Hi Erin,
Ah, yes: Certainly if you use the version that comes with SPM or FSL,
it won't be, but if you use the one in the AFNI_HOME/src/data directory,
it should be. The @auto_tlrc help says this:
NOTE: These datasets have been slightly modified
from
their original size to match the standard TLRC
dimensions (Jean Talairach and Pierre Tournoux
Co-Planar Stereotaxic Atlas of the Human Brain
Thieme Medical Publishers, New York, 1988).
That was done for internal consistency in
AFNI.
You may use the original form of these
volumes if you choose but your TLRC
coordinates
will not be consistent with AFNI's TLRC
database
(San Antonio Talairach Daemon database),
for example.
Donna
On 12/15/2005 09:13 AM, [EMAIL PROTECTED] wrote:
Hi Donna,
Using that average brain would be very nice. I just wanted to make sure that it
is in taliarch space.
Thanks,
Erin
Quoting Donna Hanlon <[EMAIL PROTECTED]>:
Hi Erin,
In most cases, you'll need to adjust the peaks caret guesses. This page
explains how to "tweak the peaks":
http://brainvis.wustl.edu/help/peak_tweaking/
My guess on the error is that your peaks were set such that some steps
produced essentially null output. If you upload your volume here, I can
provide more specific guidance about how the peaks should be set:
http://pulvinar.wustl.edu/cgi-bin/upload.cgi
But for a meta-analysis, segmentation of individual brains doesn't seem
practical. For reporting group results (unless you have segmented every
subject and done the group statistics on the surface, e.g.,
http://www.jneurosci.org/cgi/content/full/25/43/9919), it's usually more
appropriate to something like our PALS atlas
(http://sumsdb.wustl.edu/sums/download.do?id=6363278), or as described
previously, show volume foci on an average anatomical brain (e.g.,
avg152T1).
Of course, you may be considering segmentation for a project other than
your meta-analysis, but it seems worth clarifying at this stage. Don't
get me wrong: We strongly encourage researchers to segment all their
subjects and do their analysis on the surface, but we also acknowledge
the work involved with patching both hemispheres for every subject.
Trying to do this across multiple studies compounds the challenge.
Donna
On 12/14/2005 08:39 PM, [EMAIL PROTECTED] wrote:
Donna and David - thanks for your help...
I am working on the SureFit Segmentation and seem to be stuck...
First, I was curious about what exactly the Gray and White Matter Peak thing
is supposed to do. It seems to me, that both the gray and white matter
green
blobs are on white matter in my brain.
Second, when I try to perform the segmentation I am able to get past the
disconnect eye part but get stuck on the disconnect hindbrain. An error
message comes up:
Error in c:/caret5_borland/packages/source/vtk42-
LatestRelease/CommovtkImageData(3546780):GetScalarPointer;Pixel(-1,-1,0) not
in memory
Current extent = (0, 72, 0, 178, 0 123)
Does this mean anything to you?
Thanks,
Erin
P.S. this program looks like its going to be great!
Quoting Donna Hanlon <[EMAIL PROTECTED]>:
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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