[ITK] DICOM read-write intensity rescaling problems still present in ITK 4.5.2

[Eriksson, Mikael]

Hi Matt,

I tested with a couple of different sets of data: one set had bits allocated = 16, bits stored = 16, pixel representation = 1, intercept = -1024 and slope = 1, and was rewritten as expected with intercept = 0, and otherwise the same types. The other set had bits allocated = 16, bits stored = 12, pixel representation = 0, intercept = -1000 and slope = 1, and was rewritten with bits allocated = 16, bits stored = 16, pixel representation = 0, intercept = -1000 and slope = 1, so in this case the problem appeared. Another difference, although I don't think it should be the reason for this problem, is that the first data set was just a plain folder with .dcm-files, and the other data-set was a folder with extensionless files, with a DICOMDIR file in the parent directory.

In neither case did the if-block you linked to execute, since the outpixeltype had not been changed from its initialized type gdcm::PixelFormat::UNKNOWN,  but rather, the else-block on line 989 with image.SetPixelFormat(pixeltype) had been executed.

I defined both my inputPixelType as unsigned short and outputPixelType as signed short in both cases.

Can you make any sense of all this?

Best regards,
Mikael


-----Original Message-----
From: Matt McCormick [mailto:matt.mccormick at kitware.com]
Sent: 19. kesäkuuta 2014 19:44
To: Eriksson, Mikael
Cc: community at itk.org
Subject: Re: [ITK] DICOM read-write intensity rescaling problems still present in ITK 4.5.2

Hi Mikael,

The rescaling should occur here [1].  If you run your code in a debugger, does it execute as expected?

Thanks,
Matt

[1] http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/IO/GDCM/src/itkGDCMImageIO.cxx;h=e1b194934bbc6ffb7dd492448bcf9f9a70153d5a;hb=HEAD#l997

On Thu, Jun 19, 2014 at 6:00 AM, Eriksson, Mikael <mikael.k.eriksson at philips.com> wrote:
> Hi all,
>
>
>
> I’m using ITK 4.5.2, and recently noticed that in my work with
> DICOM-images, the intensities are rescaled even without any processing
> taking place between the read/write operations. I found this old
> thread from November 2007,
> http://www.itk.org/pipermail/insight-users/2007-November/024327.html,
> which does a good job explaining the cause and a workaround. The cause
> is that when reading the image volume, rescale slope and intercept is
> used to convert the stored unsigned integers (assuming the “Pixel
> representation”-tag is 0) to real-world values, but then these
> real-world values are written into the new DICOM-series, while the
> rescale-parameters are copied, so on the next read the real-world values will be different.
>
>
>
> In the thread I posted, it says that a patch was added ahead of ITK
> 3.4 to correct the problem, but I’m using ITK 4.5.2 and still have the same issues.
> By using the workaround suggested by Eliana M. Vasquez Osorio,
>
>      WriterType::DictionaryArrayRawPointer dicts =
> dcmreader->GetMetaDataDictionaryArray();
>
>      WriterType::DictionaryArrayType::const_iterator itdict;
>
>      for( itdict = dicts->begin(); itdict != dicts->end(); itdict++ )
>
>      {
>
>          WriterType::DictionaryRawPointer dicti = *itdict;
>
>          //change 0028,1052,Rescale Intercept from -1000 to 0
>
>          itk::EncapsulateMetaData<std::string>( *dicti, "0028|1052",
> "0" );
>
>      }
>
> I get the end result I want, so the intensities stay the same by
> manually setting rescale intercept to 0 in the new written series. I
> added a line to set the slope to 1 as well just to be sure, but so far
> in the data I’ve been working with the rescale slope has been 1 as for Eliana.
>
>
>
> However, my question is: is this a good way to go about correcting
> this problem, and if it was corrected already in ITK 3.4, why then do
> I see the same behaviour with ITK 4.5?
>
>
>
> Best regards,
>
> Mikael
>
>
>
>
>
> ………………………………………………………………………………………….
>
> Mikael Eriksson
>
> R&D Physicist Trainee
>
> Philips Medical Systems MR Finland, Feasibility studies
>
> mikael.k.eriksson at philips.com
>
> ………………………………………………………………………………………….
>
>
>
>
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