Thanks Donna - I'll contact the authors. Terry Sewards
----- Original Message ----- From: <[EMAIL PROTECTED]> To: <caret-users@brainvis.wustl.edu> Sent: Friday, May 05, 2006 11:00 AM Subject: caret-users Digest, Vol 32, Issue 2 > Send caret-users mailing list submissions to > caret-users@brainvis.wustl.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://pulvinar.wustl.edu/mailman/listinfo/caret-users > or, via email, send a message with subject or body 'help' to > [EMAIL PROTECTED] > > You can reach the person managing the list at > [EMAIL PROTECTED] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of caret-users digest..." > > > Today's Topics: > > 1. Re: Rif: Re: [caret-users] Re: MNI, Talairach, and other > coordinate systems (Donna Dierker) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 05 May 2006 09:34:55 -0500 > From: Donna Dierker <[EMAIL PROTECTED]> > Subject: Re: Rif: Re: [caret-users] Re: MNI, Talairach, and other > coordinate systems > To: "Caret, SureFit, and SuMS software users" > <caret-users@brainvis.wustl.edu> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=UTF-8; format=flowed > > 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 > > >>caret-users@brainvis.wustl.edu > > >> > > >>To subscribe or unsubscribe via the World Wide Web, visit > > >>http://pulvinar.wustl.edu/mailman/listinfo/caret-users > > >>or, via email, send a message with subject or body 'help' to > > >>[EMAIL PROTECTED] > > >> > > >>You can reach the person managing the list at > > >>[EMAIL PROTECTED] > > >> > > >>When replying, please edit your Subject line so it is more specific > > >>than "Re: Contents of caret-users digest..." > > >> > > >> > > >>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/20060426/865b31 a > > >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/cri c > > >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 > > >>>caret-users@brainvis.wustl.edu > > >>>http://pulvinar.wustl.edu/mailman/listinfo/caret-users > > >>> > > >>> > > >>> > > >>> > > >>-- > > >>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.) > > > > > > > > >>------------------------------ > > >> > > >>_______________________________________________ > > >>caret-users mailing list > > >>caret-users@brainvis.wustl.edu > > >>http://pulvinar.wustl.edu/mailman/listinfo/caret-users > > >> > > >> > > >>End of caret-users Digest, Vol 31, Issue 17 > > >>******************************************* > > >> > > >> > > >> > > > > > >_______________________________________________ > > >caret-users mailing list > > >caret-users@brainvis.wustl.edu > > >http://pulvinar.wustl.edu/mailman/listinfo/caret-users > > > > > > > > > > > > > > > -- > > 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.) > > > > _______________________________________________ > > caret-users mailing list > > caret-users@brainvis.wustl.edu > > http://pulvinar.wustl.edu/mailman/listinfo/caret-users > > > >------------------------------------------------------------------------ > > > >_______________________________________________ > >caret-users mailing list > >caret-users@brainvis.wustl.edu > >http://pulvinar.wustl.edu/mailman/listinfo/caret-users > > > > > > > -- > Donna L. Dierker > (Formerly Donna Hanlon; no change in marital status -- see http://home.att.net/~donna.hanlon for details.) > > > ------------------------------ > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://pulvinar.wustl.edu/mailman/listinfo/caret-users > > > End of caret-users Digest, Vol 32, Issue 2 > ****************************************** >
