[Mne_analysis] vertex numbers in source space files

[Björn Herrmann]

hey alex,
thank you for your quick response. i also did more digging and compare coordinates in label files (vertex numbers starting from 0) with the coordinates in the source space file after reading in matlab, and you are right +1 is already applied when reading in matlab.
i think I also found what makes my solutions look weird. before, i was first morphing (morph map multiplication) the solution of the reduced source space to the full fsaverage surface and did the smoothing/interpolating on this surface. now i changed the order of this approach, first smoothing/interpolating the solution of the reduced source space to the individual full surface and then I do the morphing. looks very good now.
best,
björn

------
Björn Herrmann

Auditory Cognition Group
Max Planck Institute for Human Cognitive and Brain Sciences
Stephanstrasse 1a, 04103 Leipzig, Germany

phone: ++49 (0)341 9940 2606
email: bherrmann at cbs.mpg.de

----- Original Message -----
From: "Alexandre Gramfort" <alexandre.gramfort at telecom-paristech.fr>
To: "Björn Herrmann" <bherrmann at cbs.mpg.de>
Cc: "mne analysis" <mne_analysis at nmr.mgh.harvard.edu>
Sent: Saturday, August 3, 2013 9:01:33 AM
Subject: Re: [Mne_analysis] vertex numbers in source space files

hi Björn,

if you get:

isequal(find(sspace(1).inuse),sspace(1).vertno)
ans = 1

it's that vertno is indexed starting at 1 as find returns matlab indices.

HTH
Alex

On Fri, Aug 2, 2013 at 2:14 PM, Björn Herrmann <bherrmann at cbs.mpg.de> wrote:
> dear mne users,
>
> i am using the MNE toolbox to obtain source spaces. in particular, i have a question regarding the vertex numbers in matlab.
> i am reading the source space
>
> sspace = mne_read_source_spaces(['fsurf/' subj{s} '/bem/' subj{s} '-ico-5-src.fif']);
> sspace(1)
> ans =
>               id: 101
>               np: 136746
>             ntri: 273488
>      coord_frame: 5
>               rr: [136746x3 double]
>               nn: [136746x3 double]
>             tris: [273488x3 int32]
>             nuse: 10242
>            inuse: [1x136746 int32]
>           vertno: [1x10242 int32]
>         nuse_tri: 20480
>         use_tris: [20480x3 int32]
>          nearest: []
>     nearest_dist: []
>            pinfo: []
>             dist: []
>       dist_limit: []
>
> and I calculated an inverse solution for the reduced number of vertices (n = 10242). before morphing this solution to the full 136746 vertices I do the following
>
> Vector = zeros(size(sspace(1).rr,1),1);
> Vector(sspace(1).vertno+1) = J;
>
> however, i am unsure whether it is "sspace(1).vertno" or "sspace(1).vertno+1". I had the feeling that the vertex numbers start at 0 and thus adding a 1 is correct. the vector sspace(1).inuse however points towards not adding the 1, since
>
> isequal(find(sspace(1).inuse),sspace(1).vertno)
> ans =
>      1
>
> could one of you help me regarding which one is right? i was favoring adding 1, because the morphed solution (136746 vertices) and the solution plotted for the reduced number of vertices (10242) looked more alike when i add 1 to sspace(1).vertno
>
> thanks in advance,
> björn
>
>
>
> ------
> Björn Herrmann
>
> Auditory Cognition Group
> Max Planck Institute for Human Cognitive and Brain Sciences
> Stephanstrasse 1a, 04103 Leipzig, Germany
>
> phone: ++49 (0)341 9940 2606
> email: bherrmann at cbs.mpg.de
>
>
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