[ITK] Read raw image and save as nii

[Dženan Zukić]

ITK's naming convention is opposite to DICOM's. DICOM's LPS is called RAI
in ITK. So there might not be any problem regarding that.

On Sat, May 21, 2016 at 8:59 AM, Paulo Guilherme Freire <
pauloguilhermefreire at gmail.com> wrote:

> 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."
>>
>> _______________________________________________
>> Community mailing list
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>>
>>
>> --
>> "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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