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<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Hi Dženan and Paul,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">thank you for the Information about the mesh smoothing algorithm, that helped a lot. Unfortunately I don’t completely understand the source code, since I’m not a software developer.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">In the source code you linked it says that the maximum error parameter is ignored, so I assume that the value in the program settings has no effect on the smoothing.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">(<a href="https://sourceforge.net/p/itk-snap/src/ci/master/tree/Logic/Mesh/VTKMeshPipeline.cxx#l169">https://sourceforge.net/p/itk-snap/src/ci/master/tree/Logic/Mesh/VTKMeshPipeline.cxx#l169</a>)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">As for the sigma I still don’t entirely understand why the polygon model is not smoothed below a sigma of 0.67.
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">In the preferences for ITK-SNAP at the 3D Rendering tab, there is a Gaussian image smoothing option. Activating this option will smooth the polygon model of a segmentation for sigma>=0.67.
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">Also in the source code and documentation there seems to be contradicting information, because in
<a href="https://gitlab.kitware.com/vtk/vtk/blob/master/Imaging/General/vtkImageGaussianSmooth.h">
vtkImageGaussianSmooth.h</a> sigma is in pixel units and in <a href="https://sourceforge.net/p/itk-snap/src/ci/master/tree/Logic/Mesh/VTKMeshPipeline.cxx#l166">
VTKMeshPipeline.cxx#l166</a> it is in millimeters. Which information relates to the 3D Rendering option?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">Regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">Benedikt Beyer<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><b>Von:</b> Dženan Zukić [mailto:dzenanz@gmail.com] <br>
<b>Gesendet:</b> Dienstag, 30. Mai 2017 15:38<br>
<b>An:</b> Beyer, Benedikt Alexander <benedikt.beyer@rwth-aachen.de><br>
<b>Cc:</b> community@itk.org; Paul Yushkevich <pyushkevich@gmail.com><br>
<b>Betreff:</b> Re: [ITK] Questions about ITK-Snap gaussian smoothing<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Verdana",sans-serif">Hi Benedikt,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Verdana",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Verdana",sans-serif">if you are asking about which mesh smoothing algorithm is used, I think this source code file answers that:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Verdana",sans-serif"><a href="https://sourceforge.net/p/itk-snap/src/ci/master/tree/Logic/Mesh/VTKMeshPipeline.cxx#l167" target="_blank">https://sourceforge.net/p/itk-snap/src/ci/master/tree/Logic/Mesh/VTKMeshPipeline.cxx#l167</a></span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Its <a href="https://sourceforge.net/p/itk-snap/src/ci/master/tree/Logic/Mesh/VTKMeshPipeline.h#l122" target="_blank">
declaration</a> says it is an <a href="http://www.vtk.org/doc/nightly/html/classvtkImageGaussianSmooth.html" target="_blank">vtkImageGaussianSmooth</a>. If documentation is not enough, you can find
<a href="https://gitlab.kitware.com/vtk/vtk/blob/master/Imaging/General/vtkImageGaussianSmooth.cxx" target="_blank">
its source code</a> in VTK.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">As the sigma is passed into there as a parameter, I believe the user-modifiable preferences in the program control it.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Paul (CC'd) might have more explanations.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Verdana",sans-serif">Regards,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Verdana",sans-serif">Dženan Zukić, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)</span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Tue, May 30, 2017 at 4:42 AM, Beyer, Benedikt Alexander <<a href="mailto:benedikt.beyer@rwth-aachen.de" target="_blank">benedikt.beyer@rwth-aachen.de</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="background:white"><span style="color:black">Dear ITK community,</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="color:black"> </span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="color:black">I am currently writing an academic thesis at the RWTH Aachen University and I work with STL-data that is exported with ITK-Snap. A segmented structure is exported as an STL-file
and then analyzed with VG Studio MAX. The data is used to determine measurement uncertainties created by gaussian filtering. To determine this uncertainty, I compare smoothed data to unsmoothed data. I have a few questions regarding the gaussian image smoothing
setting.</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="color:black"> </span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<span lang="EN-US">What gaussian filter algorithm does this option use? Eg. Recursive, discrete, robust, etc.</span><span style="font-size:12.0pt"><o:p></o:p></span></li><li class="MsoNormal" style="color:black;margin-left:0cm;mso-list:l0 level1 lfo1;background:white">
<span lang="EN-US">Is this filter a linear or surface filter?</span><span style="font-size:12.0pt"><o:p></o:p></span></li><li class="MsoNormal" style="color:black;margin-left:0cm;mso-list:l0 level1 lfo1;background:white">
<span lang="EN-US">How big is the gaussian kernel? Eg. 3x3, 5x5, etc.</span><span style="font-size:12.0pt"><o:p></o:p></span></li><li class="MsoNormal" style="color:black;margin-left:0cm;mso-list:l0 level1 lfo1;background:white">
<span lang="EN-US">What does the “approximation error max” option do? It has no visual effect on the segmentation.</span><span style="font-size:12.0pt"><o:p></o:p></span></li><li class="MsoNormal" style="color:black;margin-left:0cm;mso-list:l0 level1 lfo1;background:white">
<span lang="EN-US">There seems to be a threshold of the standard deviation at around 0.67. It seems that below this number no smoothing is applied. Is this specific to the program, or is this depende</span><span lang="EN-US" style="color:windowtext">n</span><span lang="EN-US">d
on the voxel size?</span><span lang="EN-US" style="font-size:12.0pt"><o:p></o:p></span></li><li class="MsoNormal" style="color:black;margin-left:0cm;mso-list:l0 level1 lfo1;background:white">
<span lang="EN-US">Are there any known influences on measurement uncertainty by gaussian smoothing?</span><span style="font-size:12.0pt"><o:p></o:p></span></li></ol>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="color:black"> </span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="color:black">Thank you in advance and with kind regards</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="color:#888888">Benedikt Beyer</span><span style="font-size:12.0pt;color:#888888"><o:p></o:p></span></p>
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<p style="background:white"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
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