[Insight-users] Convert NRRD into DICOM
Bill Lorensen
bill.lorensen at gmail.com
Fri Jul 3 08:26:53 EDT 2009
What is the command line you are typing?
On Fri, Jul 3, 2009 at 8:22 AM, Ezequiel Geremia<t-egerem at microsoft.com> wrote:
> Hi Bill,
> Here is the .nhdr header associated with the .raw datafile
> Regards,
> Ezequiel
>
>
> -----Original Message-----
> From: Bill Lorensen [mailto:bill.lorensen at gmail.com]
> Sent: 03 July 2009 12:45
> To: Ezequiel Geremia
> Cc: Luis Ibanez; itk
> Subject: Re: [Insight-users] Convert NRRD into DICOM
>
> Can you post the nrrd header file?
>
> On Fri, Jul 3, 2009 at 5:48 AM, Ezequiel Geremia<t-egerem at microsoft.com> wrote:
>> Hi,
>>
>>
>>
>> Thank you, I appreciate your support on this question.
>>
>>
>>
>> The images are volumes dimensions: ( 512, 512, 512 ) and pixel type is
>> short.
>>
>>
>>
>> While trying to run the task manager with the ITK conversion executable
>> there is no jump in RAM usage, this is why I think the RAW volume is not
>> even loaded in memory, the reader just does not find it.
>>
>>
>>
>> My understanding is that there is no memory problem, indeed I manage to load
>> the same image with the same executable just by moving to the directory
>> containing the NRRD volumes.
>>
>>
>>
>> Many thanks,
>>
>>
>>
>> Ezequiel
>>
>>
>>
>> From: Luis Ibanez [mailto:luis.ibanez at kitware.com]
>> Sent: 02 July 2009 23:56
>> To: Ezequiel Geremia
>> Cc: itk
>> Subject: Re: [Insight-users] Convert NRRD into DICOM
>>
>>
>>
>> Hi Ezequiel,
>>
>> Thanks for posting the error message from the Exception.
>>
>> I just verified that a NRRD header file can be moved along
>> with its associated .raw file to a different directory and still
>> be read with the NRRD reader included into ITK.
>>
>> --
>>
>>
>> Looking at the code...
>>
>> ...(Ah!, the Unbeatable Glory of Open Source)...
>>
>> We find that the error message that you posted is being
>> generated by line 161 of:
>>
>> Insight/Utilities/NrrdIO/formatNRRD.c
>>
>> that curiously is part of (160-165):
>>
>> if ((err = (char*)malloc(strlen(fname) + AIR_STRLEN_MED))) {
>> sprintf(err, "%s: couldn't open \"%s\" (data file %d of %d) for %s",
>> me, fname, nio->dataFNIndex+1, (int)_nrrdDataFNNumber(nio),
>> reading ? "reading" : "writing");
>> biffAdd(NRRD, err); free(err);
>> }
>>
>>
>>
>> Admittedly,
>> the error message is quite misleading here...
>>
>> It is clear that what is happening in these lines above
>> is that the code is failing to allocate enough memory
>> for your image.
>>
>> So...
>> please tell us:
>>
>>
>> A) How big is the image ?
>>
>> B) How much RAM do you have ?
>>
>>
>> and please run this code while you have open the
>> TaskManager, and check on how much memory
>> is available at the time the program post this message.
>>
>>
>> If memory allocation turns out to be the real problem,
>> please feel free to add a bug report suggesting
>> that this error message be replaced with something
>> that indicates that we are dealing with a Memory
>> Allocation problem, as opposed to an I/O problem.
>>
>> You can report bugs at:
>> http://public.kitware.com/Bug/my_view_page.php
>>
>>
>>
>>
>> Please let us know what you find,
>>
>>
>> Thanks
>>
>>
>> Luis
>>
>>
>> -----------------------------------------------------------------------------
>>
>> On Thu, Jul 2, 2009 at 1:31 PM, Ezequiel Geremia <t-egerem at microsoft.com>
>> wrote:
>>
>> Hi Luis,
>>
>> The reader.Update() call is inside a try\catch block.
>>
>> Here is the exception which is caught:
>>
>> ExceptionObject caught !
