[Insight-users] EncapsulateMetaData problem

[Luis Ibanez]

Hi Antoine,

If the information from the incoming DICOM image is incorrect,
you should first complain with your image provider. Even if
you are scanning animals, it is pretty sad that scanner vendors
in the 21st century can't yet get right the pixel spacing of an
image.


If you are forced to fix the pixel spacing, you should do it by
using the ChangeInformationImageFilter:

http://www.itk.org/Insight/Doxygen/html/classitk_1_1ChangeInformationImageFilter.html

Look at the methods

   SetOutputSpacing();
   ChangeSpacingOn();


The example that shows how to change tags applies to the information
that is not inherent to ITK images, such as:

      Number of pixels
      Pixel Spacing
      Origin
      Orientation (direction cosines)


These four items of the output image DICOM tags are *NOT* taken
from the MetaData dictionary. They are taken from the itk::Image
itself.

In other word, with ITK you can edit *SOME* of the DICOM tags,
but not *ALL* of them. In practice, the ones that you can't
edit with ITK is because you SHOULDN't have to edit them.




                ITK IS OPEN SOURCE:
             Please look at the code:

  You will see where we are settting the basic information
  into the DICOM tags:


    Line 920 :  of itkGDCMImageIO.cxx  pixel spacing
    Line 928 :  of itkGDCMImageIO.cxx  slice spacing

    Lines 948-954:  same file :  for Direction (orientation cosines).




To summarize, leave the DICOM tags alone.

What you should do is:



   1) Complain about the inhabilithy of the image acquirers
      for getting right basic information about an image.

      ... If you can't trust the image spacing...
          what can you trust ?


   2) In your code, just after reading the DEFECTIVE DICOM image,
      pass it through a ChangeInformationFilter and fix the spacing.

      Paradoxically enough, you are probably replacing the old values
      with new values that you obtained from the same people who
      provided you with a defective image in the first place.

      The image will then have the correct information, and you
      will not need to touch the DICOM tags. Just let ITK save this
      information into the DICOM header in a normal way.


   3) Go and complain again, with your image provider.

      The bottom line is that:

         If they can't get right the simplest piece of information
         such as pixel spacing, then how can you trust that they
         are solving correctly the other really complicated aspect
         of an image.


      The fact that this is an animal experiment is not an
      excuse for accepting mediocrity in the image acquisition.




   Regards,


      Luis



==========================
Antoine Leimgruber wrote:
> Hi Luis,
> 
> Thank you for your answer !
> 
> Unfortunately, I have to do it because the spacing tags coming out of 
> the imaging modality are incorrect. (Do not be concerned, though, we are 
> imaging animals and not patients).
> 
> I am not quite sure to understand your statement that ITK will not let 
> me do it since I understood that the DicomReadChangeHeaderWrite.cxx 
> example demonstrates the manual edition of Dicom tags:
> 
>   //This example illustrates how to read a single DICOM slice and write 
> it back
>   //with some changed header information as another DICOM slice.
> 
> It puzzles me because edition of tags (0018|1164) and (0028|0030) 
> works when I run the code a second time on the output image of the first 
> run.
> 
> Do you mean that ITK cannot be used for editing Dicom Headers, or are 
> you answering the second part of my question about using ITK to erase 
> dicom tags ? 
> 
> Antoine
> 
> 
> Le 19 mai 07 à 06:30, Luis Ibanez a écrit :
> 
>>
>> Hi Antoine,
>>
>> Are you trying to manually edit the DICOM tag
>> describing the image spacing ?
>>
>> If so,
>> ITK will not let you do that.
>>
>> ITK uses the actual image spacing of the image
>> and writes it down in the DICOM tags.
>>
>>
>>
>>    Regards,
>>
>>
>>       Luis
>>
>>
>>
>> --------------------------
>> Antoine Leimgruber wrote:
>>
>>> Dear all,
>>> I am trying to edit 3 dicoms tags (see section of code at the end of 
>>> the message).
>>> When I run the code once, the output dicom image has 2 of the 3 tags 
>>> edited. The tag 0028|0030 remains unchanged.
>>> If I run the code again with the previous output image as input, then 
>>> the third tag of the new output is also edited.
>>> What can I do to avoid running twice my code on each image ?
>>> An alternative would be to remove the tag 0018|1164 from the header. 
>>> How can I do it ?
>>> Thank you for your help
>>> Antoine
>>> [...]
>>> InputImageType::Pointer inputImage = reader->GetOutput();
>>> typedef itk::MetaDataDictionary   DictionaryType;
>>> DictionaryType & dictionary = inputImage->GetMetaDataDictionary();
>>> itk::EncapsulateMetaData<std::string>(dictionary,"0018|1164", 
>>> std::string("0.164800\\0.312500"));
>>> itk::EncapsulateMetaData<std::string>(dictionary,"0028|0030", 
>>> std::string("0.164800\\0.312500"));   
>>> itk::EncapsulateMetaData<std::string>(dictionary,"0010|0010", 
>>> std::string("y pixel size edited"));
>>> typedef itk::ImageFileWriter< InputImageType >  WriterType;
>>> WriterType::Pointer writer = WriterType::New();
>>>   writer->SetInput( reader->GetOutput() );
>>>   writer->SetFileName( argv[2] );
>>>   writer->SetImageIO( gdcmImageIO );
>>>   try
>>>     {
>>>     writer->Update();
>>> [...]
>>> _______________________________________________
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>>> Insight-users at itk.org <mailto:Insight-users at itk.org>
>>> http://www.itk.org/mailman/listinfo/insight-users
> 
>