[Insight-users] Measuring tumor diameter

Thu Dec 11 22:09:36 EST 2008

A very old technique for measuring the length of objects might be
relevant to you. The length is often hard to define precisely, so one
approach is to compute the length of the maximum geodesic and use that
as the length. In your case this could be equivalent to the maximum
diameter. This was originally proposed by Lantejoul, I believe.

I'm not sure about implementation details in the original paper -
perhaps there is a neat trick to do it efficiently. You can certainly
compute the maximum geodesic between one border point and the rest of
the tumour using fast marching methods, and then repeat the process
for all border voxels. This sounds slower than your idea of computing
the euclidean distance between all pairs of border voxels, but can
deal with more complex shapes.

On Fri, Dec 12, 2008 at 6:20 AM, Andriy Fedorov <fedorov at bwh.harvard.edu> wrote:
> On Thu, Dec 11, 2008 at 2:09 PM, Gaëtan Lehmann
> <gaetan.lehmann at jouy.inra.fr> wrote:
>> 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?
>>
>
> Gaetan,
>
> Thank you for the pointers. I was not aware of the IJ contribution you
> mentioned -- I need to study that.
>
>> 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?
>
> Yes, you are correct. Unfortunately, time IS a constraint in my
> application. And with the approach I consider, complexity will be
> (number of contour points)^2*(average contour diameter in pixels) due
> to the inside/outside checks along the line.
>
> Maybe I should I just try it out and see what it means in terms of seconds...
>
> Fedorov
>
>
>
>> 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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