Hi Leon,
Shawn has done exactly what you want to do, so if anyone knows the
pitfalls, he does. ;-)
Besides Shawn's useful notes, make sure you read sections 1.2.3 and 5.2
of this tutorial, if you haven't done so already:
CARET_TUTORIAL_SEPT-06
http://sumsdb.wustl.edu:8081/sums/directory.do?id=6585200
This tutorial includes a spec file intended for this purpose. The ones
in the Caret fmri_mapping directory are not really intended for use as
"visualization" specs; rather, Caret uses them when mapping fMRI data
onto PALS_B12. You can, however, use the average fiducial surfaces in
that directory for your foci-related purposes. Note that studies report
results in stereotactic spaces other than MNI (e.g., AFNI users report
true Talairach-Tournoux (T88) coordinates, which differs significantly
from MNI -- see http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach;
wustl.edu researchers typically use "711-2*" space -- somewhere between
T88 and MNI). See
http://brainvis.wustl.edu/help/pals_volume_normalization/ for additional
details.
Reading tutorial section 5.2 may clarify some of this, but you're likely
to have residual questions/confusion about these spaces.
On 12/08/2006 10:24 AM, Christ, Shawn E. wrote:
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
http://sumsdb.wustl.edu:8081/sums/directory.do?id=6600996
I’ve also uploaded a copy of my personal notes on how to transform
foci using Caret. They can be found at
http://www.shawnchrist.com/FociTransform.pdf
I hope this helps!
Best,
-Shawn
--------------------------
Shawn Christ, Ph.D.
Assistant Professor
Department of Psychological Sciences
University of Missouri-Columbia
210 McAlester Hall
Columbia, MO 65211
[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
------------------------------------------------------------------------
*From:* [EMAIL PROTECTED]
[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
Hi,
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 avoid?
Thanks,
Leon
----------------------------------------------------
Dr. Leon Y Deouell, MD, PhD
Department of Psychology
The Hebrew University of Jerusalem
Jerusalem 91905
Israel
Tel: +972-2-5881739
Fax: +972-2-5825659
http://pissaro.soc.huji.ac.il/~leon/Lab
<http://pissaro.soc.huji.ac.il/%7Eleon/Lab>
------------------------------------------------------------------------
_______________________________________________
caret-users mailing list
caret-users@brainvis.wustl.edu
http://pulvinar.wustl.edu/mailman/listinfo/caret-users
--
Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see
http://home.att.net/~donna.hanlon for details.)
