Erin,
Caret is designed to work with a single hemisphere. We have had some
discussions about loading and viewing both hemispheres simultaneously
but I do not know if that will ever happen. In the meantime the
following procedure should allow you to view a left and right
hemisphere and foci simultaneously.
* Load a left hemisphere into Caret.
* From the file menu, select "Export File". set the File Type to
"VTK Surface File". At the bottom of the dialog, set "Export
Selections" to "Fiducial...". Enter a name like left_hemisphere.vtk
and save the file.
* Quit Caret.
* Load a right hemisphere into Caret.
* Choose Open Data File from the File Menu. Set the File Type to
"VTK Model File". Select and load the VTK file that you saved a
previous step. You should now see both hemispheres.
* Enter/load Foci for both hemispheres.
* Save the foci file using File Menu: Save Data File. On the save
data file dialog set the File Type to "Foci Files (*.foci)" and make
sure the selection "Foci Associated With Surface Type" (at bottom of
Save Data File dialog) is set to Fiducial.
* When you start Caret in the future both the foci and VTK model file
should be listed in your spec file.
----------------------------------------------------------
John Harwell
[EMAIL PROTECTED]
314-362-3467
Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave. Box 8108
St. Louis, MO 63110 USA
On Dec 15, 2005, at 9:26 PM, [EMAIL PROTECTED] wrote:
Hi Donna,
I am so confused - I have been trying to get this right now for 4
days and its
just not working. What I need is a brain - a full brain, that I
can put some
foci on. My coordinates are in taliarch and tournoux space - so if
there is a
brain out there that I can either get in that space or change my
coordinates
for another space (like your PALS) that would be fine. However,
even looking
at your PALS brains all fiducial surfaces are half brains - and
since I need
to put the foci on a fiducial surface I'm not sure how this is
going to work.
I do appreciate your help, but as you can tell this is getting
frusterating
for me.
Thanks,
Erin
Quoting Donna Hanlon <[EMAIL PROTECTED]>:
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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