[caret-users] MedialWall and BA40

Fri Jun 12 08:48:16 CDT 2009

Traci,

This additional detail does clear up a lot of things, and it allowed me 
to quickly reproduce your problem, illustrated in the attached capture.

The problem is that the medial wall is incorrectly labeled as BROD.40 in 
the paint column "Brodmann - Human.colin.R" in the paint file 
Human.colin.Cerebral.R.COMPOSITE.03-05-25.71723.paint, in the dataset 
TUTORIAL.1.HUMAN.03-12.zip, dating, which turns six years old this month 
(June, 2003).

Yes, it looks like you fixed it, using the steps I gave you, which 
solves the "relabel the bad BA40 without relabeling the good BA40" 
problem David described (without drawing any borders).

But I don't know a good way of fixing the already deformed ones without 
regenerating the deformed paint files.  This can be done without having 
to re-register (although re-running registration is not usually the end 
of the world).  There is the GUI Deformation: Apply deformation map 
option, and also this command line option:

    caret_command -deformation-map-apply

... often accompanied by:

    caret_command -deformation-map-path

I'm pretty sure we've covered this already, but I feel compelled to 
encourage you to move to PALS_B12 as a registration target, rather than 
continuing to use Colin.  I think you had some reasons for sticking with 
colin, but I wanted to make this clear to all caret-users.  I'm 
reasonably sure PALS_B12's composite paint files have this region 
labeled as MEDIAL.WALL already (and was very surprised the 6/2003 
colin.R's wasn't).

Donna

On 06/11/2009 03:54 PM, Sandoval, Traci I wrote:
> 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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