Re: [Freesurfer] RAS coordinates for inflated surface

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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:

...

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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