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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Dear Dzenan<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Thank you for your reply to our question. I understand from
your message you are also working with deformable models.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>However, I think I do not exactly understood your proposed workaround.
Maybe it’s possible for you to send an e-mail with a part of the ITK code for
this workaround. <o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>I think with this code it’s possible for me to understood your
workaround and maybe this workaround may be also a solution for our problem.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Kind regards – Jan <o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'>
<p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:
"Tahoma","sans-serif"'>From:</span></b><span lang=EN-US style='font-size:10.0pt;
font-family:"Tahoma","sans-serif"'> Dženan Zukić [mailto:dzenanz@gmail.com] <br>
<b>Sent:</b> donderdag 22 juli 2010 14:56<br>
<b>To:</b> Menssen, Jan<br>
<b>Cc:</b> insight-users@itk.org; Nillesen, Maartje<br>
<b>Subject:</b> Re: [Insight-users] bug in DeformableModelSimplexMesh ?<o:p></o:p></span></p>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>I discovered few weeks back, that you cannot just change
input mesh for deform filter, that is<o:p></o:p></p>
<div>
<p class=MsoNormal><span class=apple-style-span><i><span style='font-size:7.5pt;
font-family:"Courier New"'>m_DeformFilter->SetInput(m_SimplexMesh);</span></i></span><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>this line is a problem. The workaround I used was to create
unnamed block and create a new deform filter from scratch (instantiate filter
and set a bunch of parameters) instead of just setting setting input mesh and
calling update.<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>Regards,<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>Dženan<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
<div>
<p class=MsoNormal>On Wed, Jul 21, 2010 at 11:37, <<a
href="mailto:J.Menssen@cukz.umcn.nl">J.Menssen@cukz.umcn.nl</a>> wrote:<o:p></o:p></p>
<div>
<p><span lang=EN-US style='font-family:"Calibri","sans-serif"'>Dear All<span
style='color:#1F497D'><o:p></o:p></span></span></p>
<p><span lang=EN-US style='font-family:"Calibri","sans-serif"'>We are working
on a segmentation algorithm using deformable models with a refine mesh. The
deformation and refinement is done in a for loop. Our application is
based on the DeformableModel application as given in the InsightApplications
example DeformableModelSimplexMesh.<span style='color:#1F497D'><o:p></o:p></span></span></p>
<p><span lang=EN-US style='font-family:"Calibri","sans-serif"'>We modified the
for loop in de DeformMesh method (DeformableModelApplication.cxx) with a
refinement of the mesh, but this crashes. Below a part of (pseudo) code is
given.. </span><o:p></o:p></p>
<p><i><span lang=EN-US style='font-family:"Calibri","sans-serif"'>
for i=1:i<nr_iterations;i++</span></i><o:p></o:p></p>
<p><i><span lang=EN-US style='font-family:"Calibri","sans-serif"'>
{</span></i><o:p></o:p></p>
<p><i><span lang=EN-US style='font-family:"Calibri","sans-serif"'>
m_simplexMesh->DisconnectPipeline()</span></i><o:p></o:p></p>
<p><i><span lang=EN-US style='font-family:"Calibri","sans-serif"'>
m_deformFilter-SetInput(m_simplexMesh);</span></i><o:p></o:p></p>
<p><i><span lang=EN-US style='font-family:"Calibri","sans-serif"'>
m_deformFilter->Update(0;</span></i><o:p></o:p></p>
<p><i><span lang=EN-US style='font-family:"Calibri","sans-serif"'>
simplexMesh2 = m_deformFilter->GetOutput();</span></i><o:p></o:p></p>
