[Insight-users] How to calculate volume of an image

[Mario Ceresa]

Thanks, Luis, for your answer.

I think the ITK DICOM reader populates *wrongly* the spacing values:

The z spacing is always 1 for all my image set, but I'm sure that it
is not correct because the Slice Thickness tag and the number of
slices change with each scan.

Soeren Christensen, of the GDCM mail list, kindly pointed out that:

"The Thickness tag is not a reliable measure so instead the thickness is
computed from the slice locations and their distances. hence you need
more than one slice to estimate difference between them. If you get
and error, even for multiple slices, then look at image orientation
patient and image location patient tags. You can find info on how to
sort and calculate distances via a little googling and even on the
dcmtk faq I believe. There may be a problem with equidistance between
slices causing this issue. Looking at these tags should help clarify
that."

I'll try to investigate a little bit the issue, but if any has some
advice please share! :)

Thanks and regards,

Mario

On 20 April 2010 20:33, Luis Ibanez <luis.ibanez at kitware.com> wrote:
>
> Hi Mario,
>
> You should simply get the Spacing value from the itkImage, as
>
>      ImageType::SpacingType spacing =  myImage->GetSpacing();
>
>   where
>
>     spacing[0] is the spacing along X
>     spacing[1] is the spacing along Y
>     spacing[2] is the spacing along Z
>
>
> The ITK DICOM reader will populate the spacing values
> for you.
>
>
> Please note also that is you already have a segmented
> image, you could use several of the "Label" filters in ITK
> in order to compute the volume of a labeled region.
>
>
>      Regards,
>
>
>            Luis
>
>
> --------------------------
> On Tue, Apr 20, 2010 at 12:24 PM, Mario Ceresa <mrceresa at gmail.com> wrote:
>>
>> Hello everybody!
>>
>> I'm completely lost on a seemingly stupid problem: how do I calculate
>> the physical volume of an image (3D CT scan)?
>>
>> In the past I would have simply iterated over the interesting pixels
>> in the image, accumulated them in a variable, say m_Vol, and then:
>>
>> std::cout << "Volume: " << m_VolLung*spacing[0]*spacing[1]*spacing[2]
>>
>> This believing that spacing 0 and 1 came from the "Pixel Spacing" tag
>> of my DICOM header and spacing[2] from the "Slice Thickness" tag.
>>
>> But now I have some CT scan images for which the spacing along z is
>> always 1 no matter what I try, while the Slice Thickness is different.
>>
>> I spent a while dwelling into the ImageHelper::GetSpacingValue of the
>> gdcm factory but it is *really* complicated...
>>
>> Moreover a kind person from the GDCM mailing list pointed me that:
>>
>> "Pixel spacing is not guaranteed to be the same as slice thickness.
>> You can have slices that overlapped also gaps and then with the case
>> of helical CT the Slice Thickness does not make sense for the
>> reconstruction."
>>
>> So know I'm not sure which is the best way to proceed, if any of you
>> could give me an hint I would be more than grateful!
>>
>> Thanks and regards,
>>
>> Mario
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