[Insight-users] Slice spacing of DICOM series

[Mathieu Malaterre]

Andrew,

	By slice position: do you mean (0020,0032) Image Position (Patient) ? 
And by slice spacing do you mean

(0018,0088) Spacing Between Slices
or
(0018,0050) Slice Thickness

Where does those images comes from (station, vendor, modality...) ? How 
do you know the values are wrong ?

If possible could you send me a small subset of this serie ?

Thanks
Mathieu

Stephen R. Aylward wrote:
> Hi Andrew,
> 
> Are you saying, for your data, that the slice positions are wrong for 
> reconstructing the volume and that the slice thickness should be used to 
> space the slices?
> 
> Stephen
> 
> Andrew Li wrote:
> 
>> Hi, Mathieu:
>>
>> Our previous ITK lib was built in June. I updated ITK code and built the
>> ITK lib on Friday (9/2), but results were the same.
>>
>> Then, I took a closer look and the following were what I found:
>>     GDCM function GetZSpacing() is used to read slice spacing and it
>> is correct.
>>     But at later time, in function GenerateOutputInformation() in
>> file: itkImageSeriesReader.txx,
>>         slice spacing read from GetZspacing() is ignored, and
>>         slice spacing is actually derived from slice positions
>> of the first slice and of the second.
>>
>> Unfortunately for us, when slice spacing and slice position are
>> inconsistent in the headers, the latter is wrong for most of the time.
>>
>> For now, it is already good enough for us to just to know how slice
>> spacing is derived in ITK package.
>> Thank you very much for your help! 
>> -Andrew
>> -----Original Message-----
>> From: Mathieu Malaterre [mailto:mathieu.malaterre at kitware.com] Sent: 
>> Friday, September 02, 2005 10:11 AM
>> To: Andrew Li
>> Cc: insight-users at itk.org
>> Subject: Re: [Insight-users] Slice spacing of DICOM series
>>
>> Andrew,
>>
>>     Could you check you are using GDCM. GDCM was not the default
>> DICOM IO factory until very recently.
>>
>>     For more info on the ZSpacing you can check what is being done
>> in
>> gdcm/src/gdcmFile.cxx:File::GetZSpacing()
>>
>> HTH,
>> Mathieu
>>
>>
>>
>> Andrew Li wrote:
>>
>>> Hi,
>>>
>>> We use itk::ImageSeriesReader to read 3D MRI data set that is stored 
>>> as a (2D) DICOM series and then check the slice spacing in slice 
>>> direction as following:
>>>     ...
>>>     ReaderType::Pointer reader = ReaderType::New();
>>>     ...
>>>     double sliceSpacingInSliceDirection = 
>>> (reader->GetOutput()->GetSpacing())[2];
>>>     ...
>>>
>>> How slice spacing in slice direction is derived in 
>>> itk::ImageSeriesReader Class? It seems not from the tag: {0x0018, 
>>> 0x0088} (spacing between slices).
>>>
>>> Please let me know. Thanks.
>>>
>>> -Andrew
>>>
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