Hi Erin,
As you are probably aware, many people report their coordinates as
talairach coordinates, when in fact their data were registered to
another stereotaxic space (e.g., MNI305, MNI152, 711-2B). So be on the
look-out for such cases, because there is considerable difference in the
bounding boxes of those spaces
(http://www.mrc-cbu.cam.ac.uk/Imaging/Common/mnispace.shtml).
The inline replies below assume you're really dealing with T&T
coordinates, and that you prefer rendering the foci with a slice backdrop.
One advantage, however, to rendering them on the surface -- possibly a
mildly inflated surface which reveals buried sulci, but doesn't lose too
much detail -- is that you render foci that come from a variety of
stereotaxic spaces (i.e., mix mni152 and true T&T). The trick is to
project the foci using an average fiducial surface that accurately
reflects the stereotaxic space used in the study. Once projected, foci
latch onto a surface tile, so they can be rendered on any configuration
of the surface (fiducial, inflated, flat, or spherical). For a
meta-analysis, this is a really nice advantage.
A major disadvantage, of course, is that it doesn't work for subcortical
nuclei.
Donna
On 12/13/2005 07:03 PM, [EMAIL PROTECTED] wrote:
Hi,
I am working on a meta-analysis and would like to use your software to make a
3d brain with coloured foci of coordinates I input.
I am a little confused after reading the manuals/doing the tutorials.
First, I need to input a brain that I can put foci on in Taliarch & Tournaux
coordinates.
From the AFNI list, I know you're an AFNI user, and any of these
volumes included in your AFNI distribution could be an anatomical volume
backdrop for your volume foci:
src/data/TT_N27+tlrc.HEAD
src/data/TT_avg152T1+tlrc.HEAD
src/data/TT_icbm452+tlrc.HEAD
For a meta-analysis, I prefer group averaged MRI anatomicals (i.e.,
either of the latter two) to a particular individual's anatomy (N27),
but this is your call.
Second, I like the look of the surface and volume display, with the kind of
planes crossing each other, but would like it so that it only displays the
three slices and not the surface part.
On the D/C menu, select Surface Miscellaneous and select Drawing Mode:
Hide surface.
Is that possible? However, I also
noticed that the foci function only works on fiducial surfaces? Am I unable to
put foci on the surface and volume display?
Create a foci file as usual
(http://brainmap.wustl.edu/caret/html/file_formats/file_formats.html#cellFile
-- foci and cell formats are identical), but open it as Foci Files -
Volume (the fourth of the file types listed on the Open Data File
menu). If you don't see this option, you need to get an updated version
of caret here:
http://brainmap.wustl.edu/pub/john/
login pub
password download
Probably all you'll need is the updated binary executable (caret5_exe_*
for your platform) -- not the entire distribution. Put this in your
caret/bin directory and make sure its permissions are set such that you
can execute it (e.g., for Linux, chmod u+x caret5).
And I think I could put the foci on but... who knows, I may be asking
questions later.
Sorry, kind of new to this fMRI stuff.
Thanks for your help,
Erin
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