[Insight-users] Re: on DeformableModelSimplexMesh application

Fri Feb 1 23:10:06 EST 2008

Hi, Luis and ITK users,

Could you please give me some comments on my problem?

Problem description is as follows.

The dataset I used is "sphere.zip", which can be downloaded from 
http://appsrv.cse.cuhk.edu.hk/~dfwang/tmp/sphere.zip (the size is about 
30K). By uncompressing this file, you will see Analyze file of "sphere.hdr" 
and "sphere.img".

The parameters I used are listed as follows,

Internal Forces (Alpha): 0.8
External Forces (Beta): 0.8
Damping Forces (Gamma): 0.35
Range of Search: 2
Rigidity (Regularizing): 0.5
Number of Iterations: 1

The parameters involved in the gradient calculation of
DeformableModelSimplexMesh are keep unchanged. That is, I did not make any
change to the source code of DeformableModelSimplexMesh.

The steps to reproduce my results are listed as follows,

1. "File/Load File", select "sphere.hdr";
2. left click the center point of the upper left image, then click
"File/Create Mesh", you will see a simplex spherical mesh in the window;
3. "File/Preprocess Image", wait about two minutes to finish the preprocess;
4. Click "Settings/Deform Mesh" about 25 times. Each time after your click,
you will see that the simplex mesh deform. In this process, you can see the
problem I described in my last email.

By the way, if I set the parameter of "Number of Iterations: 1" to 25, and
click "Settings/Deform Mesh" only once. The result I got seems quite
similiar to the initial mesh, and is not like the one got by seting "Number
of Iterations: 1" to 1 and click "Settings/Deform Mesh" 25 times. I think
this is another bug in this program.

If any part in the above desription is not clear enough, please let me know
and I will try to provide more details.

Best wishes,
Defeng

----- Original Message ----- 
From: "Defeng WANG" <dfwang at cse.cuhk.edu.hk>
To: "Luis Ibanez" <luis.ibanez at kitware.com>
Sent: Friday, February 01, 2008 12:05 PM
Subject: Re: [Insight-developers] bug report on DeformableModelSimplexMesh 
application

> Hi,Luis,
>
> I apologize that the same email has been sent to you several times. 
> Actually I do not know the size limitation of each email. Finally I used a 
> link to download the sample dataset, instead of via email.
>
> Best wishes,
> Defeng
> ----- Original Message ----- 
> From: "Luis Ibanez" <luis.ibanez at kitware.com>
> To: "Defeng WANG" <dfwang at cse.cuhk.edu.hk>
> Cc: "Leila Baghdadi" <baghdadi at phenogenomics.ca>; 
> <insight-developers at itk.org>; <insight-users at itk.org>
> Sent: Friday, February 01, 2008 10:40 AM
> Subject: Re: [Insight-developers] bug report on DeformableModelSimplexMesh 
> application
>
>
>>
>> Hi Defeng,
>>
>> Can you please post in a public web site the image that
>> you are using as input, and the full set of parameters
>> that you are using for running this application ?
>>
>> Otherwise it is very hard for us to figure out how far
>> from the edge of the image you are seeing the final
>> contour stopping.
>>
>> Please give use a very clear sequence of step that we
>> could follow to reproduce your experience here.
>>
>>
>>
>>   Thanks
>>
>>
>>      Luis
>>
>>
>> -------------------
>> Defeng WANG wrote:
>>> Hi, Leila,
>>>
>>> Thanks for your reply. It seems that the parameters in the UI of
>>> DeformableModelSimplexMesh are not related to the gradient calculation. 
>>> I
>>> read the source code involved in DeformableModelSimplexMesh. As for the
>>> gradient calculation, three filters are used successively as follows,
>>>
>>>  m_GradientMagnitude->SetInput(m_CastImage->GetOutput() );
>>>  m_GradientMagnitude->SetSigma(0.5);
>>>
>>>  m_SigmoidImage->SetInput( m_GradientMagnitude->GetOutput());
>>>  m_SigmoidImage->SetOutputMinimum(0);
>>>  m_SigmoidImage->SetOutputMaximum(1);
>>>  m_SigmoidImage->SetAlpha(230);
>>>  m_SigmoidImage->SetBeta(1300);
>>>
>>>  m_GradientFilter->SetInput( m_SigmoidImage->GetOutput());
>>>  m_GradientFilter->SetSigma( 0.5);
>>>
>>>
>>> I have taken a look at the final gradent image. It seems that it is good
>>> enough to describe the
>>> edge or boundary of a sphere. So what do you think of this problem 
>>> existing
>>> in this simple example?
>>>
>>>
>>> Look forard to your response.
>>>
>>> Best wishes,
>>> Defeng
>>>
>>> ----- Original Message ----- From: "Leila Baghdadi"
>>> <baghdadi at phenogenomics.ca>
>>> To: "Defeng WANG" <dfwang at cse.cuhk.edu.hk>
>>> Cc: <insight-developers at itk.org>; <insight-users at itk.org>
>>> Sent: Thursday, January 31, 2008 10:54 PM
>>> Subject: Re: [Insight-developers] bug report on
>>> DeformableModelSimplexMesh application
>>>
>>>
>>>> Hi Defeng,
>>>>
>>>> Yes I have used that code many a times. I am not sure if I understand
>>>> what you mean by "it does not converge".
>>>>
>>>> My understanding of deformable models is
>>>>
>>>> 1. you must make sure your gradient image is created properly. Use
>>>> paraview to look at the vector image
>>>>
>>>> 2. you must play with the parameters to get the model to converge,
>>>>
>>>> This is a specific type of deformable models which uses simplex mesh.
>>>> I suggest you read about this algorithm first. This is developed based
>>>> on the paper by Herve Delingette of INRIA france.
>>>>
>>>>
>>>> Leila
>>>>
>>>> On Thu, 2008-31-01 at 22:29 +0800, Defeng WANG wrote:
>>>>
>>>>> Hello, ITK users and developers,
>>>>>
>>>>> I found that DeformableModelSimplexMesh, provided in
>>>>> InsightApplications-3.4.0, does not converge. It seems that the
>>>>> deformable mesh will not stop near the boundary of one object to be
>>>>> segmented. I tried a very simple volume data set containing a sphere
>>>>> only. The initial mesh I used is a spherical simplex mesh inside it.
>>>>> However, by increasing the number of iterations, the mesh will
>>>>> continue to expand until it reaches outside of the image and the
>>>>> program reports error.
>>>>>
>>>>> Is there anybody tried this program successfully before? Or anybody
>>>>> knows how to adjust the parameters properly to get right segmentation?
>>>>>
>>>>> Best wishes,
>>>>> Defeng
>>>>> _______________________________________________
>>>>> Insight-developers mailing list
>>>>> Insight-developers at itk.org
>>>>> http://www.itk.org/mailman/listinfo/insight-developers
>>>
>>>
>>> _______________________________________________
>>> Insight-developers mailing list
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> 