Hi itk-users,<br><br>My only fault !!! (or stupdity !!)<br><br>I would like to mention that the problem I was having with the itk::Statistics::CovarianceSampleFilter was solved. The problem was being caused by an type overflow - By changing the image pixel type from signed short to double the problem was solved. <br>
<br>typedef itk::FixedArray< double, NumberOfContrasts > ArrayPixelType;<br>typedef itk::Image< ArrayPixelType, Dimension > ArrayImageType;<br><br>instead of <br><br>typedef itk::FixedArray< signed short, NumberOfContrasts > ArrayPixelType;<br>
<br><br>Thank and sorry for bothering with this issue !!!<br>Ricardo<br><br><br> <br><br><br><br><div class="gmail_quote">On Tue, Jan 5, 2010 at 2:44 PM, <span dir="ltr"><<a href="mailto:insight-users-request@itk.org">insight-users-request@itk.org</a>></span> wrote:<br>
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Today's Topics:<br>
<br>
1. [Fwd: Help save MySQL; Sign the petition]<br>
(<a href="mailto:jpr@creatis.insa-lyon.fr">jpr@creatis.insa-lyon.fr</a>)<br>
2. Re: fast marching behavior (siqi chen)<br>
3. Re: Transformation of vtkPolyData with an itk::Transform<br>
(Lodron, Gerald)<br>
4. Still having problems with Refactoring Statistic classes !!<br>
(Ricardo Ferrari)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Tue, 5 Jan 2010 01:27:09 +0100<br>
From: <a href="mailto:jpr@creatis.insa-lyon.fr">jpr@creatis.insa-lyon.fr</a><br>
Subject: [Insight-users] [Fwd: Help save MySQL; Sign the petition]<br>
To: <a href="mailto:vtkusers@vtk.org">vtkusers@vtk.org</a>, <a href="mailto:insight-users@itk.org">insight-users@itk.org</a><br>
Message-ID:<br>
<<a href="mailto:f2c2e01ab2320db1c38900648b9f67e6.squirrel@www.creatis.insa-lyon.fr">f2c2e01ab2320db1c38900648b9f67e6.squirrel@www.creatis.insa-lyon.fr</a>><br>
Content-Type: text/plain;charset=iso-8859-1<br>
<br>
Hi!<br>
<br>
Yes, I know, the following is 100% out of topics, but, as users of free<br>
software, maybe you'll feel concerned.<br>
<br>
Sorry for the cross posting.<br>
<br>
--<br>
Jean-Pierre Roux<br>
Creatis CNRS UMR 5220, INSERM U630<br>
<br>
<br>
---------------------------- Original Message ----------------------------<br>
Subject: Help save MySQL; Sign the petition<br>
From: <a href="mailto:monty@helpmysql.org">monty@helpmysql.org</a><br>
Date: Thu, December 31, 2009 23:28<br>
To: undisclosed-recipients:;<br>
--------------------------------------------------------------------------<br>
<br>
Hi!<br>
<br>
I am contacting you because you have in the past shown interest in<br>
MySQL and from that I assume you are interested in the future<br>
well-being of MySQL.<br>
<br>
Now you have a unique opportunity to make a difference. By signing<br>
the petition at <a href="http://www.helpmysql.org" target="_blank">http://www.helpmysql.org</a> you can help affect the<br>
future of MySQL as an Open Source database.<br>
<br>
You can find more information of this on my latest blog post at:<br>
<a href="http://monty-says.blogspot.com/2009/12/help-keep-internet-free.html" target="_blank">http://monty-says.blogspot.com/2009/12/help-keep-internet-free.html</a><br>
<br>
Help us spread the world about this petition!<br>
<a href="http://www.helpmysql.org" target="_blank">http://www.helpmysql.org</a> is available in 18 languages and every vote<br>
is important, independent of from where in the world it comes!<br>
If you know people that are using MySQL, please contact them and<br>
ensure they also sign the petition!<br>
<br>
Regards,<br>
Monty<br>
Creator of MySQL<br>
<br>
PS: If you already have signed the petition or know about it, sorry for<br>
reminding you about this! Because of the importance of this issue,<br>
I am trying to contact every person that I have ever communicated<br>
with regarding MySQL.<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Mon, 4 Jan 2010 21:52:03 -0500<br>
From: siqi chen <<a href="mailto:siqichensc@gmail.com">siqichensc@gmail.com</a>><br>
Subject: Re: [Insight-users] fast marching behavior<br>
