[caret-users] too many crossovers

[Donna Dierker]

Hi again Bela,

There are a couple of instances where this problem exists:

> 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.
Compare the attached captures:

source_lateral.jpg with target_lateral.jpg : green & brown borders on 
posterior end of sylvian border in source; on anterior end in target
source_ventral.jpg with target_ventral.jpg : magenta to upper right of 
blue in source; on upper left in target

Imagine the twisting that will be needed to yank them into alignment.  
It won't work.

Donna

On 11/19/2008 01:45 PM, Donna Dierker wrote:
> 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 

-------------- next part --------------
A non-text attachment was scrubbed...
Name: source_lateral.jpg
Type: image/jpeg
Size: 91582 bytes
Desc: not available
Url : http://brainvis.wustl.edu/pipermail/caret-users/attachments/20081119/63121dcf/attachment-0004.jpg 
-------------- next part --------------
A non-text attachment was scrubbed...
Name: source_ventral.jpg
Type: image/jpeg
Size: 94327 bytes
Desc: not available
Url : http://brainvis.wustl.edu/pipermail/caret-users/attachments/20081119/63121dcf/attachment-0005.jpg 
-------------- next part --------------
A non-text attachment was scrubbed...
Name: target_lateral.jpg
Type: image/jpeg
Size: 93694 bytes
Desc: not available
Url : http://brainvis.wustl.edu/pipermail/caret-users/attachments/20081119/63121dcf/attachment-0006.jpg 
-------------- next part --------------
A non-text attachment was scrubbed...
Name: target_ventral.jpg
Type: image/jpeg
Size: 97749 bytes
Desc: not available
Url : http://brainvis.wustl.edu/pipermail/caret-users/attachments/20081119/63121dcf/attachment-0007.jpg