[Insight-users] (no subject)

[Mathieu Malaterre]

Wordon,

	I am definitely convinced now you are using a -broken- converter from 
ACR/NEMA to DICOMV3.

	Here is a list of problem:

- Transfer Syntax UID declare the image BigEndian but is in fact Little 
Endian (biggest issue !)
- Media Storage SOP Class UID and SOP Class UID declare the image being 
MR, but Modality specify 'OT' instead.
- Your image have a High Bit of 0
Some other error from dciodvfy:
Warning - Value dubious for this VR - (0x0008,0x0090) PN Referring 
Physician's Name  PN [0] = <Anonymized> - Retired Person Name form
Warning - Value dubious for this VR - (0x0010,0x0010) PN Patient's Name 
  PN [0] = <Anonymized> - Retired Person Name form
MRImage
Error - Missing attribute Type 2 Required Element=<PatientID> 
Module=<Patient>
Error - Missing attribute Type 2 Required Element=<PatientBirthDate> 
Module=<Patient>
Error - Missing attribute Type 2 Required Element=<PatientSex> 
Module=<Patient>
Error - Missing attribute Type 2 Required Element=<StudyDate> 
Module=<GeneralStudy>
Error - Missing attribute Type 2 Required Element=<StudyTime> 
Module=<GeneralStudy>
Error - Missing attribute Type 2 Required Element=<StudyID> 
Module=<GeneralStudy>
Error - Missing attribute Type 2 Required Element=<AccessionNumber> 
Module=<GeneralStudy>
Warning - Unrecognized defined term <OT> for attribute <Modality>
Error - Missing attribute Type 2C Conditional Element=<PatientPosition> 
Module=<GeneralSeries>
Error - Missing attribute Type 1 Required Element=<FrameOfReferenceUID> 
Module=<FrameOfReference>
Error - Missing attribute Type 2 Required 
Element=<PositionReferenceIndicator> Module=<FrameOfReference>
Error - Unrecognized enumerated value <ORIGINAL> for attribute <Image Type>
Error - Unrecognized enumerated value <PRIMARY> for attribute <Image Type>
Error - Missing attribute Type 1 Required 
Element=<ImageOrientationPatient> Module=<ImagePlane>
Error - Missing attribute Type 1 Required Element=<ImagePositionPatient> 
Module=<ImagePlane>
Warning - Unrecognized defined term <MONOCHROME2> for attribute 
<Photometric Interpretation>
Error - Unrecognized enumerated value <MONOCHROME2> for attribute 
<Photometric Interpretation>
Error - Missing attribute Type 1 Required Element=<ScanningSequence> 
Module=<MRImage>
Error - Missing attribute Type 1 Required Element=<SequenceVariant> 
Module=<MRImage>
Error - Missing attribute Type 2 Required Element=<ScanOptions> 
Module=<MRImage>
Error - Missing attribute Type 2 Required Element=<MRAcquisitionType> 
Module=<MRImage>
Error - Missing attribute Type 2 Required Element=<EchoTime> 
Module=<MRImage>
Error - Missing attribute Type 2 Required Element=<EchoTrainLength> 
Module=<MRImage>


So please keep your ACR/NEMA in original format, do not try to convert 
them to a broken DICOM type. gdcm perfectly handles ACR/NEMA, so if you 
use ITK, you can load your ACR/NEMA.

Or if you still want a batch program to convert your ACR/NEMA to 
DICOMv3, please use gdcm (with very few lines of code you should be all 
set).

Could you please confirm that this is indeed the case ? If so I will not 
consider this as a bug, and gdcm won't have to support this 
pseudo-'DICOM' file.

Thanks
Mathieu


Mathieu Malaterre wrote:
> Wordon,
> 
>     I had a look at your image, and for some reason it is declared as 
> Explicit VR - Big Endian (1.2.840.10008.1.2.2) but is indeed Explicit VR 
> - Little Endian (1.2.840.10008.1.2.1).
> 
>     Could you tell us where this image is coming from ?
> 
>     To fix your problem, you could use a program like hexedit on unix 
> and search for the string '1.2.840.10008.1.2.2' and replace it with 
> '1.2.840.10008.1.2.1'. Or recompile gdcm after changing the function:
> 
> gdcm::Document::SwitchByteSwapCode()
> 
>     To always have SwapCode = 1234 (on little endian system).
> 
> ----------------------------------------------------------------
> 
>     I'll try to find a way in gdcm to make it clearer that reading 
> failed. So that user could see right away where is the problem. Thanks 
> for the report and the sample image.
> 
> HTH
> Mathieu
> 
> wordon wrote:
> 
>> Hi, Mathieu:
>> I use the code to read the file as below.
>> But the output file only has header part.
>> Can you give me some point?
>> The DICOM file as attached file.
>> ================================================================
>> typedef signed short InputPixelType;
>>   const unsigned int   InputDimension = 3;
>>   typedef itk::Image< InputPixelType, InputDimension > InputImageType;
>>   typedef itk::ImageFileReader< InputImageType > ReaderType;
>>   ReaderType::Pointer reader = ReaderType::New();
>>   reader->SetFileName( argv[1] );
>>   typedef itk::GDCMImageIO           ImageIOType;
>>   ImageIOType::Pointer gdcmImageIO = ImageIOType::New();
>>   reader->SetImageIO( gdcmImageIO );
>>   reader->Update();
>>
>>   typedef itk::ImageFileWriter< InputImageType >  Writer1Type;
>>   Writer1Type::Pointer writer1 = Writer1Type::New();
>>   writer1->SetFileName( argv[2] );
>>   writer1->SetInput( reader->GetOutput() );
>>   writer1->SetImageIO( gdcmImageIO );
>>     writer1->Update();
>>  
>>     return EXIT_FAILURE;
>>     }
>> ==========================================================
>>
>> -----Original Message-----
>> From: Mathieu Malaterre [mailto:mathieu.malaterre at kitware.com] Sent: 
>> Thursday, September 29, 2005 10:34 PM
>> To: wordon
>> Cc: ITK Mailing List
>> Subject: Re: [Insight-users] (no subject)
>>
>> wordon wrote:
>>
>>> Hi,all :
>>>
>>> I has a problem about :
>>>
>>> How to read a DICOM file it has several image in one file?
>>
>>
>>
>> If you refer to multiframe DICOM, then the different slices are 
>> actually the whole (generally 3D) image. All you need to do is 
>> allocate the proper image type (Dimension and PixelType). And the 
>> reader should do the work for you.
>>
>> HTH
>> Mathieu
> 
> 
>