[Paraview] Volume Rendering with opacity mapping and specular highlights

Wed Sep 23 15:34:45 EDT 2015

Aashish - thanks for the reply

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.

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:

Colour:
Value	R-G-B
-1024	0-0-0
99		0-0-0
100		1-0-0
200		1-0-0
201		0-0-0
3071	0-0-0

Opacity:
Value	Opacity
-1024	0
99		0
100		1
200		1
201		0
3071	0

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.

Ideally, I would want to emulate something along the lines of this: http://www.cemuva.com/img/uploads/malformacion-arteriovenosa-cerebral-3d.jpg <http://www.cemuva.com/img/uploads/malformacion-arteriovenosa-cerebral-3d.jpg>

Again, cheers for the help
Mathew

> On 23 Sep 2015, at 18:24, Aashish Chaudhary <aashish.chaudhary at kitware.com> wrote:
> 
> Matthew, 
> 
> * 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? 
> 
> * Are you using OpenGL2 version? 
> 
> - Aashish
> 
> On Wed, Sep 23, 2015 at 1:18 PM, Mathew Guilfoyle <mrguilfoyle at gmail.com <mailto:mrguilfoyle at gmail.com>> wrote:
> 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.
> 
> 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.
> 
> 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?
> 
> Many thanks
>> On 21 Sep 2015, at 15:10, David E DeMarle <dave.demarle at kitware.com <mailto:dave.demarle at kitware.com>> wrote:
>> 
>> Two suggestions:
>> * try contour filter instead of threshold if contour isn't available, apply cell to point first.
>> * try the clip filter with the clip type set to scalar.
>> hth
>> 
>> David E DeMarle
>> Kitware, Inc.
>> R&D Engineer
>> 21 Corporate Drive
>> Clifton Park, NY 12065-8662
>> Phone: 518-881-4909 <tel:518-881-4909>
>> On Mon, Sep 21, 2015 at 9:40 AM, Mathew Guilfoyle <mrguilfoyle at gmail.com <mailto:mrguilfoyle at gmail.com>> wrote:
>> I would be grateful for some advice on volume and surface rendering in Paraview.
>> 
>> 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.
>> 
>> 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.
>> 
>> 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.
>> 
>> Any pointers would be very welcome
>> 
>> M
>> _______________________________________________
>> Powered by www.kitware.com <http://www.kitware.com/>
>> 
>> Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html <http://www.kitware.com/opensource/opensource.html>
>> 
>> Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView <http://paraview.org/Wiki/ParaView>
>> 
>> Search the list archives at: http://markmail.org/search/?q=ParaView <http://markmail.org/search/?q=ParaView>
>> 
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/paraview <http://public.kitware.com/mailman/listinfo/paraview>
>> 
> 
> 
> _______________________________________________
> Powered by www.kitware.com <http://www.kitware.com/>
> 
> Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html <http://www.kitware.com/opensource/opensource.html>
> 
> Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView <http://paraview.org/Wiki/ParaView>
> 
> Search the list archives at: http://markmail.org/search/?q=ParaView <http://markmail.org/search/?q=ParaView>
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview <http://public.kitware.com/mailman/listinfo/paraview>
> 
> 
> 
> 
> -- 
> | Aashish Chaudhary 
> | Technical Leader         
> | Kitware Inc.            
> | http://www.kitware.com/company/team/chaudhary.html <http://www.kitware.com/company/team/chaudhary.html>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/paraview/attachments/20150923/1faa0f03/attachment.html>