Hi Erin,
It's frustrating, because you're looking for a feature Caret really
doesn't support yet.
Surface-wise, Caret currently displays a hemisphere -- not a full
brain. It is possible to display both hemispheres at the same time -- I
think importing one of them as a VTK file while the other one is already
open as a fiducial coord file. But this is something I haven't tried
myself; as I recall, it was tricky to do. But John Harwell has been
working on several major upgrades to Caret's functionality, and full
brain support happens to be one of them. Since there are several items
on his plate, I'm not really sure where this one falls on the priority
list, or what the status is.
If David or John know how to get both left and right hemispheres of the
PALS atlas to display (and you don't have to be one of them to pull it
off), then they will chime in, because they also read this list. If we
don't hear from them, then these are your options, as I see it:
1. Consider treating the left and right hemispheres separately (i.e.,
live with Caret's current functionality). Not the end of the world, but
probably not the most satisfying solution.
2. Use the surface_volume display (i.e., slice views with surface turned
off), but then you're limited to different brains for different spaces
(i.e., treat avg152 coords separately from true T&T).
3. Same as #2, but figure out how to convert, say, avg152 to T&T or vice
versa (and so on for other stereotaxic spaces, such as Wash U's 711-2*,
with all being converted to a single target space).
This is all that comes to mind at the moment, but perhaps one of our
brilliant users will have other ideas.
Caret could actually be used to do #3 (e.g., load foci with appropriate
avg fiducial surface; project foci; save as fociproj; load avg fiducial
for target space; and save foci using the target fiducial as the
reference surface). But it would be a pain to do it this way. It's
possible Ziad Saad or one of the other AFNI gods has scripts for this
purpose, and the Cambridge page cited earlier
(http://www.mrc-cbu.cam.ac.uk/Imaging/Common/mnispace.shtml) also has
some suggestions. There are probably many solutions to these problems,
but it's not something I've ever needed to do.
This gives me the opportunity to point out a little-known, but often
very useful Caret feature: You can save foci and borders, once
projected, in alternate configurations. For example, several users at
wustl.edu have wanted to draw borders on the flat map, but get the
border points in fiducial configuration. Just project them using the
appropriate source config in the main window, but make sure your target
coord is loaded, and save the border or foci file using the target coord.
Donna
On 12/15/2005 09:26 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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