To: insight-users <<a href="mailto:Insight-users@itk.org">Insight-users@itk.org</a>><br>
Message-ID:<br>
<<a href="mailto:5a74a9fd1001041852g51a663c0oa0df61145e1cabaa@mail.gmail.com">5a74a9fd1001041852g51a663c0oa0df61145e1cabaa@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
I read a few more papers and thought about the question number 2 again. I<br>
think there is misinterpretation on my part. The 4 neighbors of [49.7,49.8]<br>
along their exact distance value should be set as Alive Points instead of<br>
Trial Points. Then the neighbors of the 4 neighbors (another layer around<br>
the 4 neighbors) are set as trial points, their initial tentative values are<br>
calculated using upwind difference method. When I check the result distance<br>
map, a few things to notice:<br>
1. The distance value of the 4 neighbors of [49.7, 49.8] are correct. This<br>
is obvious since I set them as Known instead of Trial.<br>
2. The distance value of the neighbors of the 4 neighbors (the input trial<br>
points) still changed. I think this is due to the inherent FMM accuracy and<br>
update method.<br>
<br>
You can try this with the following code.<br>
<a href="http://www.rpi.edu/%7Echens/download/main3.cpp" target="_blank">http://www.rpi.edu/~chens/download/main3.cpp</a><br>
<br>
Thanks<br>
Siqi<br>
<br>
On Mon, Jan 4, 2010 at 6:03 PM, siqi chen <<a href="mailto:siqichensc@gmail.com">siqichensc@gmail.com</a>> wrote:<br>
<br>
><br>
> To better illustrate my questions regarding fast marching, I put 2 example<br>
> code in the attachment.<br>
><br>
> In main1.cpp, I simply compute a distance map to point [50,50]. As you can<br>
> see from the output, the distances from the 4 neighbors of [50,50] to<br>
> [50,50] are correct, obviously the result is 1. However, the distance from<br>
> [51,51] to [50,50] is 1.707 instead of 1.414, which is obviously wrong. I<br>
> think this is due to the fast marching accuracy itself. If we switch to<br>
> higher order FMM, the result should be improved.<br>
><br>
> In main2.cpp, I perturb the target point a little bit. Instead, I want to<br>
> compute the distance map to point [49.7,49.8]. From my point of<br>
> understanding, I need to initialize the 4 neighbors of [49.7, 49.8] and put<br>
> them into the TrialPoints. As you can see, I compute the exact distance from<br>
> these 4 neighbors to [49.7,49.8] and put them into TrialPoints. However,<br>
> when I go back and check the result distance map, some thing is different.<br>
> The distances from these 4 neighbors to [49.7,49.8] are changed. As you can<br>
> see, the distance from [50,50] to [49.7,49.8] remains correct. This is<br>
> because this value is the smallest in the TrialPoints, therefore it is<br>
> pushed in to the AlivePoints heap first and the value is frozen since then.<br>
> I think there is something wrong here about whether to update trial points<br>
> value or not. If this trial point is user specified, then the value should<br>
> not be updated. I noticed a related discussion a couple of months ago in the<br>
> mailing list,<br>
> <a href="http://www.itk.org/pipermail/insight-users/2009-May/030282.html" target="_blank">http://www.itk.org/pipermail/insight-users/2009-May/030282.html</a><br>
><br>
> <a href="http://www.rpi.edu/%7Echens/download/main1.cpp" target="_blank">http://www.rpi.edu/~chens/download/main1.cpp</a><<a href="http://www.rpi.edu/%7Echens/download/main1.cpp" target="_blank">http://www.rpi.edu/%7Echens/download/main1.cpp</a>><br>
> <a href="http://www.rpi.edu/%7Echens/download/main2.cpp" target="_blank">http://www.rpi.edu/~chens/download/main2.cpp</a><<a href="http://www.rpi.edu/%7Echens/download/main2.cpp" target="_blank">http://www.rpi.edu/%7Echens/download/main2.cpp</a>><br>
><br>
> Any input is appreciated.<br>
> Siqi<br>
><br>
><br>
><br>
> On Mon, Jan 4, 2010 at 3:32 PM, Dan Mueller <<a href="mailto:dan.muel@gmail.com">dan.muel@gmail.com</a>> wrote:<br>
><br>
>> Hi Siqi,<br>
>><br>
>> Indeed I am familiar with Fast Marching. I saw your question to the<br>
