> On Fri, May 20, 2016 at 12:36 PM, Paulo Guilherme Freire
>> <pauloguilhermefreire at gmail.com> wrote:
>> > Hello, everyone.
>> >
>> > I am trying to do something quite simple: I have a raw image (and its
>> > corresponding .nhdr file) and I want to read it and save it in .nii
>> format.
>> > The image type, according to the .nhdr file, is short. Below is the
>> code I'm
>> > using.
>> >
>> > My question is: what am I missing here? After I save the image to file
>> and
>> > open it, I don't get the expected result; rather, I get an image that
>> > reminds a TV static.
>> >
>> > Could you please help me?
>> >
>> > Thanks in advance!
>> >
>> > Best,
>> > Paulo
>> >
>> > #include <iostream>
>> > #include <itkImage.h>
>> > #include <itkImageFileWriter.h>
>> > #include <itkImageFileReader.h>
>> >
>> > int main(int argc, char* argv[])
>> > {
>> >
>> >   typedef itk::Image<short, 3> ImageType;
>> >
>> >   if(argc < 3)
>> >   {
>> >     // programName <filename>.nhdr <filename>.nii
>> >     std::cerr << "Usage: " << argv[0] << " Output1.nhdr Output2.nii\n";
>> >     return EXIT_FAILURE;
>> >   }
>> >
>> >   // Read .nhdr file
>> >   typedef itk::ImageFileReader< ImageType > ReaderType;
>> >   ReaderType::Pointer reader = ReaderType::New();
>> >   reader->SetFileName(argv[1]);
>> >   reader->Update();
>> >
>> >   // Save it as nii
>> >   typedef itk::ImageFileWriter< ImageType > WriterType;
>> >   WriterType::Pointer writer = WriterType::New();
>> >   writer->UseInputMetaDataDictionaryOn(); // is this necessary?
>> >   writer->SetInput(reader->GetOutput());
>> >   writer->SetFileName(argv[2]);
>> >
>> >   try
>> >   {
>> >     writer->Update();
>> >   }
>> >   catch(itk::ExceptionObject e)
>> >   {
>> >     std::cout << "Could not save image to file\n";
>> >   }
>> >
>> >   return EXIT_SUCCESS;
>> > }
>> >
>> >
>> > --
>> > "Se podes olhar, vê. Se podes ver, repara."
>> >
>> > _______________________________________________
>> > Community mailing list
>> > Community at itk.org
>> > http://public.kitware.com/mailman/listinfo/community
>> >
>>
> --
> "Se podes olhar, vê. Se podes ver, repara."
>
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>
>
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