[Insight-users] Measuring tumor diameter

Thu Dec 11 14:09:35 EST 2008

Le 11 déc. 08 à 18:18, Andriy Fedorov a écrit :

> Marcus,
>
> I have been thinking along these lines too.
>
> The problem I can see is that the bounding sphere diameter will not be
> the same as the maximum shape diameter. I can understand why the
> method you suggest works in collision detection, but in tumor
> measurement we need precision.
>
> Going back to my counter-examples, if you think of a T-shaped contour
> in 2D, the max diameter will be the length of the longer segment in T.
> If you imagine a sphere with all points inside, its radius will exceed
> the max diameter.... The method you suggest will give some estimate,
> but not *the* maximum diameter.
>
> Fedorov

Hi,

The point 1 can easily be done with the itk::SliceBySliceImageFilter  
class (in ITK's Review directory) - http://www.itk.org/Doxygen/html/classitk_1_1SliceBySliceImageFilter.html 
  and http://insight-journal.org/browse/publication/133.
You may want to look at http://insight-journal.org/browse/publication/176 
  for the point 2 and 3, and more precisely to the FeretDiameter of  
the itk::ShapeLabelObject class. The value is computed by  
itk::ShapeLabelMapFilter or a class which run it -  
itk::BinaryImageToShapeLabelMapFilter or  
itk::LabelImageToShapeLabelMapFilter.
The point 4 would require some more work though, as it is not  
implemented in that contribution, but it should be quite easily  
extended.
I'm much concerned by the point 5, which seems quite difficult to do  
in a reasonable time, but time may not be a big constraint for you. If  
I understand it well, it mean s counting the pixels on the line for  
all the pairs of points on the contour. I'm right?