<p><i><span lang=EN-US style='font-family:"Calibri","sans-serif"'>
</span></i><o:p></o:p></p>
<p><i><span lang=EN-US style='font-family:"Calibri","sans-serif"'>
m_refineMesh->SetInput(simplexMesh2);</span></i><o:p></o:p></p>
<p><i><span lang=EN-US style='font-family:"Calibri","sans-serif"'>
m_refineMesh->Update();</span></i><o:p></o:p></p>
<p><i><span lang=EN-US style='font-family:"Calibri","sans-serif"'>
m_simplexMesh=m_refineMesh->GetOutput();</span></i><o:p></o:p></p>
<p><i><span lang=EN-US style='font-family:"Calibri","sans-serif"'> }</span></i><o:p></o:p></p>
<p><span lang=EN-US style='font-family:"Calibri","sans-serif"'>m_deformFilter
is a</span><span lang=EN-US> </span><span style='font-family:"Calibri","sans-serif"'>DeformableSimplexMesh3DGradientConstraintForceFilter,</span>
<o:p></o:p></p>
<p><span style='font-family:"Calibri","sans-serif"'>m_RefineMesh is a
itkSimplexMeshAdaptTopologyFilter</span><o:p></o:p></p>
<p><span lang=EN-US> <i> </i></span><o:p></o:p></p>
<p><span lang=EN-US style='font-family:"Calibri","sans-serif"'>To isolate the
bug, we started with a little modification of the DeformMesh method in
DeformableModelApplication.cxx. The modifications are given below (line 522 in
original file, InsightApplciations 3.16). Running this code results also in a
crash</span><o:p></o:p></p>
<p><span lang=EN-US style='font-family:"Calibri","sans-serif"'>*----------------------------------------------------------------------------------------------------------------------------------------</span><o:p></o:p></p>
<p><i><span style='font-size:7.5pt;font-family:"Courier New"'>SimplexMeshType::Pointer
simplexMesh2 = m_SimplexMesh;</span></i><o:p></o:p></p>
<p><i><span style='font-size:7.5pt;font-family:"Courier New";color:blue'>const</span>
</i><i><span style='font-size:7.5pt;font-family:"Courier New";color:blue'>unsigned</span>
</i><i><span style='font-size:7.5pt;font-family:"Courier New";color:blue'>int</span></i><i><span
style='font-size:7.5pt;font-family:"Courier New"'> numberOfIterationsToGo =
atoi(m_IterationsValueInput->value()); </span></i><o:p></o:p></p>
<p><i><span style='font-size:7.5pt;font-family:"Courier New";color:blue'>for</span></i><i><span
style='font-size:7.5pt;font-family:"Courier New"'>(</span> </i><i><span
style='font-size:7.5pt;font-family:"Courier New";color:blue'>unsigned</span> </i><i><span
style='font-size:7.5pt;font-family:"Courier New";color:blue'>int</span></i><i><span
style='font-size:7.5pt;font-family:"Courier New"'> i=0;
i<numberOfIterationsToGo; i++ )</span></i><o:p></o:p></p>
<p><i><span style='font-size:7.5pt;font-family:"Courier New"'>{</span></i><o:p></o:p></p>
<p><i><span style='font-size:7.5pt;font-family:"Courier New"'>
std::cout <<</span> </i><i><span style='font-size:7.5pt;font-family:"Courier New";
color:#A31515'>" Iteration "</span></i><i><span
style='font-size:7.5pt;font-family:"Courier New"'> << i <<
std::endl;</span></i><o:p></o:p></p>
<p><i><span style='font-size:7.5pt;font-family:"Courier New"'>
</span></i><o:p></o:p></p>
<p><i><span style='font-size:7.5pt;font-family:"Courier New";color:green'>//*
-------------- start modified code -------------------------------------------</span></i><o:p></o:p></p>
<p><i> </i><i><span style='font-size:
7.5pt;font-family:"Courier New";color:green'>// THIS IS MODIFIED CODE THAT (WE
THINK) DOESN'T VIOLATE THE ITK RULES BUT THIS</span></i><o:p></o:p></p>
<p><i> </i><i><span style='font-size:7.5pt;font-family:"Courier New";
color:green'>// CODE CRASHES</span></i><o:p></o:p></p>
<p><i>
</i><i><span style='font-size:7.5pt;
font-family:"Courier New"'>m_SimplexMesh->DisconnectPipeline();</span></i><o:p></o:p></p>
<p><i>
</i><i><span style='font-size:7.5pt;
font-family:"Courier New"'>m_DeformFilter->SetInput(m_SimplexMesh);</span></i><o:p></o:p></p>
