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 CautionDear 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
External Email - Use Caution
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 CautionDear 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
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
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Giulia Liberati