[caret-users] Landmark Issue

[Donna Dierker]

Hi Traci,

John Harwell and I can't think of a cause for the scattered border points.  Two suggestions come to mind:

1) Upload your dataset/directory to http://pulvinar.wustl.edu/cgi-bin/upload.cgi (in zip file form).  Maybe something in the borderproj filename, contents, or spec file entry will yield a clue.

2) Try flattening again.  This time, after you get the compressed medial wall surface with the template cuts, delete the template medial wall and calcarine borders; draw new ones; project them; and save them as a filename named like "forFlattening" (as opposed to "fromFlattening").

There is no point deleting the border points individually; you could just delete the whole border, since none of it is worth saving.  But by nibbling, I meant deleting border points at the medial wall dorsal and medial wall ventral gaps, as well as at the posterior termination of the calcarine sulcus.  See this page for more details:

http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html/

Donna


----- Original Message ----
From: "Sandoval, Traci I" <traci.sandoval at student.utdallas.edu>
To: "Caret, SureFit,and SuMS software users" <caret-users at brainvis.wustl.edu>
Sent: Wednesday, July 30, 2008 2:09:23 PM
Subject: Re: [caret-users] Landmark Issue

They look fine on the inflated surface, but when I draw the other
landmarks then append the landmarks from flattening I get the scattered
border points, then I just deleted the borders from flattening and drew
all six landmarks, but when I open the subjects spec with the colin
atlas to run spherical surface deformation, I get an error that states I
don't have the same number of landmarks on my subjects vs the colin
atlas. I was thinking this was due to the splattered border points I had
been deleting. I feel I am missing something in this process. 

Also, when you say nibble away, are you suggesting that I can just clean
up the splattered border points by deleting the points individually?

Thank you for all your help. Traci


Traci Sandoval
Research Assistant
NPR Lab
Center for Brain Health
University of Texas at Dallas
University of Texas Southwestern




-----Original Message-----
From: caret-users-bounces at brainvis.wustl.edu
[mailto:caret-users-bounces at brainvis.wustl.edu] On Behalf Of Donna
Dierker
Sent: Wednesday, July 30, 2008 12:54 PM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] Landmark Issue

The borderproj looks suspect to me, too, but it is better to view the 
from flattening borders on a medial view of the inflated surface.  These

are typically appended AFTER you have drawn the other landmarks (CeS, 
sylvian, and aSTG) on the flat map and projected them.  At that point, 
you don't really need the flat map anymore, and can switch to the 
inflated view; append your flattening borders; and nibble away.

When you view your from flattening borders on the flat map, you lose 
points along the cuts -- sometimes too many along the medial wall
dorsal.

But none of this explains your scattered border point problem.  Still, 
humor me and look at them on the inflated.

On 07/30/2008 12:31 PM, Sandoval, Traci I wrote:
>
> Attached is the borderproject file 
> (LANDMARKS.fromflattening.borderproj) on the flattened image. The 
> scattered white points do not look the same as the landmark examples 
> created from flattening in the tutorial. Perhaps I am not cutting 
> correctly, or saving something incorrectly. Either way, I feel 
> something is going wrong. Please advise.
>
>
>  
>
> Traci Sandoval
>
> Research Assistant
>
> NPR Lab
>
> Center for Brain Health
>
> University of Texas at Dallas
>
> University of Texas Southwestern
>
>  
>
>  
>
>
>
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> caret-users mailing list
> caret-users at brainvis.wustl.edu
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>  

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