[caret-users] Translucent fiducial surface?
Donna Dierker
donna at brainvis.wustl.edu
Thu Jul 3 08:52:26 CDT 2008
Hi Leeland,
See inline comments below.
Donna
Amusing quote of the day: "Okay, slowwwwwly I'm starting to not see the
PALS brains as an ugly piece of dried food." -- Dr. James Lewis, 10/5/2005
On 07/02/2008 12:34 PM, Leeland Ekstrom wrote:
> Hi John / David / Donna,
>
> Thanks for all your suggestions. I was playing around with a couple
> ideas to make a schematic illustration (I do have flattened versions of
> the surface, but it's not always easy to explain that to an unfamiliar
> audience).
Here are a few ways authors have made flat maps more accessible:
Figure 1
http://www.jneurosci.org/cgi/reprint/23/10/4005
Harold Burton, "Visual Cortex Activity in Early and Late Blind People,"
The Journal of Neuroscience, May 15, 2003 • 23(10):4005– 4011
(attached as burton.gif)
Also, Alan Anticevic's figures 3 and 8 in this paper are good examples:
http://dx.doi.org/10.1016/j.neuroimage.2008.02.052
> As to whether it would be useful, this is the first time in
> 2 years I've tried to do something like that and it's more for artistic
> purposes than for data analysis - if it were an easy addition to a
> future version, then I'd say it would be useful, but if requires a lot
> additional coding, I'd say not worth the time.
>
> Two other things:
> 1) Having an inverse of the Identify Window would be useful (i.e.
> instead of clicking on a node and getting the coordinates pop up, have a
> dialog box where you could enter 3D coordinates and that node, or the
> nearest one to it, is identified; if it's a nearest one, then indicating
> the distance would be helpful)
>
Layers: Foci: Map stereotaxic focus is probably not as simple as what
you want, but it is more robust. You can leave many fields blank. Note
that the 3D fiducial surface is typically loaded in the main window when
you do this. Projecting the foci enables you to view them on other
configurations (flat, inflated, etc.).
> 2) In v5.6, there seems to be a bug on D/C --> Scene page. Setting the
> Window Positioning to 'Use all Window Positions' doesn't seem to resize
> the main window correctly, whereas setting to 'Do not Move Main Window'
> resizes and repositions the main window as the first option used to in
> previous versions.
>
I was unable to reproduce this behavior (i.e., window positions seemed
to behave as before for me), but I'm running Linux and John just rebuilt
Caret yesterday (i.e., perhaps he already fixed it).
> Thanks,
> Leeland
>
> John Harwell wrote:
>
>> 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.
>>
>>
>> -----------------------------------
>> 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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