Hi Shawn,


Just what I was hoping for. Many thanks. 









[mailto:[EMAIL PROTECTED] On Behalf Of Christ, Shawn
Sent: Friday, December 08, 2006 6:25 PM
To: caret-users@brainvis.wustl.edu
Subject: RE: [caret-users] using caret for a meta-analysis


Hi Leon,


I have been working with David, Donna, and John on utilizing Caret for
precisely this purpose with respect to an ALE-type meta-analysis on
deception that we have submitted for publication.  You can download a copy
of our spec file, etc. at


I've also uploaded a copy of my personal notes on how to transform foci
using Caret.  They can be found at


I hope this helps!







Shawn Christ, Ph.D.

Assistant Professor

Department of Psychological Sciences

University of Missouri-Columbia

210 McAlester Hall

Columbia, MO 65211




[mailto:[EMAIL PROTECTED] On Behalf Of Leon Deouell
Sent: Friday, December 08, 2006 9:50 AM
To: caret-users@brainvis.wustl.edu
Subject: [caret-users] using caret for a meta-analysis



I am in the process of doing a meta-analysis of imaging data. I am a
complete novice to Caret, but from a quick look it seems it's stereotaxic
foci functions would be ideal to log the peak activity data from different
studies. Eventually I would like to display symbols for each peak on a 3D
brain rendering of some sort. Perhaps Naively, I thought I could load a
template brain (open a spec file), add foci (assuming for a moment I have
all coordinates in MNI space) using for example 'layers>foci>map
stererotaxic focus', and see them pop-out on the brain. However, at first
pass, I run into the following questions:

a) What brain (spec file) should I load from the fMRI_mapping folder? There
are so many of them. Is there anywhere a text file describing what these
different files are?

b) If I enter a focus with coordinates which happen to be under the surface
by a few millimeters, they don't show up on the surface. Is there a way to
project them to the surface or to make the brain 'transparent'?

c) Once I have the foci entered, can I project them to an inflated brain,
and if so, how?

Finally, I assume I am not the first to want to use Caret for this purpose -
does someone have a 'recipe' for such a project or tips on what pitfalls to




Dr. Leon Y Deouell, MD, PhD

Department of Psychology

The Hebrew University of Jerusalem

Jerusalem 91905


Tel: +972-2-5881739

Fax: +972-2-5825659


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