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

Mon Apr 26 10:14:24 EDT 2010

I believe it does support Enhanced MR/CT. I added it back in January.

Bill

On Mon, Apr 26, 2010 at 9:17 AM, Mathieu Malaterre
<mathieu.malaterre at gmail.com> wrote:
> 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
>