I will try to to show you an example of the issue, so it may be clearer.

Let's say I have a contact in the left posterior insula with MNI coordinates -33, -12, 13.

This corresponds to vertex 4983.

RAS coordinates on a pial surface: -35.1280 -10.8052 12.6963

RAS coordinates on an inflated surface: -14.9530 18.1240 -12.5924

As you can see from the enclosed figures, if I plot the coordinates on a pial surface, they are indeed in the posterior insula.

If I plot the on the inflated surface, they are completely off.

2018-05-25 7:15 GMT+02:00 Giulia Liberati <giulia.liberati@uclouvain.be>:

Thank you Bruce,

Yes, this is what I did.

Because the insular contacts are not in the insula anymore after I use the vertex to find the RAS coordinates for the inflated surface, my conclusion is that this only works with surface electrodes, not depth electrodes.

Best wishes,

Giulia

On Thu, 24 May 2018 at 23:22, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
Hi Giulia

find the vertex index of the vertex you are interested in, then read the
surface whose RAS coordinates you want (e.g. the white or pial) and
lookup the RAS coords of the vertex at that index.

cheers
Bruce
On Thu, 24 May 2018,
Giulia Liberati wrote:

>
> External Email - Use Caution
>
> Dear FreeSurfer experts,
> How can you obtain RAS coordinates for an inflated surface when you have vertex #?
>
> I am using the function read_surf('lh.inflated') to find the coordinates of some electrode contacts
> located in the left insula. However, when I plot the coordinates using plotPialSurf (iElVis), these
> locations are completely off (i.e., far outside from the insula).
>
> I don't understand what is going wrong.
>
> Any possible explanation?
>
> Thanks in advance!
>
> Giulia
>
>
>
>
> --
> Giulia Liberati, PhD
>
> Institute of Neuroscience (IoNS)
> Université catholique de Louvain
> Avenue Mounier 53 bte B1.53.02 à 1200 Woluwe-Saint-Lambert
> Claude Bernard; Etage 02; Local 0826; Site Bruxelles Woluwe
> Brussels, Belgium
>
>
--
Giulia Liberati, PhD

Institute of Neuroscience (IoNS)
Université catholique de Louvain
Avenue Mounier 53 bte B1.53.02 à 1200 Woluwe-Saint-Lambert
Claude Bernard; Etage 02; Local 0826; Site Bruxelles Woluwe
Brussels, Belgium

Giulia Liberati, PhD

Institute of Neuroscience (IoNS)

Université catholique de Louvain

Avenue Mounier 53 bte B1.53.02 à 1200 Woluwe-Saint-Lambert

Claude Bernard; Etage 02; Local 0826; Site Bruxelles Woluwe

Brussels, Belgium