Hi Gari, those look correct (make sure that your indices are not off by
1 (ie, FS uses 0-based indexing, and matlab uses 1-based). I would not
expect them to be the same since #1 includes a non-linear transform, and
they are only off by about 1.5cm (not bad by affine standards). Not sure
that one is better than the other, but #2 is probably more like what is
in the liturature.


On 11/16/2016 04:53 PM, Garikoitz Lerma-Usabiaga wrote:
> Hi all,
> I have fMRI data in individual space, converted to individual surface
> using vol2surf and to fsaverage surface using surf2surf (commands [1]
> and [2] below). With Matlab, I obtain the vertex with the maximum
> value: max_Vtx and max_Vtx305. If I would like to obtain the MNI152
> coordinate of this vertex (for comparison with the literature), I
> think I have two options:
>
> 1.- Work in the individual space:
>      >> max_SurfaceRAS = lhwhite(max_Vtx, :);
>      >> max_RAS = T1.vox2ras*inv(T1.tkrvox2ras)*[max_SurfaceRAS';1];
>      I can check in freeview that the result is correct.
>      >> max_RAS305 = TalXFM  *  max_RAS;
>      I can check in tkmedit that this is right too.
>      At last, using the MNI305to152 matrix provided by Doug in the wiki:
>      >> max_RAS152  = MNI305to152 * max_RAS305;
>
> 2.- Work in the fsaverage (305) space
>       >> max_SurfaceRAS305 = lhwhite305(max_Vtx305, :);
>       as Surface RAS is the same as RAS, we only have to convert it to 152
>       >> max_RAS152_305  = MNI305to152 * max_SurfaceRAS305 ;
>
> The results are:
> For 1: [-15.57, -93.62, -2.84]
> For 2: [-23.06, -97.06,  1.35]
>
> Is this method ok? is this the way it should work? As the results are
> not the same, is one of the methods inherently better than the other?
> Many thanks!
> Gari
>
>
> [1]  mri_vol2surf --srcsubject S001 --projfrac 0.5 --interp trilinear
> --hemi lh --regheader S001 --mov fMRI.img --o fMRI.mgh
>
> [2]  mri_surf2surf --srcsubject S001 --srchemi lh --srcsurfreg
> sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg
> --sval fMRI.mgh --tval fMRI305.mgh    --sfmt curv --noreshape --no-cortex
>
>
>
>
>
>
> _______________________________________________
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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