Hi Doug,

I tried what you suggested, but it did not work (see below for details of what we tried). We have TkReg RAS coordinates (or vertex points) for our electrode contacts; most contacts are deep within the brain (e.g., hippocampus and amygdala). We want to get a variable in Matlab that will give us the anatomical labels as a function of the TkReg RAS coordinates (or vertex points). How can we do this?

Thanks!

Sparsh

What I tried: I read the 'rh.aparc.2009a.annot' file in matlab using read_annotation.m. That gave me 76 labels for right hemisphere, which I believe correspond to the surface parcellations only. In freeview I loaded the orig.mgz, aparc.a2009s+aseg.mgz, rh.pial and rh.inflated. I then clicked on a cortical surface point to see if I can get the corresponding vertex number or structure ID. On doing so, I found a value in the Vertex row under rh.pial of freeview but this number wasn't found in the matlab output (in the colortable.label or colortable.table). I think I am looking in the wrong place to find the vertex # on freeview.

Also, I did not find a readable file for the segmentation data. I tried to read the aparc.a2009s+aseg.mgz on Matlab but that didn't work.

Show quoted text

On Thu, 7 Feb 2019, 16:10 Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu wrote:

First, you'll have to find the closest vertex for each point in
fsavarage. You can do this with by creating a label file then using
mri_label2label with the --paint option.

To find the label associated with each vertex, it is probably easiest
to use matlab using read_surf.m and read_annotation.m

On 2/5/19 11:17 AM, Sparsh Jain wrote:
>
> External Email - Use Caution
>
> Good afternoon
>
> Is there is way to automatically extract the anatomical locations
> corresponding to a set of RAS coordinates using Freesurfer's atlas? I
> have a set of 200 points and I am trying to get their anatomical
> labels automatically.
>
> Thank you
> Sparsh
>
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