[Insight-users] Re: on DeformableModelSimplexMesh application

Mon Feb 4 15:29:45 EST 2008

Defeng,

>From the description you provided, it sounds like this program is
actually broken. I have not checked this program since last year as I
was off work.

I think here is what you should do for now,

instead of using the Deformable Model application try running the
Deformable test code. 

I will try looking and fixing the deformable model code when I have a
chance but it might take sometime as I have just started working again
and have lots going on.

HTH

Leila

On Sat, 2008-02-02 at 12:10 +0800, Defeng WANG wrote:
> 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
> >>> Insight-developers at itk.org
> >>> http://www.itk.org/mailman/listinfo/insight-developers
> >>>
> > 
> 
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