[caret-users] draw borders for spherical registration

[John Harwell]

Hi Julia,

It is not unusual for there a few red highlights around the edges at  
this stage of the flattening process.  You could continue the  
flattening process and it might turn out okay.

If there are no topological problems with the original 3D fiducial  
surface, then all surfaces derived from it (spherical, etc) should be  
topologically correct.  Load the original 3D surface into Caret's  
main window and select Surface Menu->Topology->Topology Error Report  
(it may take a minute to execute).  If the "Number of Handles" is  
zero, then the 3D surface and the "derived" surfaces (spherical,  
flat) are topologically correct and you can proceed with flattening.

If the 3D surface does contain handles, the best solution is to go  
back to the original segmentation volume and make corrections.   
However, since your surface was not generated within Caret, there is  
a new feature in Caret that may help.  With the original 3D surface  
in Caret's main window, Select Surface Menu->Topology->Correct  
Fiducial Surface Topology (Remove Handles).  This process will  
attempt to re-tessellate the surface in order to remove any handles  
and will create new coordinate and topology files that will need to  
be saved.  This is a new process, so examine the corrected surface to  
verify that the process has not done anything bad.  If things look  
good, use the new coordinate and topology file and restart the  
flattening process.

When I have time, I will modify Caret so that the beginning of the  
flattening process will check for topological problems.

----------------------------------------------------------
John Harwell
john at brainvis.wustl.edu
314-362-3467

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

On Jul 3, 2007, at 10:22 AM, Julia Molony wrote:

> John,
>
> Your answer was very helpful.  Now I'm stuck with an initial flat  
> map that has red highlights on a few of the edges.  The tutorial  
> says this means there are handles that need to be corrected in the  
> segmentation volume.  I don't have a volume.  I have Freesurfer  
> surfaces that I'm using to compare warping methods.  Is there any  
> solution to this cross over correction problem for already created  
> surfaces?
>
> There's just a little bit of red.  Here's a picture.  I can send  
> more information, if that would be helpful.
>
> Thank you.
>
> Julia
>
> --
> Julia Molony
> SSCC/NIMH/NIH
>
> <Init.Surf.crossovers 5.5_Figure40.jpg>
>
>
>
>
> On Jul 2, 2007, at 12:21 PM, John Harwell wrote:
>
>>
>> Hi Julia,
>>
>> During the flattening process, the medial wall border is normally  
>> drawn on the Compressed Medial Wall Surface.  The CMW surface is a  
>> sphere with the medial portion made flat so that 2D borders can be  
>> drawn on it.  This surface should be selected from the model  
>> selection control in the main window's toolbar.
>>
>> The "Smooth Fiducial Medial Wall" option results in the fiducial  
>> surface's medial wall being smoothed during the flattening  
>> process.  Smoothing will change the shape of the medial wall so  
>> that it is relatively flat.  This option does not affect the  
>> sphere.  There is normally some distortion around on the sphere  
>> that should be removed by the morphing process that is part of  
>> flattening.
>>
>> ----------------------------------------------------------
>> John Harwell
>> john at brainvis.wustl.edu
>> 314-362-3467
>>
>> Department of Anatomy and Neurobiology
>> Washington University School of Medicine
>> 660 S. Euclid Ave.    Box 8108
>> St. Louis, MO 63110   USA
>>
>> On Jul 2, 2007, at 10:09 AM, Julia Molony wrote:
>>
>>> I'm attempting to go through Caret's spherical registration stuff  
>>> but first I need to work out how to draw all the borders.  I'm  
>>> following the 5.5 tutorial and I'm stuck trying to draw the  
>>> medial wall borders.  When I open the draw borders dialogue,  
>>> choose the border name, set type to closed and dimension to 2D,  
>>> and press apply, I can't draw the border.  I click on the sphere  
>>> and hold the left mouse button and nothing is drawn.  Any ideas  
>>> on what's going on?  I checked the D/C to see if "show borders"  
>>> was selected and it is.  I've drawn borders in the past with no  
>>> trouble, so I'm not sure what's happening here.
>>>
>>> Also, what does it mean in the "Flatten Full or Partial  
>>> Hemisphere" box when it says "Smooth Fiducial Medial Wall".  It  
>>> looks like this smoothing is causing distortions in the sphere.   
>>> It makes the sphere look sort of swirly around the medial wall area.
>>>
>>> Julia
>>>
>>>
>>> --
>>> Julia Molony
>>> SSCC/NIMH/NIH
>>>
>>> _______________________________________________
>>> caret-users mailing list
>>> caret-users at brainvis.wustl.edu
>>> http://pulvinar.wustl.edu/mailman/listinfo/caret-users
>>
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