Thanks, Doug! Got it. So FreeSurfer registers the individual scans to the MNI305 atlas but mri_surfcluster reports approx. Talairach coordinates with the default option: —fixmni

I was a little bit confused because this website (https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems) says that the following: "Note on Talairach: FreeSurferhttps://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurfer does not report true "Talairach" coordinates. The coordinates listed unter "Talairach" are actually based on Matthew Brett's 10/8/98 non-linear transform from MNI305 space (see http://www.mrc-cbu.cam.ac.uk/Imaging/mnispace.html). FreeSurferhttps://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurfer also reports "Talairach MNI" coordinates. These are MNI305 space.”

If my understanding is correct, by default, the “Talairach” coordinates reported by mri_surfcluster (with —fixmni) are non-linear transformation from the MNI305 space; they are approx. Talairach coord as you suggested. And If I ever use —nofixmni, then it is what is internally used by FreeSurfer, the MNI305 space, or the "Talairach MNI” coordinates.

Is the understanding above correct?

Thanks!

-- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.yang@yale.edu

From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, November 11, 2015 at 11:01 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] TalX TalY TalZ

If you use --fixmni, then they are reported in approximate talairach space

On 11/11/15 10:08 AM, Yang, Daniel wrote: Dear FreeSurfer Experts,

Are these coordinates reported in mri_surfcluster in MNI305 space? (with —fixmni)

Thanks, Daniel

-- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.yang@yale.edumailto:daniel.yj.yang@yale.edu

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