<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">From what I heard, there will be quite a few changes.<div><br><div>now, arnaud and kishore are dedicated to let that happen as fast as possible, and so is luis.</div><div><br></div><div>your feedback is very valuable to the process.</div><div><br></div><div>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.</div><div><br></div><div>thanks in advance.</div><div><br></div><div>alex.</div><div><br></div><div><br><div><div>On Jun 7, 2009, at 11:46 PM, Sgouritsa, Eleni wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"> <div> <!-- Converted from text/plain format --><p><font size="2">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?<br> <br> Thank you for all the help,<br> Eleni<br> <br> -----Original Message-----<br> From: alex gouaillard [<a href="mailto:alexandre_gouaillard@hms.harvard.edu">mailto:alexandre_gouaillard@hms.harvard.edu</a>]<br> Sent: Sun 6/7/2009 10:35 PM<br> To: Sgouritsa, Eleni<br> Cc: Arnaud Joel Florent Gelas; <a href="mailto:insight-users@itk.org">insight-users@itk.org</a>; Luis Ibanez; Kishore Rao Rao Mosaliganti<br> Subject: Re: [Insight-users] itkScalarChanAndVeseSparseLevelSetImageFilter<br> <br> hi eleni,<br> <br> you can monitor cvs changes in the review directory using this link :<br> <a href="http://public.kitware.com/cgi-bin/viewcvs.cgi/Code/Review/?root=Insight&sortby=date#dirlist">http://public.kitware.com/cgi-bin/viewcvs.cgi/Code/Review/?root=Insight&sortby=date#dirlist</a><br> <br> There should be a lot of changes in the next days, so it might be <br> unpractical for us to let you know everytime we commit a change. We <br> will try to do it though.<br> <br> cheers.<br> <br> alex.<br> <br> <br> <br> On Jun 7, 2009, at 11:28 PM, Sgouritsa, Eleni wrote:<br> <br> > Thank you very much.<br> > Yes, I think too that my problem was coming from the foreground term.<br> > Is it possible to notify me when you finish with the other changes <br> > of the class so I can work directly with the corrected version?<br> ><br> > Regards,<br> > Eleni<br> ><br> ><br> > -----Original Message-----<br> > From: Arnaud Gelas [<a href="mailto:arnaud_gelas@hms.harvard.edu">mailto:arnaud_gelas@hms.harvard.edu</a>]<br> > Sent: Sun 6/7/2009 6:48 PM<br> > To: Sgouritsa, Eleni<br> > Cc: Kishore Mosaliganti; <a href="mailto:insight-users@itk.org">insight-users@itk.org</a>; Luis Ibanez<br> > Subject: Re: [Insight-users] <br> > itkScalarChanAndVeseSparseLevelSetImageFilter<br> ><br> > Dear Eleni,<br> ><br> > I have corrected a bug in the formula of the foreground constant<br> > calculation. This error could really affect the results of your<br> > segmentation process.<br> > You can get the new version from the cvs repository.<br> ><br> > Note that this code may change a lot in the next couple of days<br> > (Kishore and I will be fixing various parts of the code).<br> ><br> > Arnaud<br> ><br> > On Jun 7, 2009, at 6:12 PM, Sgouritsa, Eleni wrote:<br> ><br> > > What I understand is that the result should be independent of how we<br> > > define the distance function (negative inside or outside). And if we<br> > > initialize the level set totally inside the data , the level set<br> > > should expand according to equation (7) of the paper where you<br> > > describe the method, whereas if we initialize outside it should<br> > > shrink. In insight journal it happens like that but not in the itk<br> > > release.<br> > > Thank you very much,<br> > > Eleni<br> > ><br> > ><br> > > -----Original Message-----<br> > > From: Sgouritsa, Eleni<br> > > Sent: Sun 6/7/2009 3:30 PM<br> > > To: Kishore Mosaliganti<br> > > Cc: Luis Ibanez; <a href="mailto:insight-users@itk.org">insight-users@itk.org</a><br> > > Subject: RE: [Insight-users]<br> > > itkScalarChanAndVeseSparseLevelSetImageFilter<br> > ><br> > > Hello,<br> > > thank you very much for the help. Unfortunately I work with medical<br> > > data that I am not supposed to give.