[Insight-users] itkScalarChanAndVeseSparseLevelSetImageFilter

alex gouaillard Alexandre_Gouaillard at hms.harvard.edu
Sun Jun 7 23:52:48 EDT 2009 

 From what I heard, there will be quite a few changes.

now, arnaud and kishore are dedicated to let that happen as fast as  
possible, and so is luis.

your feedback is very valuable to the process.

if you wouldn't mind, we would like you to try to use the filter and  
give feedback like you did before everyday or so. That would greatly  
speed up the process.

thanks in advance.

alex.


On Jun 7, 2009, at 11:46 PM, Sgouritsa, Eleni wrote:

> Ok, thank you!I ll check there for the changes. Just your opinion:  
> Do you think I can start working with the current version and get  
> the newer later, or the upcoming corrections are very important and  
> affect the segmentation result?
>
> Thank you for all the help,
> Eleni
>
> -----Original Message-----
> From: alex gouaillard [mailto:alexandre_gouaillard at hms.harvard.edu]
> Sent: Sun 6/7/2009 10:35 PM
> To: Sgouritsa, Eleni
> Cc: Arnaud Joel Florent Gelas; insight-users at itk.org; Luis Ibanez;  
> Kishore Rao Rao Mosaliganti
> Subject: Re: [Insight-users]  
> itkScalarChanAndVeseSparseLevelSetImageFilter
>
> hi eleni,
>
> you can monitor cvs changes in the review directory using this link :
> http://public.kitware.com/cgi-bin/viewcvs.cgi/Code/Review/?root=Insight&sortby=date#dirlist
>
> There should be a lot of changes in the next days, so it might be
> unpractical for us to let you know everytime we commit a change. We
> will try to do it though.
>
> cheers.
>
> alex.
>
>
>
> On Jun 7, 2009, at 11:28 PM, Sgouritsa, Eleni wrote:
>
> > Thank you very much.
> > Yes, I think too that my problem was coming from the foreground  
> term.
> > Is it possible to notify me when you finish with the other changes
> > of the class so I can work directly with the corrected version?
> >
> > Regards,
> > Eleni
> >
> >
> > -----Original Message-----
> > From: Arnaud Gelas [mailto:arnaud_gelas at hms.harvard.edu]
> > Sent: Sun 6/7/2009 6:48 PM
> > To: Sgouritsa, Eleni
> > Cc: Kishore Mosaliganti; insight-users at itk.org; Luis Ibanez
> > Subject: Re: [Insight-users]
> > itkScalarChanAndVeseSparseLevelSetImageFilter
> >
> > Dear Eleni,
> >
> > I have corrected a bug in the formula of the foreground constant
> > calculation. This error could really affect the results of your
> > segmentation process.
> > You can get the new version from the cvs repository.
> >
> > Note that this code may change a lot in the next couple of days
> > (Kishore and I will be fixing various parts of the code).
> >
> > Arnaud
> >
> > On Jun 7, 2009, at 6:12 PM, Sgouritsa, Eleni wrote:
> >
> > > What I understand is that the result should be independent of  
> how we
> > > define the distance function (negative inside or outside). And  
> if we
> > > initialize the level set totally inside the data , the level set
> > > should expand according to equation (7) of the paper where you
> > > describe the method, whereas if we initialize outside it should
> > > shrink. In insight journal it happens like that but not in the itk
> > > release.
> > > Thank you very much,
> > > Eleni
> > >
> > >
> > > -----Original Message-----
> > > From: Sgouritsa, Eleni
> > > Sent: Sun 6/7/2009 3:30 PM
> > > To: Kishore Mosaliganti
> > > Cc: Luis Ibanez; insight-users at itk.org
> > > Subject: RE: [Insight-users]
> > > itkScalarChanAndVeseSparseLevelSetImageFilter
> > >
> > > Hello,
> > > thank you very much for the help. Unfortunately I work with  
> medical
> > > data that I am not supposed to give.
> > > Can you explain a little more point 2. You mean that I have to
> > > define my level set as inside positive and outside negative to  
> have
> > > the opposite propagation direction?
> > > I tried it but it did not work. I both cases, if I initialize  
> the LS
> > > inside the boundary of my data, it shrinks. I use mu=0, nu=0, l1=1
> > > and l2=1. Do I need negative l1?When I initialize almost the whole
> > > LS outside my data it seems to work in some cases.Generally, I get
> > > different results from the insight journal that I was getting
> > correct.
> > >
> > > Thank you,
> > > Eleni
