[Insight-users] Slice spacing of DICOM series

[Stephen R. Aylward]

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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-- 
===========================================================
Dr. Stephen R. Aylward
Associate Professor of Radiology
Adjunct Associate Professor of Computer Science and Surgery
http://caddlab.rad.unc.edu
aylward at unc.edu
(919) 966-9695