Tumor measurement with python module

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Tumor measurement with python module

Marina Cebollero
Dear Slicer developers,

My name is Marina, and I'm studying Biomedical Engineering in Spain.
I'm writing this email because I'm a beginner in Slicer development, and I would really appreciate if you could help me.

As a part of a class project, I'm designing a python scriptable module for measuring tumors using RECIST 1.1.
I know there is the CLI module called LabelDiameterEstimation created by Fedorov and Kikinis for slicer3, but I want something for slicer4 that simply allows obtaining the largest diameter in the axial plane.
Therefore, I think that, as explained in the description of LabelDiameterEstimation, the best way to calculate it will be obtaining the largest tumor slice in the axial plane, and then calculating the two most distant points in that slice.

So my first question is: do you agree with this?
And the next question is: once I get a label with the segmented tumor, how could I find that area with python?

Thanks in advance!

--
Marina Ceboller
​o​
​Biomedical Engineering Student
Universidad Politécnica de Madrid

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Re: Tumor measurement with python module

Dzenan Zukic
Hi Marina,

there is a module called "Label Statistics" in Slicer. If you apply it to a one-slice image, the "volume" statistic should give you area (when you divide it by slice thickness).

If you want to restrict your diameter estimate to axial slices only, the best way is to calculate diameter in each slice and pick the maximum.

I defer to Andrey for the CLI module you mentioned.

Regards

Dženan Zukić, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)

On Fri, Dec 30, 2016 at 1:28 PM, Marina Cebollero <[hidden email]> wrote:
Dear Slicer developers,

My name is Marina, and I'm studying Biomedical Engineering in Spain.
I'm writing this email because I'm a beginner in Slicer development, and I would really appreciate if you could help me.

As a part of a class project, I'm designing a python scriptable module for measuring tumors using RECIST 1.1.
I know there is the CLI module called LabelDiameterEstimation created by Fedorov and Kikinis for slicer3, but I want something for slicer4 that simply allows obtaining the largest diameter in the axial plane.
Therefore, I think that, as explained in the description of LabelDiameterEstimation, the best way to calculate it will be obtaining the largest tumor slice in the axial plane, and then calculating the two most distant points in that slice.

So my first question is: do you agree with this?
And the next question is: once I get a label with the segmented tumor, how could I find that area with python?

Thanks in advance!

--
Marina Ceboller
​o​
​Biomedical Engineering Student
Universidad Politécnica de Madrid

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Re: Tumor measurement with python module

andrey.fedorov
In reply to this post by Marina Cebollero
Hi Marina,

indeed that CLI module has not been ported to Slicer4. Your approach
of implementing the functionality in python makes sense, since it is
definitely more powerful for developing end-user module, and is
potentially more manageable.

AF

On Fri, Dec 30, 2016 at 2:13 PM, Dzenan Zukic <[hidden email]> wrote:

> Hi Marina,
>
> there is a module called "Label Statistics" in Slicer. If you apply it to a
> one-slice image, the "volume" statistic should give you area (when you
> divide it by slice thickness).
>
> If you want to restrict your diameter estimate to axial slices only, the
> best way is to calculate diameter in each slice and pick the maximum.
>
> I defer to Andrey for the CLI module you mentioned.
>
> Regards
>
> Dženan Zukić, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)
>
> On Fri, Dec 30, 2016 at 1:28 PM, Marina Cebollero
> <[hidden email]> wrote:
>>
>> Dear Slicer developers,
>>
>> My name is Marina, and I'm studying Biomedical Engineering in Spain.
>> I'm writing this email because I'm a beginner in Slicer development, and I
>> would really appreciate if you could help me.
>>
>> As a part of a class project, I'm designing a python scriptable module for
>> measuring tumors using RECIST 1.1.
>> I know there is the CLI module called LabelDiameterEstimation created by
>> Fedorov and Kikinis for slicer3, but I want something for slicer4 that
>> simply allows obtaining the largest diameter in the axial plane.
>> Therefore, I think that, as explained in the description of
>> LabelDiameterEstimation, the best way to calculate it will be obtaining the
>> largest tumor slice in the axial plane, and then calculating the two most
>> distant points in that slice.
>>
>> So my first question is: do you agree with this?
>> And the next question is: once I get a label with the segmented tumor, how
>> could I find that area with python?
>>
>> Thanks in advance!
>>
>> --
>> Marina Ceboller
>> o
>> Biomedical Engineering Student
>> Universidad Politécnica de Madrid
>>
>> _______________________________________________
>> slicer-devel mailing list
>> [hidden email]
>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
>> To unsubscribe: send email to [hidden email] with
>> unsubscribe as the subject
>>
>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ
>
>
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Re: Tumor measurement with python module

mosx
In reply to this post by Marina Cebollero
Hi Marina Cebollero,
my name is Marco.
I'm interesting to your work. In particular I would create my python module
to estimate the dimension of tumor from segmentation.

I create the segment with this tutorial:  segmentation video
<https://www.youtube.com/watch?v=lawaJUGEf5A>    

Now I want to calculate the volume of this using the idea of the
LabelDiameterEstimation that you suggest.

I create a base python and I obtain the vtkMRMLLabelMapVolumeNode with
selected it from qMRMLNodeComboBox.
Now my question is:
How can I obtain the label?


Thank you for the help.



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Re: Tumor measurement with python module

mosx
This post has NOT been accepted by the mailing list yet.
In reply to this post by Marina Cebollero
Hi Marina Cebollero,
my name is Marco.
I'm interesting to your work. In particular I would create my python module to estimate the dimension of tumor from segmentation.

I create the segment with this tutorial: segmentation video 

Now I want to calculate the volume of this using the idea of the LabelDiameterEstimation that you suggest.

I create a base python and I obtain the vtkMRMLLabelMapVolumeNode with selected it from qMRMLNodeComboBox.
Now my question is:
How can I obtain the label?


Thank you for the help.