>> mailing list, but did not respond because I have not experienced what<br>
>> you describe: when I set the trial point value, that is the value in<br>
>> the arrival function.<br>
>><br>
>> Perhaps you could post to the mailing list a minimal example<br>
>> (code+cmake+data) demonstrating your issue. That would make it really<br>
>> easy for me to help you!<br>
>><br>
>> Cheers, Dan<br>
>><br>
>> 2010/1/4 siqi chen <<a href="mailto:siqichensc@gmail.com">siqichensc@gmail.com</a>>:<br>
>> > Hi, Dan,<br>
>> ><br>
>> > Sorry to bother you. From the ITK mailing list, I noticed you reported a<br>
>> bug<br>
>> > about FastMarchingImageFilter couple of months ago. So I guess you are a<br>
>> > fast marching expert : )<br>
>> ><br>
>> > I am trying to use FastMarchingImageFilter to calculate a distance map<br>
>> to a<br>
>> > set of points which have non-integer coordinates and I want the result<br>
>> to be<br>
>> > as accurate as possible. Here is what I did, but the result is not very<br>
>> > accurate.<br>
>> ><br>
>> > First I find the integer points which are the neighbors of the target<br>
>> points<br>
>> > and set these integer points as trial points. Then I use some<br>
>> interpolation<br>
>> > method to initialize the distance from these trial points to the target<br>
>> > points, which are assumed to be "exactly correct". The TrialPoints in<br>
>> the<br>
>> > FastMarchingImageFilter is defined as this set of trial points and their<br>
>> > corresponding distances to the target points. The AlivePoints is empty.<br>
>> When<br>
>> > I check the result distance map, I find that the distance value of these<br>
>> > trial points are changed, they are no longer what their initial states<br>
>> are.<br>
>> > Therefore, the iso curve deviate the original input a little bit. I am<br>
>> quite<br>
>> > confusing about this result.<br>
>> ><br>
>> > I noticed you mentioned on the mailing list about neighbor update, that<br>
>> is<br>
>> > to distinguish between user-specified trial points and<br>
>> algorithm-generated<br>
>> > trial points. here is the discussion,<br>
>> > <a href="http://www.itk.org/pipermail/insight-users/2009-May/030282.html" target="_blank">http://www.itk.org/pipermail/insight-users/2009-May/030282.html</a> . I<br>
>> wonder<br>
>> > if you have any suggestions about my problem.<br>
>> ><br>
>> > Any input is appreciated.<br>
>> ><br>
>> > Thanks<br>
>> > Siqi Chen<br>
>> ><br>
>><br>
><br>
><br>
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<br>
Message: 3<br>
Date: Tue, 5 Jan 2010 07:50:08 +0100<br>
From: "Lodron, Gerald" <<a href="mailto:Gerald.Lodron@joanneum.at">Gerald.Lodron@joanneum.at</a>><br>
Subject: Re: [Insight-users] Transformation of vtkPolyData with an<br>
itk::Transform<br>
To: Sajendra <<a href="mailto:sajendra@gmail.com">sajendra@gmail.com</a>><br>
Cc: "<a href="mailto:insight-users@itk.org">insight-users@itk.org</a>" <<a href="mailto:insight-users@itk.org">insight-users@itk.org</a>>,<br>
"<a href="mailto:vtkusers@vtk.org">vtkusers@vtk.org</a>" <<a href="mailto:vtkusers@vtk.org">vtkusers@vtk.org</a>><br>
Message-ID:<br>
<E70FE8EA6EBE9241BDB4CA6D8D12E1D86B7EF09841@RZJC1EX.jr1.local><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi,<br>
<br>
Unfortunatelly i am using the bspline transform. I know that the exact inverse is not given but is there a possibility to approximate the inverse of that transform?<br>
<br>
Best regards<br>
<br>
-----Urspr?ngliche Nachricht-----<br>
Von: Sajendra [mailto:<a href="mailto:sajendra@gmail.com">sajendra@gmail.com</a>]<br>
Gesendet: Donnerstag, 17. Dezember 2009 17:57<br>
An: Lodron, Gerald<br>
Cc: <a href="mailto:insight-users@itk.org">insight-users@itk.org</a>; <a href="mailto:vtkusers@vtk.org">vtkusers@vtk.org</a><br>
Betreff: Re: [Insight-users] Transformation of vtkPolyData with an itk::Transform<br>
<br>
Hello Gerald,<br>
<br>
You will likely need to use the inverse of the transform computed from itk registration to transform your vtk polydata.<br>