>>
>> itk::ExceptionObject (00A0E9A8)
>> Location: "void __thiscall itk::NrrdImageIO::ReadImageInformation(void)"
>> File: ..\..\..\src\Code\IO\itkNrrdImageIO.cxx
>> Line: 264
>> Description: itk::ERROR: NrrdImageIO(025D1DC0): ReadImageInformation: Error
>> read
>> ing C:\Downloads\MS-Lesion-Segmentation-2008\Extracted-Files\Test
>> ing-Data\CHB_test1_Part1\CHB_test1_Case01\CHB_test1_Case01_FLAIR.nhdr:
>> [nrrd] nrrdLoad: trouble reading "C:\Downloads\MS-Lesion-Segmenta
>> tion-2008\Extracted-Files\Testing-Data\CHB_test1_Part1\CHB_test1_Case01\CHB_test
>> 1_Case01_FLAIR.nhdr"
>> [nrrd] nrrdRead: trouble reading NRRD file
>> [nrrd] _nrrdFormatNRRD_read: couldn't open the first datafile
>> [nrrd] nrrdIoStateDataFileIterNext: couldn't open
>> "./CHB_test1_Case01_FLAIR.raw"
>> (data file 1 of 1) for reading
>>
>> In this case, the reader does not seem to add the path of the header file
>> (i.e.
>> "C:\Downloads\MS-Lesion-Segmentation-2008\Extracted-Files\Testing-Data\CHB_test1_Part1\CHB_test1_Case01\")
>> to the filename found in the header file and which is in the same directory
>> (i.e. "./CHB_test1_Case01_FLAIR.raw").
>>
>> Many thanks,
>>
>> Ezequiel
>>
>> -----Original Message-----
>> From: Luis Ibanez [mailto:luis.ibanez at kitware.com]
>>
>> Sent: 02 July 2009 17:51
>> To: Ezequiel Geremia; Insight Users
>> Subject: Re: [Insight-users] Convert NRRD into DICOM
>>
>>
>> Hi Ezequiel,
>>
>> Thanks for the update.
>>
>> I haven't seen this problem before.
>>
>> I would be very surprised if the reader relies on absolute
>> paths, because that will mean that it is impossible to
>> move NRRD files from one computer to another,... and even
>> from one directory to another in the same machine.
>>
>>
>>
>> Did you got an error message ?
>>
>> If so,
>> Could you please post it to the mailing list ?
>>
>> Are you placing the Update() call of the reader
>> inside a try/catch block ?
>>
>>
>>
>> Please let us konw
>>
>>
>> Thanks
>>
>>
>> Luis
>>
>>
>> ------------------------
>> Ezequiel Geremia wrote:
>>> Hi Luis,
>>>
>>> Thank you for answering my mail,
>>>
>>> I managed to read NRRD format by passing the header .nhdr or .mhd files
>>> and to convert them into DICOM series.
>>>
>>> The NRRD format I got form the MS Segmentation Challenge 2008 & Liver
>>> Tumor Segmentation Challenge 2008 websites seem to be specified as the union
>>> of a header and a RAW data file.
>>>
>>> However I experienced another issue concerning the reader. When I pass the
>>> header, which contains the relative filename of the .raw file to be
>>> converted, as an input, the reader is not able to find it (maybe because the
>>> reader relies on absolute filenames).
>>>
>>> Do you know a way out of this ?
>>>
>>> Regards,
>>>
>>> Ezequiel
>>>
>>>
>>>
>>> -----Original Message-----
>>> From: Luis Ibanez [mailto:luis.ibanez at kitware.com]
>>> Sent: 30 June 2009 22:27
>>> To: Ezequiel Geremia
>>> Cc: insight-users at itk.org
>>> Subject: Re: [Insight-users] Convert NRRD into DICOM
>>>
>>>
>>>
>>> Hi Ezequiel,
>>>
>>>
>>> If your input file is in NRRD format,
>>> why are you passing a RAW format as input ?
>>>
>>>
>>> ITK is expecting that a NRRD file will be called
>>>
>>> LTS_IMG05.nrrd
>>>
>>> not to be called:
>>>
>>> LTS_IMG05.raw
>>>
>>>
>>>
>>> Also, is this image 2D or 3D ?
