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

Mon Apr 26 09:17:13 EDT 2010

GDCM 1.3 does not support properly Enhanced MR/CT Image Storage. In
those cases, it is possible to have correct Z-Spacing in a single file
(not single slice).

HTH

On Mon, Apr 26, 2010 at 2:35 PM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
> Mario,
>
> What do you expect to do with the "z spacing" value since you are only
> using a single slice?
>
>
> On Mon, Apr 26, 2010 at 4:26 AM, Mario Ceresa <mrceresa at gmail.com> wrote:
>> 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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>>>>>
>>>>>
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>>>
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-- 
Mathieu