<p><i>
</i><i><span style='font-size:7.5pt;font-family:"Courier New"'>m_DeformFilter->SetIterations(1);</span></i><o:p></o:p></p>
<p><i>
</i><i><span style='font-size:7.5pt;
font-family:"Courier New"'>m_DeformFilter->Update();</span></i><o:p></o:p></p>
<p><i>
</i><i><span style='font-size:7.5pt;
font-family:"Courier New"'>simplexMesh2 = m_DeformFilter->GetOutput();</span></i><o:p></o:p></p>
<p><i>
</i><i><span style='font-size:7.5pt;
font-family:"Courier New"'>SimplexMesh2->DisconnectPipeline(0</span></i><o:p></o:p></p>
<p style='margin-left:108.0pt'><i><span style='font-size:7.5pt;font-family:
"Courier New"'>m_DeformFilter->SetInput(simplexMesh2);</span></i><o:p></o:p></p>
<p><i>
</i><i><span style='font-size:7.5pt;
font-family:"Courier New"'>m_DeformFilter->SetIterations(1);</span></i><o:p></o:p></p>
<p><i>
</i><i><span style='font-size:7.5pt;
font-family:"Courier New"'>m_DeformFilter->Update();</span></i><o:p></o:p></p>
<p><i>
</i><i><span style='font-size:7.5pt;
font-family:"Courier New"'>m_SimplexMesh = m_DeformFilter->GetOutput();</span></i><o:p></o:p></p>
<p><i><span style='font-size:7.5pt;font-family:"Courier New";color:green'>//
--------------------- end modified code --------------------------------------
*/</span></i><o:p></o:p></p>
<p><i><span style='font-size:7.5pt;font-family:"Courier New"'>
m_SimplexMeshToShow = m_SimplexMesh;</span></i><o:p></o:p></p>
<p><i><span style='font-size:7.5pt;font-family:"Courier New"'> </span>
</i><i><span style='font-size:7.5pt;font-family:"Courier New";color:blue'>this</span></i><i><span
style='font-size:7.5pt;font-family:"Courier New"'>->RefreshMeshVisualization();</span></i><o:p></o:p></p>
<p><i><span style='font-size:7.5pt;font-family:"Courier New"'>
</span></i><o:p></o:p></p>
<p><i><span style='font-size:7.5pt;font-family:"Courier New"'> </span>
</i><i><span style='font-size:7.5pt;font-family:"Courier New";color:green'>//
force a redraw</span></i><o:p></o:p></p>
<p><i><span style='font-size:7.5pt;font-family:"Courier New"'>
axialView->redraw();</span></i><o:p></o:p></p>
<p><i><span style='font-size:7.5pt;font-family:"Courier New"'>
coronalView->redraw();</span></i><o:p></o:p></p>
<p><i><span style='font-size:7.5pt;font-family:"Courier New"'>
sagittalView->redraw();</span></i><o:p></o:p></p>
<p><i><span style='font-size:7.5pt;font-family:"Courier New"'>
surfaceView->redraw();</span></i><o:p></o:p></p>
<p><i><span style='font-size:7.5pt;font-family:"Courier New"'>
Fl::check(); </span></i><o:p></o:p></p>
<p><i><span style='font-size:10.0pt;font-family:"Courier New"'> }</span></i><o:p></o:p></p>
<p><span lang=EN-US>*-------------------------------------------------------------------------------------------------------------------------------------------</span><o:p></o:p></p>
<p><span lang=EN-US style='font-family:"Calibri","sans-serif"'>Error message
(using Visual Studio 2005 and/or 2008) of the crash</span><o:p></o:p></p>
<p><span lang=EN-US style='font-family:"Calibri","sans-serif"'>Debug Assertion
Failed !</span><o:p></o:p></p>
<p><span lang=EN-US> </span><span
lang=EN-US style='font-family:"Calibri","sans-serif"'>Expression map/set
iterator not dereferencable </span><o:p></o:p></p>
<p><span lang=EN-US style='font-family:"Calibri","sans-serif"'>Do we something
wrong? Using a for loop in a pipeline is dangerous but in bug 0001080, we
read it’s possible to use a for loop. Also at the Old Nabble forum I read
a message that is must be possible to use a for loop. (</span><a
href="http://old.nabble.com/Using-image-iterators-combined-with-filters-in-a-loop-td28684443.html"
target="_blank"><span lang=EN-US style='font-family:"Calibri","sans-serif"'>http://old.nabble.com/Using-image-iterators-combined-with-filters-in-a-loop-td28684443.html</span></a><span
