[caret-users] Translucent fiducial surface?

[John Harwell]

Leeland,

At this time, there is no direct method for setting the opacity of a  
surface.

First, did you try a flat surface?  It allows one to view all of the  
cortex.

Secondly, as David hinted, you can try the following:

* Load the inflated surface into the main window and make the  
appropriate overlay selections.
* Select File Menu->Save Data File.  On the Save Data File Dialog, set  
the File Type to VTK Surface File (*.vtk).  Verify that the Export  
Surface Option's Surface is set to the inflated or other desired  
surface.  Enter a File Name and press the Save button.
* Select File Menu->Open Data File.  Set the File Type to VTK Model  
File (*.vtk *.vtp), select the name of the file saved in the previous  
step, and press the Open button.
* On the Display Control's Surface Miscellaneous page, set the Drawing  
Mode to Hide Surface (this will hide the caret surface)
* In the Main Window, set the Model to the Fiducial Surface (VTK Model  
Files are only displayed when a fiducial surface is selected for  
display even though the caret surface is hidden).
* On the Display Control's Model Settings page, set the Opacity as  
desired (0.3 is used in the attached image).

Lastly, If you or others find having an overall surface opacity  
useful, please let us know and we can look into adding this into Caret.

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-----------------------------------
John Harwell
john at brainvis.wustl.edu

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave   Box 8108
Saint Louis, MO 63110




On Jun 29, 2008, at 10:18 PM, David Van Essen wrote:

> Leeland,
>
> You can get translucency by converting to a vtk model using the Save
> option for the Caret coordinate file.  This can also preserve surface
> coloration.  I don't have a lot of experience with this, but John may
> be able to provide additional tips now that he is back from Australia.
>
> David VE
>
> On Jun 26, 2008, at 8:46 AM, Donna Dierker wrote:
>
>> Hi Leeland,
>>
>> I don't think so, but David will correct me if I'm wrong.  (John will
>> return from Australia next week; he would know best.)
>>
>> There is a way under D/C: Surface Miscellaneous to turn the drawing
>> mode
>> to Nodes or Hide Surface, but neither of these will give you what you
>> want.  You could toggle back and forth the Partial View options, but
>> this isn't any better than just toggling Toolbar:L and Toolbar:M to
>> switch sides.  Would selecting Window: Window 2 and setting Window 2
>> to
>> medial view, main window to lateral work?
>>
>> If you actually want to combine/sum the metrics on either side,  
>> then I
>> would generate the sum directly as a new combined metric overlay.
>> With
>> more knowledge of the surface type and how the respective sides
>> relate/align, I could elaborate.
>>
>> Here is an example of how it might work:  Let's say the surface is a
>> sphere.  Metric 1 is good; we like it like it is.  Metric 2 is one we
>> want to flip along some axis and sum with metric 2.  We project
>> Metric 2
>> to a volume via Attributes: Metric.  We either flip the volume along
>> the
>> axis of interest, or we flip the surface and map the volume to the
>> flipped surface.  Now we can sum metric 1 and metric 2 to create
>> metric
>> 3 (sum metric1 + [xyz]-flipped metric 2).
>>
>> I may be way off track, but at least now you know how to steer my
>> thinking.
>>
>> Donna
>>
>> On 06/25/2008 05:30 PM, Leeland Ekstrom wrote:
>>> Hi,
>>>
>>> Is there some way in Caret to alter the opacity of the fiducial
>>> surface
>>> itself (i.e. when viewing a 3D inflated surface, reduce the opacity
>>> of
>>> the surface itself to something like 50%, so that metric blobs on
>>> both
>>> medial and lateral sides of the brain could be seen simultaneously)?
>>> The 'opacity' parameter on the 'Overlay/Underlay - Surface' dialog
>>> seems
>>> to only alter overlays and underlays, and not the base surface  
>>> itself
>>> upon which these different surfaces are visualized.
>>>
>>> Thanks for your help,
>>> Leeland
>>>
>>>
>>
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