[Insight-users] cannot open DICOM with ITK 4.3.1

Tue Jun 4 11:05:18 EDT 2013

I tried your code with the same issue. What ITK version are you using,
under which platform?
In my linux system it works only with ITK4.2.1 but not with 4.3.x or 4.4.0.

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On 4 June 2013 15:53, Dženan Zukić <dzenanz at gmail.com> wrote:

> I can read it without any problem using this tool:
>
> http://itk-insight-users.2283740.n2.nabble.com/How-to-compare-the-result-of-segmentation-with-ground-truth-tp7583172p7583184.html
>
>
> On Mon, Jun 3, 2013 at 2:04 PM, Luca Tersi <lucatersi at gmail.com> wrote:
>
>> Has anybody tried to read my image file (available here<https://dl.dropboxusercontent.com/u/9312078/frame0001.dcm>)?
>>
>> Do you think my problem is related to the image itself or to my ITK
>> compilation?
>>
>> Thanks
>>
>> Luca
>>
>>
>> ---
>>
>> ----------------------------------------------------------------------------------------------------------
>>
>>
>> On 21 May 2013 17:35, Luca Tersi <lucatersi at gmail.com> wrote:
>>
>>> Ok, you can download it from here<https://dl.dropboxusercontent.com/u/9312078/frame0001.dcm>
>>> .
>>> It is part of a DICOM series already processed and saved with ITK.
>>> Thanks for your help.
>>> L
>>>
>>>
>>> ---
>>>
>>> ----------------------------------------------------------------------------------------------------------
>>>
>>>
>>> On 21 May 2013 17:22, Bill Lorensen <bill.lorensen at gmail.com> wrote:
>>>
>>>> The compiler should not matter.
>>>>
>>>> Can you share a dicom file that you cannot open?
>>>>
>>>>
>>>> On Tue, May 21, 2013 at 11:14 AM, Luca Tersi <lucatersi at gmail.com>wrote:
>>>>
>>>>> Dear Bill,
>>>>>
>>>>> I finally managed to test my code on a Windows platform (MinGW) using
>>>>> ITK 4.3.2 and everything seems to work properly.
>>>>> I tried again on linux and both 4.3.1 and 4.3.2 do not work.
>>>>>
>>>>> Might it be a compiler related issue? (gcc 4.8 on linux and 4.7 on
>>>>> windows)
>>>>>
>>>>> Thanks a lot
>>>>>
>>>>> Luca
>>>>>
>>>>>
>>>>>
>>>>> ---
>>>>>
>>>>> ----------------------------------------------------------------------------------------------------------
>>>>>
>>>>>
>>>>> On 21 April 2013 00:50, Luca Tersi <lucatersi at gmail.com> wrote:
>>>>>
>>>>>> Yes, it could be read. I can switch between 4.3.1 and 4.2.1 (same
>>>>>> cmake settings): I can open any DICOM file with 4.2.1 but not with 4.3.1.
>>>>>> Maybe I'm missing something..
>>>>>> Thanks a lot
>>>>>> Luca
>>>>>>
>>>>>> PS. I'm working on Linux Manjaro 64-bit, next week I will try to run
>>>>>> it on Windows
>>>>>>
>>>>>>
>>>>>> ---
>>>>>>
>>>>>> ----------------------------------------------------------------------------------------------------------
>>>>>>
>>>>>>
>>>>>> On 19 April 2013 21:09, Bill Lorensen <bill.lorensen at gmail.com>wrote:
>>>>>>
>>>>>>> Are you saying the same file could be read prior to the upgrade?
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Wed, Apr 17, 2013 at 5:26 AM, Luca Tersi <lucatersi at gmail.com>wrote:
>>>>>>>
>>>>>>>> Dear all,
>>>>>>>>
>>>>>>>> I've been using ITK and VTK for a while, but after a recent upgrade
>>>>>>>> to ITK4.3.1, I cannot open DICOM series or single .dcm files. I obtain the
>>>>>>>> following exception:
>>>>>>>>
>>>>>>>>
>>>>>>>> itk::ExceptionObject (0x2a12eb0)
>>>>>>>>
>>>>>>>> Location: "unknown"
>>>>>>>>
>>>>>>>> File:
>>>>>>>> /home/lt/Work/FLUORO/kitware/ITK4.3.1_src/Modules/IO/GDCM/src/itkGDCMImageIO.cxx
