[caret-users] MedialWall and BA40

Thu Jun 11 15:54:54 CDT 2009

Donna, I am working in a subjects directory, with a deformed composite paint file. It appears I only have one paint file loaded...
deformed_bh002cd_leftHuman.colin.Cerebral.R.COMPOSITE.71723.paint

This is a problem on all my data sets, I didn't realize it because my focus is not the medial wall, but once the problem arose, it is on every deformed caret brain. I tried to do as John requested, Attributes - Paint - Edit Paint Names- but I added a new name then drew a border around Med.Wall and re-assigned it, still did not fix the problem, John actually wrote to re-assign BA40 to the medialwall, but wont it re-assign all of BA40, including the part that is correctly labeled? Upon closer look, I found that the Atlas has labeled the medialwall as BA40, I am using Human.colin.Cerebral.R.ATLAS.03-12.71723, I have now re-assigned the medial wall as you originally requested, in the Atlas, and it worked on the Atlas. So I suspect that when I run deformation, this should solve the problem for the future. Do I need to redo the deformation on all the brains to fix them? I tried John's suggestion and it removed the color for both BA40 med.wall and correct BA40, what is strange is that I use the Edit Paint Names and attributes to re-draw BA areas and it works fine, just not now? Thanks for your help. Traci

-----Original Message-----
From: caret-users-bounces at brainvis.wustl.edu on behalf of Donna Dierker
Sent: Thu 6/11/2009 11:25 AM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] MedialWall and BA40

Hi Traci,

No capture came through.

I'm not sure what is going on, but here are some wild speculations: You 
have more than one paint file.  In paint file A, index 15 is 
Brodmann.40.  In paint file B, index 15 is MEDIAL.WALL.  Both paints are 
loaded.  I'm not sure how Caret deals with this conflict, but it 
probably does, or else I'd probably have encountered this problem within 
the last nine years.

While this is just speculation, it seems wise, in troubleshooting mode, 
to reduce the number of variables and cut back to a single paint file, 
if possible.

It is possible, if needed, to select your true medial wall nodes, as 
described below, and save the nodes in a ROI file (Surface: ROI menu).

This way, you can load the paint with the unpolluted Brodmann areas 
(e.g., Human.PALS_B12.RIGHT.COMPOSITE_Areas_Functional_WS.73730.paint), 
and if necessary load the save ROI file to change the medial wall node 
memberships.

But let's step back:  Are you dealing primarily with PALS_B12 tutorial 
files (coord, topo, paint, etc.), whose medial wall assignments should 
be relatively in stone in existing COMPOSITE paint files?  Or are you 
working in a subject's directory, to which you have deformed the 
COMPOSITE paint file?  Solutions to the former are simpler.

If the former, try loading just the COMPOSITE paint, replacing any 
currently loaded paint information.  (Save the old stuff, if desired, 
but it will have the problem you describe.)  See if the medial wall is 
still hosed.  It shouldn't be.  If it is, I can point you to good files 
in sumsdb.

If you think you need multiple paint files loaded concurrently, help me 
understand why.

My multiple paint file hypothesis might be wrong, but let's test it.

Donna

On 06/11/2009 11:05 AM, Sandoval, Traci I wrote:
> Hi Donna, Thank you for your response, but it did not seem to work. I have attached a pic for your viewing pleasure, while it changes the color of the medial wall, when you click it, it still states in the identify window that is it BA 40? Additionally, I tried to change the color of the medial wall before I ran deformation and it changed it back to red and BA40? Thank you
>
>
> -----Original Message-----
> From: caret-users-bounces at brainvis.wustl.edu on behalf of Donna Dierker
> Sent: Thu 6/11/2009 8:41 AM
> To: caret-users
> Subject: [caret-users] MedialWall and BA40
>  
> Traci,
>
> I don't understand why the message below bounced.  Nor do I really 
> understand how the paint indices got mixed up.
>
> But you should not need to re-draw the medial wall.  Do this:
>
> Surface: Region of interest, selection source Paint, select Brodmann.40
>
> Select node with Mouse, and click in the medial wall.
>
> Press select nodes and then Remove Islands
>
> Next
>
> Assign Paint: Column Brodmann
> Assign Name MEDIAL.WALL
>
> File: Save Data File: Paint
>
> Donna
>
> -------- Original Message --------
>
> Subject:
> MedialWall and BA40
> From:
> "Sandoval, Traci I" <traci.sandoval at student.utdallas.edu>
> Date:
> Wed, 10 Jun 2009 16:34:07 -0500
> To:
> <caret-users-bounces at brainvis.wustl.edu>
>
> Hello, I noticed that the medial wall is being defined as brodmann's 
> area 40, I am guessing it is because they have the same color assigned 
> to them. Is there a quick fix for this? Or do I need to re-draw the 
> medial wall and re-assign as something else? Thank you for your 
> continued help.Traci
>
> Traci Sandoval
> NeuroPychometric Research Lab
> Center for Brain Health
> University of Texas at Dallas
> University of Texas, Southwestern
>
>
>
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