[caret-users] problem with border file

[Donna Dierker]

Hi Sofia,

See inline replies below.

Donna

On 06/10/2008 06:18 AM, Sofia Crespi wrote:
> Hi I have a question.
> I've designed some closed border on my flat surface in order to use 
> them for surface region of interest operation.
> More precisely I've daone these operations:
> 1.Layers---->Borders---->draw Borders
> 2. I've selected a new name, closed boundaries and 2D,
>     in the closed border assignement frame-----> Voxels I've selected 
> Assign voxels within closed borders and +/-1 for the thickness.
> 3. I've choosed a color and designed my border on the flat map.
> 4.Then I saved the file with a new name as: border file Surface, 
> border file Volume, Border color file.
>  
> Now I'm able to see the border and if I select the Border Page in the 
> Dispaly control dialog I can find the name and the color of my new 
> border. Now I close caret.
> If I open caret again and load my spec file, loading also the new 
> border file already created I cannot display the new border on the 
> flat map...
> why?
If both the border file Surface and border color files that you saved in 
step 4 above were selected when you loaded the spec file, then the only 
other reason I can imagine that you don't see the border on your flat 
map is that borders are not selected on the D/C: Overlay/Underlay - 
Surface menu (scroll all the way to the bottom, until you see a borders 
checkbox); see attached capture, which shows the Borders checkbox 
toggled on at the bottom of the D/C: Overlay/Underlay - Surface page.

Depending on which Caret version you have, this checkbox may or may not 
be on by default when you load a spec with borders selected.
>  
> I opened the border file Surface just created....
> all the other border file come out as *appended* (why since are 
> different file????) the last one is not appended and I cannot see that 
> border....
This is not clear to me.  Perhaps if you uploaded your dataset, I could 
decipher what you mean.

http://pulvinar.wustl.edu/cgi-bin/upload.cgi

It sounds like one or more of the following possibilities might 
contribute to the confusion:

1. You have multiple border files loaded, which may have borders that 
intersect/duplicate with one another.
2. When you couldn't see the border upon opening, you tried loading 
again, resulting in the same borders being loaded twice.

I hope this is just a case of the borders not being turned on when you 
relaunch Caret.
>  
> Please have a look to the doc fiel attached:
No doc file was attached.
> in yellow I've underlined all the attached file...:
> *1* *why the same file "V6 border color " is appended more than 1 time?*
Something similar to possibilities 1 and 2 occurred wth the bordercolor 
file.
> *2. the appended file LO-MST-MT is refereed to 3 border That I'm not 
> able to disply any more..*
I don't understand this question, but I hope the display problem is 
resolved by the D/C checkbox.
> *3 the new border V6NEW does not result as appended ??*
Perhaps it was added after the last save?  I can't think of another 
plausible explanation.
>  
> where is my error?
Let's hope the D/C checkbox resolves 90% of your issues.
> can you help me?
Typically, we project borders after drawing them and save the resulting 
borderproj files.  This allows you to view the borders on multiple 
surfaces (e.g., fiducial, inflated).  There are definitely contexts in 
which border files have distinct advantages, however (e.g., when viewing 
on surfaces of different mesh / number of nodes than the drawing 
substrate; when using the 2D/3D coordinates for an outside application).

But you clearly state above you are trying to view your borders on the 
flat map, which is the same surface used for the drawing substrate.  
Thus, I conclude that this is probably a D/C checkbox not selected issue.
>  
> Thank you in advance
>  
> Sofia Crespi
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