> > >
> > >
> > > -----Original Message-----
> > > From: Kishore Mosaliganti [mailto:kishoreraom at gmail.com]
> > > Sent: Fri 6/5/2009 1:02 PM
> > > To: Sgouritsa, Eleni
> > > Cc: Luis Ibanez; insight-users at itk.org
> > > Subject: Re: [Insight-users]
> > > itkScalarChanAndVeseSparseLevelSetImageFilter
> > >
> > > Hi Eleni,
> > >
> > > Thank you for pointing out these problems. You are right that the
> > > Review
> > > code is not very stable as yet. We are working on fixing them.
> > > During the
> > > transfer from the IJ paper to the Review directory, a lot of
> > > modifications
> > > were made. We might have inadvertently introduced new errors.
> > >
> > > Regarding your problems:
> > >
> > > 2. The level-set function is defined by convention as inside is
> > > negative and
> > > outside is positive. So the negative values become your foreground
> > and
> > > positive values become the background. This controls the  
> propagation
> > > direction.
> > >
> > > 3. I am looking at the Halt function. Looks like the boundary case
> > > of 0
> > > iterations is not coded right.
> > >
> > > 4.  Regarding the high RMS values, the level-set function is re-
> > > initialized
> > > to a signed distance function after every few iterations. It so
> > > happens that
> > > the default setting is 1 iteration. Hence, the RMS change is being
> > > calculated after the reinitialization while it needs to be done
> > > before. We
> > > are also working on correcting this. Thank you for pointing this
> > out.
> > >
> > >
> > > Is it possible for you to post a small sample of your data for  
> us to
> > > work on
> > > the errors.
> > >
> > >
> > > Kishore
> > >
> > > On Tue, Jun 2, 2009 at 11:24 AM, Sgouritsa, Eleni
> > > <esgourit at central.uh.edu>wrote:
> > >
> > > >  Hello,
> > > > I m sorry if my point was not clear. The problems that I am  
> facing
> > > using
> > > > this class to segment 3D data are the following:
> > > >
> > > > 1. My data has negative origin (for example (-100, -100, -60).
> > > Unless I do
> > > > SetOrigin(0,0,0) (or I guess any origin >=0) my program  
> crashes. I
> > > have to
> > > > set my negative origin as zero for my program to run. Does the
> > > class assumes
> > > > positive origin of the input image?
> > > >
> > > > 2. I initialize my level set inside (so the evolution should be
> > > outwards).
> > > > In this case I can not make my level set expand (it can just
> > > shrink, or not
> > > > move). I think I should use something like
> > > SetReverseExpansionDirection to
> > > > control the propagation direction, but I can not find this  
> option
> > > in the
> > > > class public members. (This is currently my main problem where I
> > > am stuck,
> > > > any help would be very useful!)
> > > >
> > > > 3. The maximum RMS Error serves (along with the number of
> > > iterations) as a
> > > > stopping criteria inside the Halt function (of
> > > > itkMultiphaseFiniteDifferenceImageFilter.txx file).
> > > > Lets say I set maximum RMS Error = 0.01.
> > > > The Halt function returns the following:
> > > > return ( (this->GetElapsedIterations() >= this-
> > > >m_NumberOfIterations) ||
> > > >       ( this->GetMaximumRMSError() >= m_RMSChange ) );
> > > > While the Halt function returns false the evolution continues.
> > > > However, in iteration 0, I get m_RMSChange = 0, so the evolution
> > > always
> > > > stops doing 0 iterations (since the condition this-
> > > >GetMaximumRMSError() >=
> > > > m_RMSChange becomes true)
> > > > If I modify the Halt function to returm the following:
> > > > if(this->GetElapsedIterations()==0)
> > > >         return false;
> > > > else
> > > >         return ( (this->GetElapsedIterations() >=
> > > > this->m_NumberOfIterations) || ( this->GetMaximumRMSError() >=
> > > m_RMSChange )
> > > > );
> > > > then it works.
> > > > The other problem is that RMSChange in the next iterations
> > > (1,2,3...) has
> > > > very big values (like 5000) even near convergence. So the only  
> way
> > > to stop
> > > > the evolution is through the iterations number.
> > > >
> > > > I am still investigating the class and I am not absolutely sure
> > > about the