Regards,

Gaëtan

>
>
>
>
> On Thu, Dec 11, 2008 at 12:10 PM, Neuner Markus  
> <neuner.markus at gmx.net> wrote:
>> Hi,
>>
>> I would sggest an approch that is called:  "Bounding Sphere"
>> and is commonly used in graphics to calculate bounding spheres that  
>> are
>> independent of object rotations.
>>
>> Several methods exist to compute a bounding spere and some good  
>> examples of
>> how to compute and implement this is outlined in the book "Real-Time
>> Collision Detection" from Christer Ericson.
>>
>> One good method is to use the direction of maximum spread from a PCA
>> (primary component analysis) of all "contour points".
>> Then you pick points farhest away along this direction (1st  
>> eigenvector).
>> This is done by projection (Dot-Product) of the points onto the  
>> direction
>> vector and you increase the diameter of a shpere until all points are
>> inside.
>>
>> I dont know if PCA is implemented in ITK to compute the  
>> covariancematrix,
>> eigenvectors and eigenvalues of a point set.
>>
>>
>> Regards, Markus
>>
>>
>> Andriy Fedorov wrote:
>>>
>>> On Thu, Dec 11, 2008 at 10:17 AM, Somer, Edward <edward.somer at kcl.ac.uk 
>>> >
>>> wrote:
>>>
>>>>
>>>> Having segmented the tumour I'd try a 3D-distance transform to  
>>>> find the
>>>> interior pixel furthest from any edge of the mask. Isn't the  
>>>> maximum
>>>> diameter then twice the value of the distance transform at this  
>>>> point?
>>>>
>>>>
>>>
>>> This will not work, unfortunately. Here's a counterexample.
>>>
>>> Imagine I-like shape of some thickness in 2d. Then the maximum
>>> distance from distance transform will be half the thickness of the
>>> shape. However, the diameter will be equal to the *length* of this
>>> shape. So in this case you are getting non-maximum diameter with the
>>> approach you suggest.
>>>
>>>
>>>
>>>>
>>>> Perhaps I'm missing something,
>>>>
>>>> Ed
>>>>
>>>> Andriy Fedorov wrote:
>>>>
>>>>>
>>>>> Luis,
>>>>>
>>>>> I am actually looking for an automatic tool.
>>>>>
>>>>> The approach I am currently considering is this:
>>>>>
>>>>> 1) go through the axial slices, find the one with the largest area
>>>>> 2) extract that slice contour
>>>>> 3) go through all possible combinations of the contour points,  
>>>>> find
>>>>> the pair of most distant points, and take this as a diameter
>>>>> 4) follow the line between the points in the previous step, and
>>>>> subtract the parts of the line that are outside the contour  
>>>>> (this is
>>>>> how the tumor measurements are actually taken). This may change  
>>>>> the
>>>>> measured diameter.
>>>>> 5) repeat steps 3 and 4 until the maximum is found after taking  
>>>>> into
>>>>> account diameter parts outside the countour
>>>>>
>>>>> The problem of course is that this procedure will be quadratic  
>>>>> to the
>>>>> number of contour points, and I am looking for ways to speed  
>>>>> this up,
>>>>> or find an existing implementation, or find a better way to find  
>>>>> the
>>>>> farthest point. I thought about kd-tree to optimize point  
>>>>> location,
>>>>> but I am not sure how to use it for farthest point.
>>>>>
>>>>> Any comments are welcome
>>>>>
>>>>> Andriy Fedorov
>>>>>
>>>>>
>>>>> On Thu, Dec 11, 2008 at 9:47 AM, Luis Ibanez <luis.ibanez at kitware.com 
>>>>> >
>>>>> wrote:
>>>>>
>>>>>
>>>>>>
>>>>>> Hi Andi,
>>>>>>
>>>>>>
>>>>>> Are you looking for an automatic tool ?
>>>>>> or for an interactive method ?
>>>>>>
>>>>>> In VTK you will find 3D Widgets designed
>>>>>> for taking measurements in-plane.
>>>>>>
>>>>>>
>>>>>> Regards,
>>>>>>
>>>>>>
>>>>>>  Luis
>>>>>>
>>>>>>
>>>>>> ------------------------
>>>>>> Andriy Fedorov wrote:
>>>>>>
>>>>>>
>>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> I need to measure the longest diameter of a 3D tumor  
>>>>>>> segmentation. I
>>>>>>> was wondering, if anybody is aware of any existing tools for  
>>>>>>> this
>>>>>>> purpose? If not, are there tools to quickly measure the  
>>>>>>> diameter of a
>>>>>>> 2D projection of the segmentation?
>>>>>>>
>>>>>>> I just wanted to have the community opinion before starting to
>>>>>>> implement something myself.
>>>>>>>
>>>>>>> Andriy Fedorov
>>>>>>> _______________________________________________
>>>>>>> Insight-users mailing list
>>>>>>> Insight-users at itk.org
>>>>>>> http://www.itk.org/mailman/listinfo/insight-users
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Insight-users mailing list
>>>>> Insight-users at itk.org
>>>>> http://www.itk.org/mailman/listinfo/insight-users
>>>>>
>>>>>
>>>>
>>>> --
>>>> Edward Somer, PhD.
>>>> Senior PET Methodologist
>>>> The PET Imaging Centre St Thomas' Hospital
>>>> London, UK
>>>> SE1 7EH
>>>>
>>>> work tel: +44 (0) 20 7188 1497
>>>> work fax: +44 (0) 20 7620 0790
>>>> e-mail: Edward.Somer at kcl.ac.uk / Edward.Somer at googlemail.com
>>>>
>>>>
>>>>
>>>>
>>>
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>>>
>>>
>>
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-- 
Gaëtan Lehmann
Biologie du Développement et de la Reproduction
INRA de Jouy-en-Josas (France)
tel: +33 1 34 65 29 66    fax: 01 34 65 29 09
http://voxel.jouy.inra.fr  http://www.mandriva.org
http://www.itk.org  http://www.clavier-dvorak.org

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