<br> > > Can you explain a little more point 2. You mean that I have to<br> > > define my level set as inside positive and outside negative to have<br> > > the opposite propagation direction?<br> > > I tried it but it did not work. I both cases, if I initialize the LS<br> > > inside the boundary of my data, it shrinks. I use mu=0, nu=0, l1=1<br> > > and l2=1. Do I need negative l1?When I initialize almost the whole<br> > > LS outside my data it seems to work in some cases.Generally, I get<br> > > different results from the insight journal that I was getting <br> > correct.<br> > ><br> > > Thank you,<br> > > Eleni<br> > ><br> > ><br> > > -----Original Message-----<br> > > From: Kishore Mosaliganti [<a href="mailto:kishoreraom@gmail.com">mailto:kishoreraom@gmail.com</a>]<br> > > Sent: Fri 6/5/2009 1:02 PM<br> > > To: Sgouritsa, Eleni<br> > > Cc: Luis Ibanez; <a href="mailto:insight-users@itk.org">insight-users@itk.org</a><br> > > Subject: Re: [Insight-users]<br> > > itkScalarChanAndVeseSparseLevelSetImageFilter<br> > ><br> > > Hi Eleni,<br> > ><br> > > Thank you for pointing out these problems. You are right that the<br> > > Review<br> > > code is not very stable as yet. We are working on fixing them.<br> > > During the<br> > > transfer from the IJ paper to the Review directory, a lot of<br> > > modifications<br> > > were made. We might have inadvertently introduced new errors.<br> > ><br> > > Regarding your problems:<br> > ><br> > > 2. The level-set function is defined by convention as inside is<br> > > negative and<br> > > outside is positive. So the negative values become your foreground <br> > and<br> > > positive values become the background. This controls the propagation<br> > > direction.<br> > ><br> > > 3. I am looking at the Halt function. Looks like the boundary case<br> > > of 0<br> > > iterations is not coded right.<br> > ><br> > > 4. Regarding the high RMS values, the level-set function is re-<br> > > initialized<br> > > to a signed distance function after every few iterations. It so<br> > > happens that<br> > > the default setting is 1 iteration. Hence, the RMS change is being<br> > > calculated after the reinitialization while it needs to be done<br> > > before. We<br> > > are also working on correcting this. Thank you for pointing this <br> > out.<br> > ><br> > ><br> > > Is it possible for you to post a small sample of your data for us to<br> > > work on<br> > > the errors.<br> > ><br> > ><br> > > Kishore<br> > ><br> > > On Tue, Jun 2, 2009 at 11:24 AM, Sgouritsa, Eleni<br> > > <<a href="mailto:esgourit@central.uh.edu">esgourit@central.uh.edu</a>>wrote:<br> > ><br> > > > Hello,<br> > > > I m sorry if my point was not clear. The problems that I am facing<br> > > using<br> > > > this class to segment 3D data are the following:<br> > > ><br> > > > 1. My data has negative origin (for example (-100, -100, -60).<br> > > Unless I do<br> > > > SetOrigin(0,0,0) (or I guess any origin >=0) my program crashes. I<br> > > have to<br> > > > set my negative origin as zero for my program to run. Does the<br> > > class assumes<br> > > > positive origin of the input image?<br> > > ><br> > > > 2. I initialize my level set inside (so the evolution should be<br> > > outwards).<br> > > > In this case I can not make my level set expand (it can just<br> > > shrink, or not<br> > > > move). I think I should use something like<br> > > SetReverseExpansionDirection to<br> > > > control the propagation direction, but I can not find this option<br> > > in the<br> > > > class public members. (This is currently my main problem where I<br> > > am stuck,<br> > > > any help would be very useful!)