I agree with you.
Filippo
Donna Dierker <[EMAIL PROTECTED]>
Inviato da: [EMAIL PROTECTED]
05/05/2006 09:34 EST
Per favore, rispondere a "Caret, SureFit, and SuMS software users"
Per: "Caret, SureFit, and SuMS software users" <caret-users@brainvis.wustl.edu>
Cc:
Ccr: Filippo Carducci/Dip-Fisio_Um/Dipartimenti/Didattica/Ateneo/Uniroma1/it
Oggetto: Re: Rif: Re: [caret-users] Re: MNI, Talairach,and other coordinatesystems
Hi Dr. Carducci,
Thanks for pointing out Matthew Brett's excellent page; I've cited that
link many times myself.
But in addition to the two approaches for converting coordinates listed
on that page, there are still other methods, and papers should specify
which one(s) was(were) used.
On 05/05/2006 09:06 AM, [EMAIL PROTECTED] wrote:
> Hi,
>
> you can visit the site
> http://www.mrc-cbu.cam.ac.uk/Imaging/Common/mnispace.shtml.
>
>
>
> At this site there is also a Matlab script to convert MNI coordinates
> into Talairach space.
>
>
>
> Filippo Carducci
>
>
>
> __________________
>
> Dr. Filippo Carducci PhD
>
> University of Rome ""La Sapienza"
>
> Dept. Human Physiology and Pharmacology
>
>
>
>
>
>
>
> *Donna Dierker <[EMAIL PROTECTED]>*
> Inviato da: [EMAIL PROTECTED]
> 05/05/2006 08:21 EST
> Per favore, rispondere a "Caret, SureFit, and SuMS software users"
>
> Per: "Caret, SureFit, and SuMS software users"
> <caret-users@brainvis.wustl.edu>
> Cc:
> Ccr: Filippo
> Carducci/Dip-Fisio_Um/Dipartimenti/Didattica/Ateneo/Uniroma1/it
> Oggetto: Re: [caret-users] Re: MNI, Talairach, and other coordinate
> systems
>
>
> 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
> >
> >
> >
> >
> >
> >----- Original Message -----
> >From: <[EMAIL PROTECTED]>
> >To: <caret-users@brainvis.wustl.edu>
> >Sent: Wednesday, April 26, 2006 11:00 AM
> >Subject: caret-users Digest, Vol 31, Issue 17
> >
> >
> >
> >
> >>Send caret-users mailing list submissions to
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> >>
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> >>Today's Topics:
> >>
> >> 1. Re: help needed (shantanu ghosh)
> >> 2. Re: help needed (Donna Dierker)
> >>
> >>
> >>----------------------------------------------------------------------
> >>
> >>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"
> >><caret-users@brainvis.wustl.edu>
> >>Message-ID: <[EMAIL PROTECTED]>
> >>Content-Type: text/plain; charset="iso-8859-1"
> >>
> >>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
> >>
> >>
> >>
> >>
> >>
> >>---------------------------------
> >> Jiyo cricket on Yahoo! India cricket
> >>Yahoo! Messenger Mobile Stay in touch with your buddies all the time.
> >>-------------- next part --------------
> >>An HTML attachment was scrubbed...
> >>URL:
> >>
> >>
> >http://brainvis.wustl.edu/pipermail/caret-users/attachments/20060426/865b31a
> >c/attachment-0001.html
> >
> >
> >>------------------------------
> >>
> >>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"
> >><caret-users@brainvis.wustl.edu>
> >>Message-ID: <[EMAIL PROTECTED]>
> >>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >>
> >>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
> >>>
> >>>------------------------------------------------------------------------
> >>>Jiyo cricket on Yahoo! India cricket
> >>>
> >>>
> >>>
> ><http://us.rd.yahoo.com/mail/in/mailcricket/*http://in.sports.yahoo.com/cric
> >ket/>
> >
> >
> >>>Yahoo! Messenger Mobile
> >>>
> >>>
> >>>
> ><http://us.rd.yahoo.com/mail/in/mailmobilemessenger/*http://in.mobile.yahoo.
> >com/new/messenger/>
> >
> >
> >>>Stay in touch with your buddies all the time.
> >>>
> >>>------------------------------------------------------------------------
> >>>
> >>>_______________________________________________
> >>>caret-users mailing list
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> >>>
> >>--
> >>Donna L. Dierker
> >>(Formerly Donna Hanlon; no change in marital status -- see
> >>
> >>
> >http://home.att.net/~donna.hanlon
> <http://home.att.net/%7Edonna.hanlon> for details.)
> >
> >
> >>------------------------------
> >>
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> >>
> >>End of caret-users Digest, Vol 31, Issue 17
> >>*******************************************
> >>
> >>
> >>
> >
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>
> --
> Donna L. Dierker
> (Formerly Donna Hanlon; no change in marital status -- see
> http://home.att.net/~donna.hanlon
> <http://home.att.net/%7Edonna.hanlon> for details.)
>
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>
--
Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see http://home.att.net/~donna.hanlon for details.)
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