On 05/04/2006 03:30 PM, Terry Sewards wrote:

Hi Donna,

I'm a little confused about coordinates of foci reported in the literature.
You're in excellent company.

In a study by Mechelli et al. (2005)  [NeuroImage 30: 992-1002] the authors
state that "the functional images were spatially normalized to a standard
MNI-305 template using nonlinear-basis functions", but in the tables in
which the coordinates are listed it says "Co-ordinates [x, y, z] are
reported in Talairach space".  There is no mention of a coordinate
transformation from MNI to TT space.  I had assumed that "reported in
Talairach space" meant exactly that, but now I am unsure.  I would
appreciate it if you could clarify this for me.  Thanks.
You'll need to ask the authors, I'm afraid. Like you, I believe MNI-305 does not equal Talairach, and if converting one to another, it's good form to specify how in the methods. But you probably also know that many people use the term Talairach loosely, as a synonym for stereotaxic. My guess is that they used the standard SPM2 templates, which means MNI-305 is more accurate than Talairach.

So I wish I could clarify, but I'm as much in the dark as you are.  Sorry.

Terry Sewards





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Today's Topics:

  1. Re: help needed (shantanu ghosh)
  2. Re: help needed (Donna Dierker)


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Message: 1
Date: Wed, 26 Apr 2006 10:35:58 +0100 (BST)
From: shantanu ghosh <[EMAIL PROTECTED]>
Subject: Re: [caret-users] help needed
To: "Caret, SureFit, and SuMS software users"
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Dear Caret support
 How can I paint  Talairach coordinates for different tasks with
different colors onto a single cortical surface for illustration in
metaanalysis?
 thanks in advance,
 shantanu


     Shantanu Ghosh, PhD
 Department of Humanities and Social Sciences
 Indian Institute of Technology, Delhi
 Hauz Khas
 New Delhi 110016
 INDIA
 Tel.: +91-11-2659 6589
 Fax: +91-11-2659 6509





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Message: 2
Date: Wed, 26 Apr 2006 08:37:09 -0500
From: Donna Dierker <[EMAIL PROTECTED]>
Subject: Re: [caret-users] help needed
To: "Caret, SureFit, and SuMS software users"
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Hi Shantanu,

There are a couple of ways to do this.  If you're lucky enough to have
access to either a ROI or functional volume (e.g., AFNI +tlrc or FSL/SPM
avg152 space group statistical output maps), then you can map them onto
the PALS atlas using the procedure outlined in the PALS_B12 tutorial

http://sumsdb.wustl.edu:8081/sums/directory.do?dir_id=6332260

If you just have a stereotaxic coordinate, then you can use the Layers:
Foci: Map Stereotaxic Focus feature.  See page 43 of this tutorial:

Caret 5.2 Tutorial - Introduction, Installation, Visualization, and
Registration
http://brainmap.wustl.edu/caret/pdf/Caret_5_12_Tutorial_Intro.pdf

When doing metanalyses, one thing to keep in mind is that people use the
term Talairach loosely.  They may call coordinates talairach, when
they're really in another stereotaxic space (e.g., icbm 152 or Wash U's
711-2B).  The PALS atlas contains several different average fiducial
surfaces (in the Caret data_files/fmri_mapping_fils directory) to
support various grids.  See this link for more details:

http://brainvis.wustl.edu/help/pals_volume_normalization/

When mapping foci or functional data, make sure you use the average
fiducial surface that most closely resembles the space of your
coordinates/volume.  If they're different, then your results are garbage.

On 04/26/2006 04:35 AM, shantanu ghosh wrote:

Dear Caret support
How can I paint  Talairach coordinates for different tasks with
different colors onto a single cortical surface for illustration in
metaanalysis?
thanks in advance,
shantanu


Shantanu Ghosh, PhD
Department of Humanities and Social Sciences
Indian Institute of Technology, Delhi
Hauz Khas
New Delhi 110016
INDIA
Tel.: +91-11-2659 6589
Fax: +91-11-2659 6509

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