no worries, I'm glad it worked out Bruce On Fri, 25 May 2018, Giulia Liberati wrote:

External Email - Use Caution

Hi Bruce, You are right.

There was a silly bug in my plotting script which I managed to fix.

So now everything is at its place!

Thank you very much for your patience and support!

Giulia

2018-05-25 15:52 GMT+02:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: Hi Giulia,

  no, that shouldn't be the case. You don't care about the RAS coordinates
  of the inflated vertex - only its index. Use the index to look up the
  corresponding vertex on another surface like white, then use its RAS
  coords. Should work for any spot in the brain.

  cheers
  Bruce
  On Fri, 25 May 2018, Giulia
  Liberati wrote:

  >
  >         External Email - Use Caution        
  >
  > 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