> > > > points mentioned but I would like to share with you for more
> > advice.
> > > >
> > > >
> > > > Thank you very much,
> > > > Lena
> > > >
> > > >
> > > >
> > > >
> > > > -----Original Message-----
> > > > From: Luis Ibanez [mailto:luis.ibanez at kitware.com<luis.ibanez at kitware.com
> > > >
> > > > ]
> > > > Sent: Mon 6/1/2009 8:39 PM
> > > > To: Sgouritsa, Eleni
> > > > Cc: alex gouaillard; insight-users at itk.org
> > > > Subject: Re: [Insight-users]
> > > itkScalarChanAndVeseSparseLevelSetImageFilter
> > > >
> > > >
> > > > Hi Lena,
> > > >
> > > > Could you please be more specific about your problem report on
> > > > item (2) ?
> > > >
> > > > Is there a chance that you can report this in a form that
> > > > we could reproduce ?
> > > >
> > > >
> > > >     Thanks
> > > >
> > > >
> > > >        Luis
> > > >
> > > >
> > > > -----------------------------
> > > > Sgouritsa, Eleni wrote:
> > > > > Hi,
> > > > >
> > > > > I have two more questions.
> > > > > 1. In the insight journal code there was an option
> > > > > SetReverseExpansionDirection to control if the expansion of  
> the
> > > level
> > > > > set will be inwards or outwards. How can I do it using the
> > > > > itkScalarChanAndVeseSparseLevelSetImageFilter of 3.14 release?
> > > > >
> > > > > 2. I still have a problem when my 3D data have negative  
> origin.
> > > > >
> > > > > Thanks and regards,
> > > > > Lena
> > > > >
> > > > > -----Original Message-----
> > > > > From: Sgouritsa, Eleni
> > > > > Sent: Mon 6/1/2009 4:00 AM
> > > > > To: alex gouaillard
> > > > > Cc: insight-users at itk.org
> > > > > Subject: RE: [Insight-users]
> > > > itkScalarChanAndVeseSparseLevelSetImageFilter
> > > > >
> > > > > Hello,
> > > > > finally the second issue was my fault (I just had a problem
> > while
> > > > > including the header files of the review folder).
> > > > > For the first, the inconsistency is just a matter of name. The
> > > code runs
> > > > > correctly, just the name assignement in the txx is a little
> > > misleading.
> > > > >
> > > > > Thank you very much,
> > > > > Lena
> > > > >
> > > > >
> > > > > -----Original Message-----
> > > > > From: alex gouaillard
> > > [mailto:alexandre_gouaillard at hms.harvard.edu<alexandre_gouaillard at hms.harvard.edu
> > > >
> > > > ]
> > > > > Sent: Sun 5/31/2009 11:34 PM
> > > > > To: Sgouritsa, Eleni
> > > > > Cc: insight-users at itk.org
> > > > > Subject: Re: [Insight-users]
> > > > itkScalarChanAndVeseSparseLevelSetImageFilter
> > > > >
> > > > > hi eleni,
> > > > >
> > > > > we'll take a look tomorrow.
> > > > >
> > > > > thanks for the feedback.
> > > > >
> > > > > alex.
> > > > >
> > > > > On May 31, 2009, at 11:52 PM, Sgouritsa, Eleni wrote:
> > > > >
> > > > >  > Hello,
> > > > >  > I know that the review folder of the new release (3.14) is
> > not
> > > > >  > stable yet but I would just like to give two comments:
> > > > >  >
> > > > >  > 1. I found an inconsistency between the template  
> arguments of
> > > the
> > > > >  > itkScalarChanAndVeseSparseLevelSetImageFilter.h and the
> > > > >  > itkScalarChanAndVeseSparseLevelSetImageFilter.txx.
> > > > >  > Specifically, in the header file, the template is :
> > > > >  > template < class TInputImage, class TFeatureImage, class
> > > > >  > TOutputImage, class TFunction,
> > > > >  >   class TSharedData, typename TIdCell = unsigned int >
> > > > >  > whereas in the txx it is:
> > > > >  > template < class TInput, class TFeature, class TFunction,
> > > > >  > class TOutputPixel, class TSharedData, typename TIdCell >
> > > > >  > There is a change in the order of the 3rd and 4th argument.
> > > > >  >
> > > > >  > 2. I can not find this class
> > > > >  > (itkScalarChanAndVeseSparseLevelSetImageFilter)  incuded in
> > the
> > > > >  > CMakeLists of the review folder
> > > > >  >
> > > > >  > Regards,
> > > > >  > Lena
> > > > >  >
> > > > >  > <ATT00001.txt>
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > >
> >  
> ------------------------------------------------------------------------
> > > > >
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> > > >
> > >
> > >
> > >
> > > <ATT00001.txt>
> >
> >
> >
> > <ATT00001.txt>
>
>
>

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