[Insight-users] Intensity values issue : DICOM RescaleSlope

[Luis Ibanez]

Hi Michael,


Thanks for sharing your findings in this problem.

   We will need help from a DICOM Guru,
   to sort this out...

The name "Mathieu" comes to mind...     :-)



     Luis


-----------------------------------
On Wed, May 26, 2010 at 12:38 PM, Michael Pozdnyakov <mishgunn at gmail.com> wrote:
> Hi Luis,
>
> First of all, thank you for your answer.
>
> Actually my problem had been already solved, I only haven't written yet
> about it.
>
> To debug this issue, first of all I tried, as you said, to write directly
> the image I read. Result, no more problem. So then I tried to read pixels of
> output images on each stage of my code. And I discovered, that intensity
> values never become negative. So, the problem was in writing. After some
> research, I noticed, that there was RescaleSlope tag value of Dicom Meta
> Data of the fixed image, who was smaller than the moving image's one. And
> after I changed it (I took the value of moving image) I had no more problem.
>
> But it is always strange for me, that there is this kind of casting. Is
> there any explanation?
>
> Thanks,
> Mikhail
> On 25 May 2010, at 17:29, Luis Ibanez wrote:
>
>> Hi Michael,
>>
>> Thanks for the detailed description of your problem.
>>
>> Looking at your code, it seems that you are using a "float" pixel
>> type, not a "double" pixel type, as you describe in your email.
>>
>>
>> It is unlikely that this change in pixels values is produced by
>> the resampling process itself.
>>
>>
>> Could you please do the following:
>>
>> 1) Connect the Series reader output directly as input to the
>>   Series writer (that is, skip the resampling process altogether)
>>
>> 2) Look at the resulting output image, and let us know if that
>>   image does have the pixel values changed too.
>>
>>
>>  Thanks
>>
>>
>>     Luis
>>
>>
>>
>> -----------------------------------------------------------------------------------
>> On Mon, May 17, 2010 at 9:16 AM, Michael Pozdnyakov <mishgunn at gmail.com>
>> wrote:
>>>
>>> Hello,
>>>
>>> I'm working now on 3D rigid registration task and I have some issues with
>>> my
>>> program at the moment of transformation. For the better explication of
>>> the
>>> issue I will describe only transformation part.
>>>
>>> I have a body PET exam in a series of DICOM files. I read this series
>>> with
>>> GDCM and the reading goes well and I keep a 3D image in memory (in
>>> double).
>>> Then I create a ResampleImageFilter to transform the image. I define the
>>> transformation (I've tried many of them: translation, versor rigid,
>>> affine,
>>> euler and even identity) and I define the interpolator. And finally I
>>> save
>>> my transformed image in another DICOM series. Everywhere I have double
>>> data
>>> type.
>>>
>>> So, my issue is that high intensity values (bigger than ~16K) become
>>> negative. And it doesn't depend on transformation type neither on
>>> interpolator. I have always the same probleme in high intensity zones.
>>>
>>> Thanks,
>>> Mikhail
>>>
>>> PS.
>>> My configuration
>>> MacOS X 10.5.8, gcc 4.0.1
>>> ITK 3.16
>>>
>>> PPS
>>> Sources in attachement
>>>
>>>
>>>
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>
>