That converts from MNI305 to MNI152 without going through the talairach itself. When FS computes Tal coords, it does so nonlinearly.
doug


On 9/11/13 12:08 PM, Yang, Daniel wrote:
Hi Doug,

It's pretty awesome. So accordingly, 

MNI152x = (0.9975) MNI305x + (-0.0073) MNI305y + (0.0176) MNI305z + (-0.0429) * 1 
MNI152y = (0.0146) MNI305x + (1.0009) MNI305y + (-0.0024) MNI305z + (1.5496) * 1
MNI152z = (-0.0130) MNI305 + (-0.0093) MNI305y + (0.9971) MNI305z + (1.1840) * 1

The last row of the M (i.e., [-0.0429 1.5496 1.1840]') looks like some sort of offset to me, correct?

In other words, we are obtaining MNI305 first, Freesurfer convert that to TAL by default (question: is it done linearly or non-linearly?), and then we can manually convert it to MNI152 also.

Thanks so much!
Daniel

-- 
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454

On 9/10/13 6:52 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edu> wrote:

Hi Yang, I've computed a matrix that should do the trick. If you are in
matlab, then

M = [    0.9975   -0.0073    0.0176   -0.0429
     0.0146    1.0009   -0.0024    1.5496
    -0.0130   -0.0093    0.9971    1.1840
          0         0         0    1.0000]
P305 = [MNI305x MNI305y MNI305z 1]';
P152 = M*P305

Can you give this a shot and see if it makes sense? It will probably be
hard to tell since the matrix is pretty close to identity.

doug




On 09/10/2013 05:17 PM, Yang, Daniel wrote:
Thanks, Doug. I am really hoping to get MNI152 (because I also use
fsl). Are MNI305 and MNI152 the same? How can I obtain MNI152 coordinates?

Best,
Daniel

--
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454

On 9/10/13 5:14 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edu


     It is an estimate of Tal coords from the MNI305. See


     If you want MNI305, run mri_surfcluster with --nofixmni

     doug



     On 09/10/2013 05:08 PM, Yang, Daniel wrote:

         Hi all,

         The output of mri_surfcluster --sum shows TalX TalY TalZ. I am
         wondering if they are based on the Talairach system or some
         sort of
         MNI-Talairach system. If the latter, can you tell me something
         more
         about it? Like a webpage that describes its relationship
         between the
         MNI152 or the Talairach system?

         I find it confusing because mri_surfcluster said: "INFO:
         fixing MNI
         talairach coordinates"

         Thanks!
         Daniel

         --
         Yung-Jui "Daniel" Yang, PhD
         Postdoctoral Researcher
         Yale Child Study Center
         New Haven, CT
         (203) 737-5454


         _______________________________________________
         Freesurfer mailing list


     --
     Douglas N. Greve, Ph.D.
     MGH-NMR Center
     Phone Number: 617-724-2358
     Fax: 617-726-7422

     Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
     Outgoing:

     _______________________________________________
     Freesurfer mailing list


     The information in this e-mail is intended only for the person to
     whom it is
     addressed. If you believe this e-mail was sent to you in error and
     the e-mail
     contains patient information, please contact the Partners
     Compliance HelpLine at
     http://www.partners.org/complianceline . If the e-mail was sent to
     you in error
     but does not contain patient information, please contact the
     sender and properly
     dispose of the e-mail.



--
Douglas N. Greve, Ph.D.
MGH-NMR Center
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting