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

[Mario Ceresa]

Hello Xiaofeng!
thanks for your mail: I don't specify any tolerance value, at least directly.

At the moment I use gdcm as compiled in itk, or by its own example
program, not directly.

Mario





On 23 April 2010 17:35, Xiaofeng Z <xf10036 at hotmail.com> wrote:
> 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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>