<br> > > ><br> > > > 3. The maximum RMS Error serves (along with the number of<br> > > iterations) as a<br> > > > stopping criteria inside the Halt function (of<br> > > > itkMultiphaseFiniteDifferenceImageFilter.txx file).<br> > > > Lets say I set maximum RMS Error = 0.01.<br> > > > The Halt function returns the following:<br> > > > return ( (this->GetElapsedIterations() >= this-<br> > > >m_NumberOfIterations) ||<br> > > > ( this->GetMaximumRMSError() >= m_RMSChange ) );<br> > > > While the Halt function returns false the evolution continues.<br> > > > However, in iteration 0, I get m_RMSChange = 0, so the evolution<br> > > always<br> > > > stops doing 0 iterations (since the condition this-<br> > > >GetMaximumRMSError() >=<br> > > > m_RMSChange becomes true)<br> > > > If I modify the Halt function to returm the following:<br> > > > if(this->GetElapsedIterations()==0)<br> > > > return false;<br> > > > else<br> > > > return ( (this->GetElapsedIterations() >=<br> > > > this->m_NumberOfIterations) || ( this->GetMaximumRMSError() >=<br> > > m_RMSChange )<br> > > > );<br> > > > then it works.<br> > > > The other problem is that RMSChange in the next iterations<br> > > (1,2,3...) has<br> > > > very big values (like 5000) even near convergence. So the only way<br> > > to stop<br> > > > the evolution is through the iterations number.<br> > > ><br> > > > I am still investigating the class and I am not absolutely sure<br> > > about the<br> > > > points mentioned but I would like to share with you for more <br> > advice.<br> > > ><br> > > ><br> > > > Thank you very much,<br> > > > Lena<br> > > ><br> > > ><br> > > ><br> > > ><br> > > > -----Original Message-----<br> > > > From: Luis Ibanez [<a href="mailto:luis.ibanez@kitware.com">mailto:luis.ibanez@kitware.com</a><<a href="mailto:luis.ibanez@kitware.com">luis.ibanez@kitware.com</a><br> > > ><br> > > > ]<br> > > > Sent: Mon 6/1/2009 8:39 PM<br> > > > To: Sgouritsa, Eleni<br> > > > Cc: alex gouaillard; <a href="mailto:insight-users@itk.org">insight-users@itk.org</a><br> > > > Subject: Re: [Insight-users]<br> > > itkScalarChanAndVeseSparseLevelSetImageFilter<br> > > ><br> > > ><br> > > > Hi Lena,<br> > > ><br> > > > Could you please be more specific about your problem report on<br> > > > item (2) ?<br> > > ><br> > > > Is there a chance that you can report this in a form that<br> > > > we could reproduce ?<br> > > ><br> > > ><br> > > > Thanks<br> > > ><br> > > ><br> > > > Luis<br> > > ><br> > > ><br> > > > -----------------------------<br> > > > Sgouritsa, Eleni wrote:<br> > > > > Hi,<br> > > > ><br> > > > > I have two more questions.<br> > > > > 1. In the insight journal code there was an option<br> > > > > SetReverseExpansionDirection to control if the expansion of the<br> > > level<br> > > > > set will be inwards or outwards. How can I do it using the<br> > > > > itkScalarChanAndVeseSparseLevelSetImageFilter of 3.14 release?<br> > > > ><br> > > > > 2. I still have a problem when my 3D data have negative origin.<br> > > > ><br> > > > > Thanks and regards,<br> > > > > Lena<br> > > > ><br> > > > > -----Original Message-----<br> > > > > From: Sgouritsa, Eleni<br> > > > > Sent: Mon 6/1/2009 4:00 AM<br> > > > > To: alex gouaillard<br> > > > > Cc: <a href="mailto:insight-users@itk.org">insight-users@itk.org</a><br> > > > > Subject: RE: [Insight-users]<br> > > > itkScalarChanAndVeseSparseLevelSetImageFilter<br> > > > ><br> > > > > Hello,<br> > > > > finally the second issue was my fault (I just had a problem <br> > while<br> > > > > including the header files of the review folder).<br> > > > > For the first, the inconsistency is just a matter of name. The<br> > > code runs<br> > > > > correctly, just the name assignement in the txx is a little<br> > > misleading.