[Insight-users] Pixel Spacing / DICOM Series (was Re: InsightToolkit-3.12.0 problem reading Structure DCM)

[Mathieu Malaterre]

Please post your question to the ITK mailing list.

Z-spacing is computed automatically by itk.

HTH

On Tue, Sep 15, 2009 at 9:35 PM, Maximilien Renard <iixamaxii at gmail.com> wrote:
> Hi Mathieu,
>
> Thank you for your quick answer.
>
> Well, I'm pretty confused now.
> These images are slices of two cadaveric hands. So I obviously need
> the Z-Spacing too.
>
> Would you be kind enough to explain me how I should create a 3D Volume
> from these images?
>
> I've tried to do as explained in "7.12.3 Reading a 2D DICOM Series and
> Writing a Volume", then I've tried to adapt the code to open each
> single file as a single slice and then paste it into a new 3D Image.
> But I was not able to figure out how to paste a itk::Image<unsigned
> short, 2> into a itk::Image<unsigned short, 3> (I get an error when I
> set the SetDestinationIndex with a 3-dim array). And when I try to
> open each slice as a 3D image (itk::ImageFileReader<
> itk::image<unsigned short>, 3 >), it says that I cannot open a file
> with 0 Z-spacing.
>
> I'm really completely lost :/
>
> Thank you,
>
>
> Regards,
>
>
> Maximilien Renard
>
> 2009/9/15 Mathieu Malaterre <mathieu.malaterre at gmail.com>:
>> Maximilien,
>>
>> On Tue, Sep 15, 2009 at 1:46 PM, Maximilien Renard <iixamaxii at gmail.com> wrote:
>>> Hi,
>>>
>>> Sorry for my late answer.
>>>
>>> So I've checked the dicom tags of my image using
>>> DicomImageReadPrintTags and I've highlighted these lines :
>>>
>>> (0018|0050) Slice Thickness = 0.75
>>> ...
>>> (0020|000e) Series Instance UID = 1.3.12.2.1107.5.1.4.24514.4.0.2018232119198399
>>> ...
>>> (0028|0030) Pixel Spacing = 0.41015625\0.41015625
>>>
>>> So I've read a little bit on the internet and it seems that Slice
>>> Thickness is not what I'm searching for.
>>>
>>> The good way seems to be these tags :
>>>
>>> (0020|0032) Image Position (Patient) = -101.79492\-211.79492\-1107.5
>>> (0020|0037) Image Orientation (Patient) = 1\0\0\0\1\0
>>>
>>> and use them in order to :
>>>
>>> 1) compute the normal of the planes
>>> 2) use the Image Position to compute the position of the current slice
>>> on the axis (and the difference between the position of two adjacent
>>> slices gives the spacing between them).
>>>
>>> ( http://newsgroups.derkeiler.com/Archive/Comp/comp.protocols.dicom/2006-01/msg00055.html
>>> )
>>>
>>> Since I am kind of a newbie, please forgive me if I asking
>>> stupidities, here are my questions :
>>>
>>> 1) How come that despite the fact that there is this Series ID, my
>>> images are not a serie ?
>>
>> I am not sure I understand your question. Do you understand that DICOM
>> Series does *not* mean homogenous volume (i.e constant z-spacing)
>>
>>> 2) Will the method to compute the Z-Spacing that I describe above work
>>> for all kind of CT Images ?
>>
>> This is internally done you should not even need to know how it work.
>>
>>> 3) Doesn't ITK have a way to determine this spacing ?
>>
>> Yes it shoudl work by default.
>>
>> --
>> Mathieu
>>
>



-- 
Mathieu

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