<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Hi Sergio,</div><div> good. To get less noise you can do one of two things:</div><div>1. increase sigma min</div><div>2. increase gamma (by one order of magnitude at a time)</div><div>Just play with those two and check out the differences visually, you'll be able to control the behavior of the filter.</div><div>Best regards</div><div><br></div><div>Luca</div><div><br></div><br><div><div>On Oct 13, 2010, at 10:23 AM, Sergio Vera wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Ravi, Luca, thanks to both of you.<div><br></div><div>Indeed a stupid mistake, using twice the SetSigmaMinimum method... :(</div><div>Now the filter works properly :)</div><div><br></div><div>I might add another question?</div>
<div>Is there any standard procedure or trick to reduce the amount of noisy structures that the hessian filters enhance? Along with the coronary vessels and other tubes of the image, a lot of noisy blobs are enhanced..</div>
<div><br></div><div>thanks<br><br><div class="gmail_quote">On Mon, Oct 11, 2010 at 11:11 PM, Luca Antiga <span dir="ltr"><<a href="mailto:luca.antiga@gmail.com">luca.antiga@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div style="word-wrap:break-word">Hi Sergio,<div> the line</div><div>hessian->SetSigmaMinimum(2.4);</div><div>should be </div><div><div>hessian->SetSigmaMaximum(2.4);</div></div><div><br></div><div>Probably a method SetSigmaRange taking two arguments would be a safer choice to avoid this kinds of mistakes.</div>
<div><br></div><div>Hope this helps.</div><div><br></div><div>Luca</div><div><br></div><div><br></div><div><br><div><div><div></div><div class="h5"><div>On Oct 11, 2010, at 12:22 PM, Sergio Vera wrote:</div><br></div></div>
<blockquote type="cite"><div><div></div><div class="h5">Hello all<div><br></div><div>Currently I use HessianRecursiveGaussianImageFilter Hessian3DToVesselness to enhance coronary arteries in CTA images. I would like to test the multiscale hessian enhancement using MultiScaleHessianBasedMeasureImageFilter and HessianToObjectnessMeasureImageFilter, however, I'm only obtainig empty (black) images as a result of the enhancement and the scales.</div>
<div><br></div><div>Here is a snippet of the code:</div><div><div> </div><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace">typedef itk::ThresholdImageFilter<ITKImgInType> ThrFilter;</font></blockquote><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace">ThrFilter::Pointer thr = ThrFilter::New();</font></blockquote><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace">thr->SetInput(&a_imgIn);</font></blockquote><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace">thr->SetLower(80); </font></blockquote><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace">thr->SetUpper(10000); // remove other parts of the image with low values</font> </blockquote><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace"><br></font></blockquote><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace">typedef itk::CastImageFilter<ITKImgInType, F1d3ITKImgType> CastFilter;</font></blockquote><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace">CastFilter::Pointer cast2float = CastFilter::New();</font></blockquote><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace">cast2float->SetInput(thr->GetOutput());</font></blockquote><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace"><br></font></blockquote><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace">typedef itk::SymmetricSecondRankTensor<float, 3> HessianPixelType;</font></blockquote><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace">typedef itk::Image<HessianPixelType, 3> HessianImage;</font></blockquote><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace"><br></font></blockquote><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace">typedef itk::MultiScaleHessianBasedMeasureImageFilter </font><span style="font-family:'courier new', monospace"><F1d3ITKImgType, HessianImage, F1d3ITKImgType> HessianFilter;</span></blockquote>
<blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace">HessianFilter::Pointer hessian = HessianFilter::New();</font></blockquote><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace">hessian->SetInput(cast2float->GetOutput());</font></blockquote><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace">hessian->SetNumberOfSigmaSteps(6);</font></blockquote><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace">hessian->SetSigmaStepMethodToEquispaced();</font></blockquote><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace">hessian->SetSigmaMinimum(1.1);</font></blockquote><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace">hessian->SetSigmaMinimum(2.4); // This sizes in mm?</font></blockquote><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace">hessian->SetGenerateHessianOutput(true);</font></blockquote><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace">hessian->SetGenerateScalesOutput(true);</font></blockquote><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace"><br></font></blockquote><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<span style="white-space:pre-wrap"><font face="'courier new', monospace">ty</font></span><font face="'courier new', monospace">pedef itk::HessianToObjectnessMeasureImageFilter </font><span style="font-family:'courier new', monospace"><HessianImage, F1d3ITKImgType> ObjectnessFilter;</span></blockquote>
<blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace">ObjectnessFilter::Pointer vesselFilter = ObjectnessFilter::New();</font></blockquote><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace">vesselFilter->SetScaleObjectnessMeasure(false);</font></blockquote><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace">vesselFilter->SetBrightObject(true);</font></blockquote><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace">vesselFilter->SetAlpha(0.5);</font></blockquote><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace">vesselFilter->SetBeta(0.5);</font></blockquote><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace">vesselFilter->SetGamma(5.0);</font></blockquote><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace">vesselFilter->SetObjectDimension(1); // vessels</font></blockquote><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<span style="white-space:pre-wrap"><font face="'courier new', monospace"> </font></span></blockquote><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace">hessian->SetHessianToMeasureFilter(vesselFilter);</font></blockquote><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<span style="white-space:pre-wrap"><font face="'courier new', monospace"> </font></span></blockquote><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace">try {</font></blockquote><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace"><span style="white-space:pre-wrap"> </span>hessian->Update();</font></blockquote><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace">} catch (const itk::ExceptionObject& e) {</font></blockquote><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace"><span style="white-space:pre-wrap"> </span>std::cerr << __FUNCTION__ << ": itk::ExceptionObject caught: " << e.what() </font><span style="font-family:'courier new', monospace"><< '\n';</span></blockquote>
<blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace"><span style="white-space:pre-wrap"> </span>return eErrorITKExceptionRunningSegmentation;</font></blockquote><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace">} catch (...) {</font></blockquote><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace"><span style="white-space:pre-wrap"> </span>std::cerr << __FUNCTION__ << ": '...' exception caught.\n";</font></blockquote>
<blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace"><span style="white-space:pre-wrap"> </span>return eErrorUnknownExceptionStartingSegmentation;</font></blockquote><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace">}</font></blockquote><blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace">spy::WriteFile<F1d3ITKImgType></font><span style="font-family:'courier new', monospace">(__FUNCTION__, "Vesselness.mhd", *(hessian->GetOutput()), true);</span></blockquote>
<blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace">spy::WriteFile<F1d3ITKImgType></font><font face="'courier new', monospace">(__FUNCTION__, "Scales.mhd", *(hessian->GetScalesOutput()), true);</font></blockquote>
<blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204, 204, 204);border-left-style:solid;padding-left:1ex">
<font face="'courier new', monospace">spy::WriteFile<F1d3ITKImgType></font><span style="font-family:'courier new', monospace">(__FUNCTION__, "Converted2Float.mhd", *(cast2float->GetOutput()), true);</span></blockquote>
</div><div><br></div><div>The two first images written to disk are empty. Correct size and spacing but only black voxels. Converted2Float.mhd seems to be correcttly converted</div><div>Thanks in advance<br>-- <br>Sergio Vera<br>
<br> Alma IT Systems<br> C/ Vilana, 4B, 4º 1ª<br> 08022 Barcelona<br> T. (+34) 932 380 592<br> <a href="http://www.alma3d.com/" target="_blank">www.alma3d.com</a><br>
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</div></blockquote></div><br></div></div></blockquote></div><br><br clear="all"><br>-- <br>Sergio Vera<br><br> Alma IT Systems<br> C/ Vilana, 4B, 4º 1ª<br> 08022 Barcelona<br> T. (+34) 932 380 592<br> <a href="http://www.alma3d.com/">www.alma3d.com</a><br>
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