[caret-users] beginner question

[jessica f cantlon]

Thank you David...I started over and everything looks to be working now. 
    I guess my problem was that it wasn't clear from the tutorial where 
the PubMed IDs were being pulled from and which files needed to line up 
with each other.

I was wondering if there is any info about how to estimate peaks as 
spheres and then flatten them.  I saw an article that did something to 
this effect (Lewis, J., 2006, Cortical networks related to human use of 
tools, The Neuroscientist, 12(3), p. 211).  However, I couldn't find any 
info on how to do this in the tutorials.  Maybe there isn't anything in 
which case I can try to figure something out myself.

thanks again!
Jessica

David Van Essen wrote:
> Jessica,
> 
> On Jan 20, 2008, at 7:18 PM, jessica f cantlon wrote:
> 
>> I have a beginner's question about using caret to project foci to the 
>> PALS atlas.  When I go to do that I get the message "These foci do not 
>> have associated stereotaxic spaces:" and it lists all of them, even 
>> though I have gone through and individually selected the space format 
>> in the "Study Metadata Editor" for every study.  Is there something 
>> obvious I'm not doing?
> 
> I suspect the problem is that the linkage between the individual foci 
> and the corresponding studies is not complete.  Each focus gets linked 
> to a unique study using the PubMed ID (PMID) number (or a ProjID that is 
> automatically assigned if there is no PMID number).  If the individual 
> foci all have a 'Name' entry that matches the Study Name, then you can 
> automatically fill in all of the PMID numbers using:
> Select Layers: Foci: Update Focus PubMed ID if Focus Study Name Matches 
> Study Name, then select Confirm in the popup window.
> 
> This will populate the PubMed ID column with the PMID number (or the 
> Project ID number if no PMID is available) and the stereotaxic space (if 
> entered into the study file).
> 
> This step may not be adequately explained in the current tutorials, so 
> we will try to get that fixed.
> 
> If this doesn't work, let us know; it might then become useful to take a 
> look at your actual dataset.
> 
> As a heads-up, a number of important refinements are well underway with 
> regard to stereotaxic foci.  One is that we are incorporating flexible 
> 'Foci search' capabilities within Caret that are proving to be very 
> helpful for comparisons across the 14,000 published foci currently 
> accessible via SumsDB.  We are aiming to have a new Caret release and 
> associated tutorial available in the late-winter/early-spring time frame.
> 
> David VE
> 
>>
>>
>> thanks,
>> jessica
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> 
> 
> 
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