[caret-users] draw borders for spherical registration

[Donna Dierker]

Hi Julia,

On your initial flat map, none of the red patches along the edges would 
worry me, but we would check the ones I've circled in the attached 
capture.  By check, I mean click on the red patch in the main window, 
but use an inflated view in Window 2 to locate the crossover region in 
the inflated surface.  The patch in the upper left may end up being 
nothing, but the one in the lower right looks like a handle connecting 
cortical regions that are separated by a significant geodesic distance.

If you're processing enough subjects that a case or two like this is 
down in the noise, then this isn't a show stopper.  But this is 
something we'd fix in the segmentation and regenerate the surface, for 
one of our own studies.

Donna

On 07/03/2007 02:01 PM, John Harwell wrote:
> 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
>>>>

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