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

[Xiaofeng Z]

Hi, Mario,

Did you give a tolerance to z-spacing when you do IPPSort?

In my experience, this is the source of sort failure in the most of times.

Xiaofeng

--------------------------------------------------
From: "Mario Ceresa" <mrceresa at gmail.com>
Sent: Friday, April 23, 2010 4:16 AM
To: "Luis Ibanez" <luis.ibanez at kitware.com>
Cc: <insight-users at itk.org>
Subject: Re: [Insight-users] How to calculate volume of an image

> 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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>>
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