<div dir="ltr"><div>Hi Dženan,</div><div><br></div>I actually found that I had to put <font face="monospace, monospace">objectnessFilter->SetScaleObjectnessMeasure(false);</font><font face="arial, helvetica, sans-serif">. I already had </font><span style="font-family:monospace,monospace">objectnessFilter-></span><wbr style="font-family:monospace,monospace"><span style="font-family:monospace,monospace">SetBrightObject(false); </span><font face="arial, helvetica, sans-serif">and </font><span style="font-family:monospace,monospace">objectnessFilter->SetObjectDim</span><wbr style="font-family:monospace,monospace"><span style="font-family:monospace,monospace">ension(1);</span><font face="arial, helvetica, sans-serif">. Now the output, which I've attached, is much better, though it still shows some of the blobs. Thanks for all your help.</font><div><font face="arial, helvetica, sans-serif"><br></font></div><div><font face="arial, helvetica, sans-serif">Jeanna</font></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Aug 10, 2016 at 4:59 AM, Dženan Zukić <span dir="ltr"><<a href="mailto:dzenanz@gmail.com" target="_blank">dzenanz@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 dir="ltr"><div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small">Hi Jeanna,</div><div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small"><br></div><div class="gmail_default" style="font-size:small"><span style="font-family:verdana,sans-serif">by taking a look at the output, you need </span><font face="monospace, monospace">objectnessFilter-><wbr>SetBrightObject(false);</font><span style="font-family:verdana,sans-serif"> and a larger size of </span><font face="monospace, monospace">objectnessFilter->SetObjectDim<wbr>ension();</font></div><div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small"><br></div><div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small">HTH,</div><div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small">Dženan</div></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Aug 10, 2016 at 12:01 AM, Jeanna S. <span dir="ltr"><<a href="mailto:jeannasheen@gmail.com" target="_blank">jeannasheen@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 dir="ltr"><div>Thanks for letting me know. I've changed the output image type to float and now it no longer shows up as just black. I've attached my output image (the image on the left is the input image; the image on the right is the output image). However, the filter seems not to detect blood vessels like I hoped, even after testing various values of Alpha, Beta, and Gamma. I was wondering if anybody has suggestions on how to improve the vessel detection?<br></div><div><br></div><div>Thanks,</div><div>Jeanna</div></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Aug 9, 2016 at 6:29 AM, Dženan Zukić <span dir="ltr"><<a href="mailto:dzenanz@gmail.com" target="_blank">dzenanz@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 dir="ltr"><div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small">Hi Jeanna,</div><div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small"><br></div><div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small">output of this filter is in [0,1] range, and if your output image type is not float then you will get an all-black image. Here is an example invocation:</div><div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small"><br></div><div class="gmail_default" style="font-family:verdana,sans-serif;font-size:small"><div class="gmail_default"> typedef itk::HessianToObjectnessMeasur<wbr>eImageFilter< HessianImageType, FloatImageType > ObjectnessFilterType;</div><div class="gmail_default"> ObjectnessFilterType::Pointer objectnessFilter = ObjectnessFilterType::New();</div><div class="gmail_default"> objectnessFilter->SetBrightObj<wbr>ect(true);</div><div class="gmail_default"> objectnessFilter->SetScaleObje<wbr>ctnessMeasure(false);</div><div class="gmail_default"> objectnessFilter->SetObjectDim<wbr>ension(2.5);</div><div class="gmail_default"> objectnessFilter->SetAlpha(0.5<wbr>);</div><div class="gmail_default"> objectnessFilter->SetBeta(1.0)<wbr>;</div><div class="gmail_default"> objectnessFilter->SetGamma(5.0<wbr>);</div><div class="gmail_default"> objectnessFilter->SetInput(hc-<wbr>>GetOutput());</div><div class="gmail_default"> objectnessFilter->Update();</div><div