>>>
>>>
>>> You may have to retouch the example code in order
>>> to manage 3D images.
>>>
>>>
>>> Regards,
>>>
>>>
>>> Luis
>>>
>>>
>>> --------------------------
>>> Ezequiel Geremia wrote:
>>>
>>>>Hi,
>>>>
>>>>
>>>>
>>>>I tried to convert NRRD, which is ITK supported format, data volumes
>>>>into DICOM volumes using the generic converter given in
>>>>/ImageReadWrite.exe/ with the following arguments
>>>>
>>>>- Input file: LTS_IMG05.raw
>>>>
>>>>- Output file: LTS_IM05.dcm (also tried .dic and .dicom file
>>>>extensions)
>>>>
>>>>- Exception:
>>>>
>>>>itk::ImageFileReaderException (0146EEC0)
>>>>
>>>>Location: "void __thiscall itk::ImageFileReader<class
>>>>itk::Image<short,3>,class itk::DefaultConvertPixelTraits<short>
>>>> >::GenerateOutputInformation(void)"
>>>>
>>>>File:
>>>>c:\users\t-egerem\software\insighttoolkit-3.14.0\src\code\io\itkImageFileReader.txx
>>>>
>>>>Line: 144
>>>>
>>>>Description: Could not create IO object for file
>>>>C:\Users\t-egerem\Downloads\3D-Liver-Tumor-Segmentation-Challenge-2008\Extracted-Files\Testing-Data\LTS_IMG05.raw
>>>>
>>>> Tried to create one of the following:
>>>>
>>>> GDCMImageIO
>>>>
>>>> MetaImageIO
>>>>
>>>> PNGImageIO
>>>>
>>>> VTKImageIO
>>>>
>>>> GiplImageIO
>>>>
>>>> BioRadImageIO
>>>>
>>>> LSMImageIO
>>>>
>>>> AnalyzeImageIO
>>>>
>>>> NiftiImageIO
>>>>
>>>> StimulateImageIO
>>>>
>>>> JPEGImageIO
>>>>
>>>> TIFFImageIO
>>>>
>>>> NrrdImageIO
>>>>
>>>> BMPImageIO
>>>>
>>>> DICOMImageIO2
>>>>
>>>> You probably failed to set a file suffix or set the suffix to an
>>>>unsupported type.
>>>>
>>>>
>>>>
>>>>Then I tried to shortcut the pluggable factory mechanism and it does not
>>>>as well with the same data it throws the following error message
>>>>
>>>> itk::ExceptionObject (0122F614)
>>>>
>>>>Location: "void __thiscall itk::ImageFileReader<class
>>>>itk::Image<short,3>,class itk::DefaultConvertPixelTraits<short>
>>>> >::EnlargeOutputRequestedRegion(class itk::DataObject *)"File:
>>>>c:\users\t-egerem\software\insighttoolkit-3.14.0\src\code\io\itkImageFileReader.txx
>>>>
>>>>Line: 342
>>>>
>>>>Description: itk::ERROR: ImageFileReader(0172F7C0): ImageIO returns IO
>>>>region that does not fully contain the requested regionRequested region:
>>>>ImageRegion (0122F8D8)
>>>>
>>>> Dimension: 3
>>>>
>>>> Index: [0, 0, 0]
>>>>
>>>> Size: [0, 0, 0]
>>>>
>>>>StreamableRegion region: ImageRegion (0172F8A4)
>>>>
>>>> Dimension: 3
>>>>
>>>> Index: [0, 0, 0]
>>>>
>>>> Size: [0, 0, 0]
>>>>
>>>>
>>>>
>>>>If you can think of a solution can you please point it out to me ?
>>>>
>>>>
>>>>
>>>>Regards,
>>>>
>>>>
>>>>
>>>>Ezequiel Geremia
>>>>
>>>>
>>>>
>>>>
>>>>------------------------------------------------------------------------
>>>>
>>>>_____________________________________
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>>>>
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>>>
>>>
>>>
>>
>>
>>
>> _____________________________________
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>>
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>
>
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