lang=EN-US style='font-family:"Calibri","sans-serif"'>)</span><o:p></o:p></p>
<p><span lang=EN-US style='font-family:"Calibri","sans-serif"'>Even if we
changed the code in the original example DeformableModelApplication according
to the above referenced Old Nabble article the application crashes (see
below)</span><o:p></o:p></p>
<p><span style='font-size:10.0pt;font-family:"Courier New"'>
</span><o:p></o:p></p>
<p><i><span style='font-size:10.0pt;font-family:"Courier New"'>m_DeformFilter->SetInput(
m_SimplexMesh );</span></i><o:p></o:p></p>
<p><i><span style='font-size:10.0pt;font-family:"Courier New"'> </span>
</i><i><span style='font-size:10.0pt;font-family:"Courier New"'>m_DeformFilter->SetIterations(1);
</span></i><o:p></o:p></p>
<p><i><span style='font-size:10.0pt;font-family:"Courier New"'>
m_DeformFilter->Update();</span></i><o:p></o:p></p>
<p><i><span style='font-size:10.0pt;font-family:"Courier New"'> </span>
</i><i><span style='font-size:10.0pt;font-family:"Courier New"'>m_SimplexMesh
= m_DeformFilter->GetOutput(); </span></i><o:p></o:p></p>
<p><i> </i><i><span style='font-size:
10.0pt;font-family:"Courier New"'>m_SimplexMesh->DisconnectPipeline();</span></i><o:p></o:p></p>
<p><span lang=EN-US style='font-family:"Calibri","sans-serif"'>So is there a
bug in the original ITK sources? As far as we now, ITK doesn’t allow to change
the input of a filter and we think this is what happened in the original
DeformableSimplexMesh application.</span><o:p></o:p></p>
<p><span lang=EN-US style='font-family:"Calibri","sans-serif"'>Can someone help
us with our problem ?</span><o:p></o:p></p>
<p><span lang=EN-US style='font-family:"Calibri","sans-serif"'>We tested with
ITK 2.8, ITK 3.16 and 3.18 and all crashes</span><o:p></o:p></p>
<p><b> </b><b><span style='font-size:10.0pt;font-family:"Univers","serif";
color:#215868'>Jan Menssen</span><br>
</b><i><span style='font-size:10.0pt;font-family:"Univers","serif";color:#444444'>Research
assistant</span></i><o:p></o:p></p>
<p><b><span style='font-size:7.5pt;font-family:"Univers","serif";color:#215868'>Radboud
University Nijmegen Medical Centre</span></b><br>
<b><span style='font-size:7.5pt;font-family:"Univers","serif";color:#444444'>Clinical
Physics Lab -</span></b> <span style='font-size:7.5pt;font-family:"Univers","serif";
color:#444444'>Peadiatrics</span><br>
<span style='font-size:7.5pt;font-family:"Univers","serif";color:#444444'>Huispost
833, route 833<br>
P.O box 9101<br>
6500 HB Nijmegen<br>
Telefoon: +31 24 36 19063<br>
E-mail</span> <a href="mailto:J.Menssen@cukz.umcn.nl" target="_blank"><span
style='font-size:7.5pt;font-family:"Univers","serif"'>J.Menssen@cukz.umcn.nl</span></a><span
style='font-size:7.5pt;font-family:"Univers","serif";color:#444444'> </span><o:p></o:p></p>
<p><a href="http://www.umcn.nl/" target="_blank"><span style='font-size:7.5pt;
font-family:"Univers","serif"'>http://www.umcn.nl</span></a><o:p></o:p></p>
<p class=MsoNormal><br clear=all>
<o:p></o:p></p>
<div>
<p><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>Het UMC St
Radboud staat geregistreerd bij de Kamer van Koophandel in het handelsregister
onder nummer 41055629.<br>
The Radboud University Nijmegen Medical Centre is listed in the Commercial
Register of the Chamber of Commerce under file number 41055629.<o:p></o:p></span></p>
</div>
</div>
<p class=MsoNormal style='margin-bottom:12.0pt'><br>
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Het UMC St Radboud staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629.<BR> The Radboud University Nijmegen Medical Centre is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.<BR>
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