class="gmail_default"> FloatImageType::Pointer objectness = objectnessFilter->GetOutput();</div></div></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Aug 8, 2016 at 9:38 PM, Jeanna S. <span dir="ltr"><<a href="mailto:jeannasheen@gmail.com" target="_blank">jeannasheen@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 dir="ltr"><div style="font-size:12.8px"><span style="font-size:12.8px">Actually, I found a way to display the images to the screen. However, </span><span style="font-size:12.8px">I am still not quite sure how to detect the blood vessels in my image. When I apply the </span><span style="font-size:12.8px">itkHessianToObjectnessMeas<wbr>ureI</span><span style="font-size:12.8px">mageFilter on my image, it just turns out black. I was wondering if this is because there is not enough contrast between the vessels and the background. If so, is there any setting or threshold on the filter I can change so that it can detect the blood vessels?</span></div><div style="font-size:12.8px"><br><div>Thanks,</div><div>Jeanna</div></div></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Aug 8, 2016 at 4:37 PM, Jeanna S. <span dir="ltr"><<a href="mailto:jeannasheen@gmail.com" target="_blank">jeannasheen@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 dir="ltr">Hi Timothee,<div><br></div><div>I'm using the itk:HessianToObjectnessMeasure<wbr>ImageFilter that you suggested. I was wondering if there is any way for me to view the image on the screen after it has been run through the filter, and if you have any examples of the filter working on an image.</div><div><br></div><div>Thanks,</div><div>Jeanna</div></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Sun, Aug 7, 2016 at 4:13 PM, Jeanna S. <span dir="ltr"><<a href="mailto:jeannasheen@gmail.com" target="_blank">jeannasheen@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 dir="ltr">Hi Timothee,<div><br></div><div>Thank you for replying. I will look into these methods.</div><div><br></div><div>Jeanna</div></div><div class="gmail_extra"><div><div><br><div class="gmail_quote">On Wed, Aug 3, 2016 at 1:59 AM, Timothee Evain <span dir="ltr"><<a href="mailto:tevain@telecom-paristech.fr" target="_blank">tevain@telecom-paristech.fr</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hello Jeanna,<br>
<br>
I think this will be difficult just with the LabelMap framework.<br>
Usually to filter vessels you rely on some measures based on their shape, but in the ShapeLabelObject, the elongation measure is "the ratio of the longest physical size of the region [i.e. the bounding box] on one dimension and its smallest physical size". This is a quite coarse measure, sensitive to rotation, and I doubt it will be useful in your case.<br>
Aside from the attribute problem, you also have to detect the vessels prior to filtering them (i.e. getting a binary or a label image of vessels), and the LabelMap framework doesn't do that.<br>
<br>
I would suggest taking a look at these other methods:<br>
-Frangi's vesselness (implemented in itk through these filter : itkHessianToObjectnessMeasureI<wbr>mageFilter or itkHessian3DToVesselnessMeasur<wbr>eImageFilter)<br>
-Ranking Orientation Responses of Path Openings, aka RORPO (<a href="http://path-openings.github.io/RORPO/" rel="noreferrer" target="_blank">http://path-openings.github.i<wbr>o/RORPO/</a>)<br>
-Fast Marching (itkFastMarchingImageFilter)<br>
<br>
HTH,<br>
<br>
Tim<br>
<br>
----- Mail original -----<br>
De: "Jeanna S." <<a href="mailto:jeannasheen@gmail.com" target="_blank">jeannasheen@gmail.com</a>><br>
À: <a href="mailto:community@itk.org" target="_blank">community@itk.org</a><br>
Envoyé: Mercredi 3 Août 2016 03:08:42<br>
Objet: [ITK] ITK Example ShapeOpeningLabelMapFilter<br>
<br>
Hello,<br>
<br>
I am trying to process the attached image using the ShapeOpeningLabelMapFilter for the Insight Toolkit . The image is of a retina, and I want to use the image filter to remove the blood vessels from the picture (the blood vessels are the long, skinny, branching lines). I was wondering if the example code for the ShapeOpeningLabelMapFilter ( here ) would be able to do this with a little modification, and if so, which attribute would be the most useful to identify and remove the blood vessels.<br>
<br>
Thanks in advance.<br>
<br>
<br>
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