The transform you have maps points from the fixed image space into the moving image space (so that it can be used to resample the moving image). If you want to transform points from the moving image space into the fixed image space, you need the inverse of that transform.<br>
<br>
Regards,<br>
Sajendra<br>
<br>
<br>
<br>
On Thu, Dec 17, 2009 at 5:27 AM, Lodron, Gerald <<a href="mailto:Gerald.Lodron@joanneum.at">Gerald.Lodron@joanneum.at</a>> wrote:<br>
> Hello<br>
><br>
> I currently made a point selector which stores it's points into a vtkPolyData structure.<br>
><br>
> Now I successfully made a image registration which converted the vtk image into itk, registered (transformed with itk::ResampleImageFilter) it and converted it back to vtk for visualization. Now the points of the vtkPolyData object are misaligned and I need to transform them. My point transformation implementation looks like this:<br>
><br>
><br>
><br>
> The problem is that the points does not fit to their old position, so there must be something wrong with the transformPoint operation?<br>
><br>
<br>
<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Tue, 5 Jan 2010 14:52:52 -0200<br>
From: Ricardo Ferrari <<a href="mailto:rjf.araraquara@gmail.com">rjf.araraquara@gmail.com</a>><br>
Subject: [Insight-users] Still having problems with Refactoring<br>
Statistic classes !!<br>
To: <a href="mailto:insight-users@itk.org">insight-users@itk.org</a><br>
Message-ID:<br>
<<a href="mailto:dc387afe1001050852u2b254536p7fe38658345ebc9a@mail.gmail.com">dc387afe1001050852u2b254536p7fe38658345ebc9a@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi itk-users,<br>
<br>
Previously (Digest Vol 68, Issue 109), I reported a problem I was having<br>
with the itk::Statistics::CovarianceSampleFilter. Although, I have not got<br>
any feedback on that issue and I could not figure it out by myself, I have<br>
overcome the problem by writing my own function to compute the covariance<br>
matrix.<br>
<br>
Now, I have faced another issue when using the<br>
itk::Statistics::GaussianMixtureModelComponent and the<br>
itk::Statistics::ExpectationMaximizationMixtureModelEstimator<br>
<br>
Attached I am sending a minimal code to illustrate the problem. For testing<br>
the code, I have downloaded two minc images (t1 and a t2 contrasts) from the<br>
brainweb projects and converted them to dicom.<br>
<br>
The program call and the result are presented bellow<br>
<br>
ferrari@ferrari-workstation:~/Desktop/Test$ bin/test<br>
t1_icbm_normal_1mm_pn3_rf20.dcm t2_icbm_normal_1mm_pn3_rf20.dcm<br>
1<br>
1a<br>
1b<br>
Segmentation fault<br>
ferrari@ferrari-workstation:~/Desktop/Test$<br>
<br>
<br>
Again, I really appreciate any help on clarifying these issues. Am I using<br>
the itk::Statistics::ImageToListSampleAdaptor class appropriately ?<br>
<br>
<br>
Thank you very much,<br>
Ricardo<br>
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CMAKE_MINIMUM_REQUIRED(VERSION 2.7)<br>
<br>
SET( ProgramName "test" )<br>
<br>
PROJECT( ${ProgramName} )<br>
<br>
FIND_PACKAGE (ITK REQUIRED)<br>
IF (ITK_FOUND)<br>
INCLUDE( ${USE_ITK_FILE} )<br>
SET(ITK_LIBRARIES ITKCommon ITKBasicFilters ITKIO ITKMetaIO ITKNumerics ITKStatistics itkvnl)<br>
ENDIF(ITK_FOUND)<br>
<br>
FIND_PACKAGE (VTK REQUIRED)<br>
IF (VTK_FOUND)<br>
INCLUDE( ${USE_VTK_FILE} )<br>
SET(VTK_LIBRARIES vtkRendering vtkGraphics vtkWidgets vtkHybrid vtkImaging vtkIO vtkFiltering vtkCommon)<br>
ENDIF( VTK_FOUND)<br>
<br>
INCLUDE_DIRECTORIES(<br>
${CMAKE_CURRENT_SOURCE_DIR}<br>
)<br>
<br>
SET( SRCS<br>
)<br>
<br>
ADD_EXECUTABLE( ${ProgramName}<br>
main.cpp<br>
${SRCS}<br>
)<br>
<br>
TARGET_LINK_LIBRARIES( ${ProgramName}<br>
${VTK_LIBRARIES}<br>
${ITK_LIBRARIES}<br>
)<br>
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<br>
------------------------------<br>
<br>
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End of Insight-users Digest, Vol 69, Issue 11<br>
*********************************************<br>
</blockquote></div><br>