[caret-users] Landmark Issue

[Donna Dierker]

John Harwell did think of something else:  Did you go back and fix 
something in the segmentation; retessellate; and open the borderproj 
drawn on the old mesh on the new mesh flat map?  This could explain what 
you are seeing.

On 07/30/2008 02:51 PM, Donna Dierker wrote:
> 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>
> [mailto: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