<br> > > > ><br> > > > > Thank you very much,<br> > > > > Lena<br> > > > ><br> > > > ><br> > > > > -----Original Message-----<br> > > > > From: alex gouaillard<br> > > [<a href="mailto:alexandre_gouaillard@hms.harvard.edu">mailto:alexandre_gouaillard@hms.harvard.edu</a><<a href="mailto:alexandre_gouaillard@hms.harvard.edu">alexandre_gouaillard@hms.harvard.edu</a><br> > > ><br> > > > ]<br> > > > > Sent: Sun 5/31/2009 11:34 PM<br> > > > > To: Sgouritsa, Eleni<br> > > > > Cc: <a href="mailto:insight-users@itk.org">insight-users@itk.org</a><br> > > > > Subject: Re: [Insight-users]<br> > > > itkScalarChanAndVeseSparseLevelSetImageFilter<br> > > > ><br> > > > > hi eleni,<br> > > > ><br> > > > > we'll take a look tomorrow.<br> > > > ><br> > > > > thanks for the feedback.<br> > > > ><br> > > > > alex.<br> > > > ><br> > > > > On May 31, 2009, at 11:52 PM, Sgouritsa, Eleni wrote:<br> > > > ><br> > > > > > Hello,<br> > > > > > I know that the review folder of the new release (3.14) is <br> > not<br> > > > > > stable yet but I would just like to give two comments:<br> > > > > ><br> > > > > > 1. I found an inconsistency between the template arguments of<br> > > the<br> > > > > > itkScalarChanAndVeseSparseLevelSetImageFilter.h and the<br> > > > > > itkScalarChanAndVeseSparseLevelSetImageFilter.txx.<br> > > > > > Specifically, in the header file, the template is :<br> > > > > > template < class TInputImage, class TFeatureImage, class<br> > > > > > TOutputImage, class TFunction,<br> > > > > > class TSharedData, typename TIdCell = unsigned int ><br> > > > > > whereas in the txx it is:<br> > > > > > template < class TInput, class TFeature, class TFunction,<br> > > > > > class TOutputPixel, class TSharedData, typename TIdCell ><br> > > > > > There is a change in the order of the 3rd and 4th argument.<br> > > > > ><br> > > > > > 2. I can not find this class<br> > > > > > (itkScalarChanAndVeseSparseLevelSetImageFilter) incuded in <br> > the<br> > > > > > CMakeLists of the review folder<br> > > > > ><br> > > > > > Regards,<br> > > > > > Lena<br> > > > > ><br> > > > > > <ATT00001.txt><br> > > > ><br> > > > ><br> > > > ><br> > > > ><br> > > > ><br> > > <br> > ------------------------------------------------------------------------<br> > > > ><br> > > > > _____________________________________<br> > > > > Powered by <a href="http://www.kitware.com">www.kitware.com</a><br> > > > ><br> > > > > Visit other Kitware open-source projects at<br> > > > > <a href="http://www.kitware.com/opensource/opensource.html">http://www.kitware.com/opensource/opensource.html</a><br> > > > ><br> > > > > Please keep messages on-topic and check the ITK FAQ at:<br> > > > <a href="http://www.itk.org/Wiki/ITK_FAQ">http://www.itk.org/Wiki/ITK_FAQ</a><br> > > > ><br> > > > > Follow this link to subscribe/unsubscribe:<br> > > > > <a href="http://www.itk.org/mailman/listinfo/insight-users">http://www.itk.org/mailman/listinfo/insight-users</a><br> > > ><br> > > ><br> > > > _____________________________________<br> > > > Powered by <a href="http://www.kitware.com">www.kitware.com</a><br> > > ><br> > > > Visit other Kitware open-source projects at<br> > > > <a href="http://www.kitware.com/opensource/opensource.html">http://www.kitware.com/opensource/opensource.html</a><br> > > ><br> > > > Please keep messages on-topic and check the ITK FAQ at:<br> > > > <a href="http://www.itk.org/Wiki/ITK_FAQ">http://www.itk.org/Wiki/ITK_FAQ</a><br> > > ><br> > > > Follow this link to subscribe/unsubscribe:<br> > > > <a href="http://www.itk.org/mailman/listinfo/insight-users">http://www.itk.org/mailman/listinfo/insight-users</a><br> > > ><br> > > ><br> > ><br> > ><br> > ><br> > > <ATT00001.txt><br> ><br> ><br> ><br> > <ATT00001.txt><br> <br> <br> </font> </p> </div> </blockquote></div><br></div></div></body></html>