>>>>>>>>
>>>>>>>> Line: 335
>>>>>>>>
>>>>>>>> Description: itk::ERROR: GDCMImageIO(0x3180830): Cannot read
>>>>>>>> requested file
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> This is my code:
>>>>>>>>
>>>>>>>>  QString filename = QFileDialog::getOpenFileName(currentDir, "*",
>>>>>>>> this, "Open file dialog", "Choose Input DICOM File" );
>>>>>>>>   if ( filename.length()  == 0 )
>>>>>>>>     {
>>>>>>>>       cout<<"aborted"<<endl;
>>>>>>>>       return;
>>>>>>>>     }
>>>>>>>>
>>>>>>>>   typedef itk::Image< IntPixelType, voxelDimension >
>>>>>>>> IntVolumeType;
>>>>>>>>   typedef itk::ImageFileReader< IntVolumeType >
>>>>>>>> IntVolumeReaderType;
>>>>>>>>   IntVolumeReaderType::Pointer reader=IntVolumeReaderType::New();
>>>>>>>>   reader->SetFileName ( filename.latin1() );
>>>>>>>>   ImageIOType::Pointer gdcmImageIO = ImageIOType::New();
>>>>>>>>   reader->SetImageIO ( gdcmImageIO );
>>>>>>>>
>>>>>>>>   try
>>>>>>>>   {
>>>>>>>>     reader->Update();
>>>>>>>>   }
>>>>>>>>   catch ( itk::ExceptionObject & excp )
>>>>>>>>   {
>>>>>>>>     std::cerr << "Error reading the images " << std::endl;
>>>>>>>>     std::cerr << excp << std::endl;
>>>>>>>>     return;
>>>>>>>>   }
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> If I do not specify any IO object (it was working with ITK4.2.1) I
>>>>>>>> get:
>>>>>>>>
>>>>>>>> itk::ImageFileReaderException (0x13a7510)
>>>>>>>>
>>>>>>>> Location: "void itk::ImageFileReader<TOutputImage,
>>>>>>>> ConvertPixelTraits>::GenerateOutputInformation() [with TOutputImage =
>>>>>>>> itk::Image<short unsigned int, 3u>; ConvertPixelTraits =
>>>>>>>> itk::DefaultConvertPixelTraits<short unsigned int>]"
>>>>>>>>
>>>>>>>> File:
>>>>>>>> /home/lt/Work/FLUORO/kitware/ITK4.3.1_src/Modules/IO/ImageBase/include/itkImageFileReader.hxx
>>>>>>>>
>>>>>>>> Line: 143
>>>>>>>>
>>>>>>>> Description: Could not create IO object for file
>>>>>>>> /run/media/lt/CODONICS/DICOM/ST000000/SE000015/XA000000
>>>>>>>>
>>>>>>>> Tried to create one of the following:
>>>>>>>>
>>>>>>>> JPEGImageIO
>>>>>>>>
>>>>>>>> GDCMImageIO
>>>>>>>>
>>>>>>>> BMPImageIO
>>>>>>>>
>>>>>>>> LSMImageIO
>>>>>>>>
>>>>>>>> PNGImageIO
>>>>>>>>
>>>>>>>> TIFFImageIO
>>>>>>>>
>>>>>>>> VTKImageIO
>>>>>>>>
>>>>>>>> StimulateImageIO
>>>>>>>>
>>>>>>>> BioRadImageIO
>>>>>>>>
>>>>>>>> MetaImageIO
>>>>>>>>
>>>>>>>> NiftiImageIO
>>>>>>>>
>>>>>>>> NrrdImageIO
>>>>>>>>
>>>>>>>> GiplImageIO
>>>>>>>>
>>>>>>>> HDF5ImageIO
>>>>>>>>
>>>>>>>> You probably failed to set a file suffix, or
>>>>>>>>
>>>>>>>> set the suffix to an unsupported type.
>>>>>>>>
>>>>>>>> Is anybody having the same issue? Do you have any hints?
>>>>>>>>
>>>>>>>> Thanks in advance
>>>>>>>>
>>>>>>>> Luca
>>>>>>>> ---
>>>>>>>>
>>>>>>>> *Luca Tersi, Ph.D.*
>>>>>>>> *Health Sciences and Technologies - Interdepartmental Center for
>>>>>>>> Industrial Research (HST - ICIR) *
>>>>>>>> *Alma Mater Studiorum - University of Bologna; *Via Cavalcavia
>>>>>>>> 797, I-47521 Cesena (FC) - Italy
>>>>>>>>
>>>>>>>> ----------------------------------------------------------------------------------------------------------
>>>>>>>>
>>>>>>>>
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>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Unpaid intern in BillsBasement at noware dot com
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Unpaid intern in BillsBasement at noware dot com
>>>>
>>>
>>>
>>
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