[caret-users] too many crossovers

[Donna Dierker]

Hi Bela,

I haven't looked at your target dataset, but right away I can see some 
impending nightmares in your source dataset borders.

The attached captures show junctions where separate landmarks meet or 
come into close proximity with one another.  This spells trouble.  You 
want some spacing at the landmark junctions.  I used to get crossovers 
in the medial wall until I following the core 6 landmark guidelines on 
trimming the medial wall near the frontal and calcarine junctions 
(http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html/#mw).  
Obviously, you're doing something more customized (not using core 6 
landmarks, using colin as target), but the same principle applies.

See what trimming some points (on both source and target) near these 
junctions does for reducing your crossovers.

Other causes of crossovers include:

* errors/defects in the spheres themselves, especially along the landmarks
* big spacing in the landmark border points, which can happen if you 
project borders from a flat surface (instead of drawing on flat; 
projecting; and appending to in-tact medial wall/calcarine borders on a 
closed topo surface)
* oddities in the borders besides hooks/kinks/reversed polarity: 
closted/nested borders; borders crossing over each other; there's no way 
to topologically match borders without twisting the surface, because 
landmarkA is right of landmark B in source, but vice versa in target.
* misidentifying the hemisphere in the spec files

Donna

On 11/19/2008 12:29 PM, Bela Bhatia wrote:
> Donna,
>
> I checked by spinning the borders and they look ok - no kinks or sharp 
> turns.
> I have uploaded 2 zip files
> NPRArchive.tar.gz
> Right_Hem_Atlas_11_final.tar.gz
>
> What are the variables that affect crossovers during spherical 
> Registration?
>
> Thanks for your help!
>
> Bela
>
> Donna Dierker wrote:
>
>
>   
>> Hi Bela,
>>
>> One thing you can do is view your source (and target, if non-standard) 
>> borders on the source sphere.  Then, select D/C: Surface Miscellaneous: 
>> Drawing mode: Hide surface.  Spin the sphere around (or use the toolbar 
>> buttons to switch from medial, lateral, etc.), and make sure there are 
>> no hard right turns or kinks in any of your borders.  The medial wall 
>> ventral is a common trouble spot for hooks/kinks.  Make sure you turn 
>> Drawing Mode back to Tiles and lighting when you're done inspecting the 
>> borders.
>>
>> If you see no problems, then send me a zipped archive of your source 
>> dataset (including all the files selected on the registration menu).  
>> Also, either enumerate the source settings or give me a screen capture 
>> of the source tab on the registration dialog, so I know which files you 
>> selected.  Upload the zipped archive here:
>>
>> http://pulvinar.wustl.edu/cgi-bin/upload.cgi
>>
>> If you're using a standard atlas target, like the PALS_B12.LR borders, 
>> then just say so and no upload is necessary for the atlas target.  
>> Otherwise, I'll need that, too.
>>
>> I'll try it on my end and let you know what I find.
>>
>> Donna
>>
>> On 11/19/2008 11:27 AM, Bela Bhatia wrote:
>>     
>>> Hello,
>>>
>>> I am getting too many crossovers while processing spherical 
>>> registration.
>>>
>>> The border starting points are all corect.
>>>
>>> What else can I do?
>>>
>>> Thanks
>>> Bela
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>>>   
>>>       
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