<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Aashish - thanks for the reply<div class=""><br class=""></div><div class="">I am using the latest OS X binary download (4.4.0) - is this OpenGL2? When I switch ‘Volume Rendering Mode’ to GPU rendering all images disappear so I presume I’m only able to use CPU rendering. I am on a 2014 Macbook Pro with Nvidia GT750M.</div><div class=""><br class=""></div><div class="">I’m using contrast enhanced volumetric CT imaging. I want to render blood vessels in red; within the scan they appear in approximately the 100-200 Hounsfield unit range. The full range of scalar data is [-1024, 3071]. On this basis I’ve set up the following colour and opacity mappings:</div><div class=""><br class=""></div><div class="">Colour:</div><div class="">Value<span class="Apple-tab-span" style="white-space:pre"> </span>R-G-B</div><div class="">-1024<span class="Apple-tab-span" style="white-space:pre"> </span>0-0-0</div><div class="">99<span class="Apple-tab-span" style="white-space:pre"> </span>0-0-0</div><div class="">100<span class="Apple-tab-span" style="white-space:pre"> </span>1-0-0</div><div class="">200<span class="Apple-tab-span" style="white-space:pre"> </span>1-0-0</div><div class="">201<span class="Apple-tab-span" style="white-space:pre"> </span>0-0-0</div><div class="">3071<span class="Apple-tab-span" style="white-space:pre"> </span>0-0-0</div><div class=""><br class=""></div><div class="">Opacity:</div><div class="">Value<span class="Apple-tab-span" style="white-space:pre"> </span>Opacity</div><div class="">-1024<span class="Apple-tab-span" style="white-space:pre"> </span>0</div><div class="">99<span class="Apple-tab-span" style="white-space:pre"> </span>0</div><div class="">100<span class="Apple-tab-span" style="white-space:pre"> </span>1</div><div class="">200<span class="Apple-tab-span" style="white-space:pre"> </span>1</div><div class="">201<span class="Apple-tab-span" style="white-space:pre"> </span>0</div><div class="">3071<span class="Apple-tab-span" style="white-space:pre"> </span>0</div><div class=""><br class=""></div><div class="">None of the voxels appear to be fully opaque in the rendering. When I increase the specular from 0 to 1 it has no effect at all on the image.</div><div class=""><br class=""></div><div class="">Ideally, I would want to emulate something along the lines of this: <a href="http://www.cemuva.com/img/uploads/malformacion-arteriovenosa-cerebral-3d.jpg" class="">http://www.cemuva.com/img/uploads/malformacion-arteriovenosa-cerebral-3d.jpg</a></div><div class=""><br class=""></div><div class="">Again, cheers for the help</div><div class="">Mathew</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On 23 Sep 2015, at 18:24, Aashish Chaudhary <<a href="mailto:aashish.chaudhary@kitware.com" class="">aashish.chaudhary@kitware.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Matthew, <div class=""><br class=""></div><div class="">* Can you send us the exact number you are putting in for the transfer function? Make sure that you have values for the entire range of scalar values? </div><div class=""><br class=""></div><div class="">* Are you using OpenGL2 version? </div><div class=""><br class=""></div><div class="">- Aashish</div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Wed, Sep 23, 2015 at 1:18 PM, Mathew Guilfoyle <span dir="ltr" class=""><<a href="mailto:mrguilfoyle@gmail.com" target="_blank" class="">mrguilfoyle@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word" class="">Thanks for the suggestions. After looking into it further the type of visualisation I am after is volume rendering of the data with an opacity transfer function based on the scalar data values.<div class=""><br class=""></div><div class="">I have set up my volume rendering to have full (i.e =1) opacity through the range of scalar values I’m interested in, reducing to near transparency either side of this. I also want specular highlighting of the opaque tissues.</div><div class=""><br class=""></div><div class="">However, despite these settings Paraview does not seem to render any voxels as fully opaque and there is certainly no specular highlighting. Is this a known limitation?</div><div class=""><br class=""></div><div class="">Many thanks<br class=""><div class=""><blockquote type="cite" class=""><div class="">On 21 Sep 2015, at 15:10, David E DeMarle <<a href="mailto:dave.demarle@kitware.com" target="_blank" class="">dave.demarle@kitware.com</a>> wrote:</div><br class=""><div class=""><div dir="ltr" class="">Two suggestions:<div class="">* try contour filter instead of threshold if contour isn't available, apply cell to point first.</div><div class="">* try the clip filter with the clip type set to scalar.</div><div class="">hth</div></div><div class="gmail_extra"><br clear="all" class=""><div class=""><div class="">David E DeMarle<br class="">Kitware, Inc.<br class="">R&D Engineer<br class="">21 Corporate Drive<br class="">Clifton Park, NY 12065-8662<br class="">Phone: <a href="tel:518-881-4909" value="+15188814909" target="_blank" class="">518-881-4909</a></div></div>
<br class=""><div class="gmail_quote">On Mon, Sep 21, 2015 at 9:40 AM, Mathew Guilfoyle <span dir="ltr" class=""><<a href="mailto:mrguilfoyle@gmail.com" target="_blank" class="">mrguilfoyle@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">I would be grateful for some advice on volume and surface rendering in Paraview.<br class="">
<br class="">
I am trying to generate 3D skull models from CT data. The reason for using Paraview is to take advantage of the detailed fly-through/movie capability. I can generate an acceptable 3D model that I can interact with in OsiriX and 3D Slicer, both of which I believe use VTK. However, in Paraview I am struggling to create a 3D model that looks any good.<br class="">
<br class="">
When I apply a threshold filter and view as a ‘Surface’ the image is a lot more ‘blocky’ than in the other two applications. The image is dominated by the artifactual lines due to the original data being acquired as axial slices; whereas in OsiriX and 3D Slicer this gets smoothed out and the ‘genuine’ surface skull features (sutures etc) stand out.<br class="">
<br class="">
I realise this is probably question of apply the correct series of filters and that the other two apps do this ‘under the hood’. However, i have tried to apply Decimation and Smooth to the extracted surface and am not making any headway.<br class="">
<br class="">
Any pointers would be very welcome<br class="">
<br class="">
M<br class="">
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<br class=""></blockquote></div><br class=""><br clear="all" class=""><div class=""><br class=""></div>-- <br class=""><div class="gmail_signature"><div dir="ltr" class=""><font face="trebuchet ms, sans-serif" class=""><i class="">| Aashish Chaudhary <br class="">| Technical Leader <br class="">| Kitware Inc. <br class=""></i></font><div class=""><i class=""><font face="trebuchet ms, sans-serif" class="">| </font><a href="http://www.kitware.com/company/team/chaudhary.html" target="_blank" class="">http://www.kitware.com/company/team/chaudhary.html</a></i></div></div></div>
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