[Insight-users] Re: on DeformableModelSimplexMesh application

[Defeng WANG]

Hi, Luis,

As you suggested, I tried to describe my problem clearly, but so far still 
no reply comes for this question.

What do you think of the problem? Any comments or suggestions are 
appreciated.

best,
Defeng

----- Original Message ----- 
From: "Defeng WANG" <dfwang at cse.cuhk.edu.hk>
To: "Luis Ibanez" <luis.ibanez at kitware.com>; <insight-users at itk.org>
Sent: Saturday, February 02, 2008 12:10 PM
Subject: Re: on DeformableModelSimplexMesh application


> 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
>>>>
>>>>
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>>
>