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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