[ITK] Read raw image and save as nii

Sat May 21 16:53:32 EDT 2016

Thanks for the clarification, Dženan! I didn't know that. So the problem is
not in the orientation. I wish I could get a grasp on what's wrong with my
code. Unfortunately, I'm clueless so far.

Best,
Paulo

Dženan Zukić <dzenanz at gmail.com> schrieb am Sa., 21. Mai 2016, 11:06:

> 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
>>> Community at itk.org
>>> http://public.kitware.com/mailman/listinfo/community
>>>
>>>
>>> --
>>> "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."
>>
>
> --
"Se podes olhar, vê. Se podes ver, repara."
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