[ITK] Read raw image and save as nii

[Paulo Guilherme Freire]

Hello, Timothee. Thank you for your suggestions.

I opened the new file on ITK-Snap and saw that the LPS orientation was not
successfully streamed to it. The orientation ITK-Snap is showing the image
is in is RAI. I tried changing the LPS orientation to RAS in the .nhdr file
(since according to http://teem.sourceforge.net/nrrd/format.html#space,
there is no support to RAI). By doing so, I wasn't even able to save the
image to a new file.

Regarding the filter that is causing this problem, I believe that the
reader is to blame. If I open the raw image on ITK-Snap and manually input
the .nhdr information, the image is loaded (almost) succesfully. I say
almost because the orientation still remains RAI instead of LPS.

Best,
Paulo

On Sat, May 21, 2016 at 8:47 AM Timothee Evain <tevain at telecom-paristech.fr>
wrote:

> Hi Paulo,
>
> Some suggestions:
> -Is the LPS orientation of your data streamed successfully to your new
> file ?
> -Which filter is in cause ? the reader or the writer ? Are you able to
> visualize your data after loading it but before writing it (with VTK for
> example) ?
>
> Tim
>
>
>
> ----- Mail original -----
> De: "Paulo Guilherme Freire" <pauloguilhermefreire at gmail.com>
> À: "Dženan Zukić" <dzenanz at gmail.com>
> Cc: community at itk.org
> Envoyé: Vendredi 20 Mai 2016 22:54:44
> Objet: Re: [ITK] Read raw image and save as nii
>
> Hello, Dženan. Thank you for your suggestion. I just tried using endian:
> big, but still no success.
>
> Best,
> Paulo
>
> On Fri, May 20, 2016 at 5:46 PM Dženan Zukić < dzenanz at gmail.com > wrote:
>
>
>
> 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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>
>
> --
> "Se podes olhar, vê. Se podes ver, repara."
>
> _______________________________________________
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>
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