[Mne_analysis] Fwd: Source space cration failed

[Maria Felber]

Hello Alex,

I am using freesurfer 5.1.0. 
I tried the command mne_setup_source_space --subject im14 --ico 6 --cps --overwrite, however I got the exact same error message as before. 
Could this have something to do with the fact, that this subject appears to have some extra tissue right outside the brain in freesurfer?
Thanks for your help,
Maria

----- Original Message -----
From: "Alexandre Gramfort" <gramfort at nmr.mgh.harvard.edu>
To: "Maria Felber" <felber at cbs.mpg.de>
Cc: "mne analysis" <mne_analysis at nmr.mgh.harvard.edu>
Sent: Tuesday, November 22, 2011 7:25:11 PM
Subject: Re: [Mne_analysis] Source space cration failed

hello maria,

this looks like a corner case with the use of the freesurfer recon.
what version of freesurfer did you use? can you try using the
option "--ico -6" like used here:

http://martinos.org/mne/command_line_tutorial.html#command-line-tutorial

Alex

On Tue, Nov 22, 2011 at 9:16 AM, Maria Felber <felber at cbs.mpg.de> wrote:
> Dear all,
>
> I tried to create a BEM with the following command:
>
> mne_setup_source_space --subject im14 --ico 5 --cps --overwrite
>
> I got the following lines shown in my shell:
>
> Setting up the source space with the following parameters:
>
> SUBJECTS_DIR = /SCR3/charlie/imesapp/freesurfer/
> Subject      = im14
> Surface      = white
> Icosahedron subdivision grade 5
> Create a source space with patch information
>
>>>> 1. Creating the source space file /SCR3/charlie/imesapp/freesurfer//im14/bem/im14-ico-5-src.fif...
>
> mne_make_source_space version 2.5 compiled at Sep 30 2010 16:56:44
>
> Loading /SCR3/charlie/imesapp/freesurfer//im14/surf/lh.white...
> Triangle file : created by felber on Tue Nov  1 23:10:36 2011 nvert = 131982 ntri = 263960
>        Triangle and vertex normals and neighboring triangles...[done]
>        Vertex neighbors...[done]
>        Distances between neighboring vertices...[791880 distances done]
> Doing the icosahedral vertex picking...
> Loading geometry from /SCR3/charlie/imesapp/freesurfer//im14/surf/lh.sphere...
> Triangle file : created by felber on Wed Nov  2 00:31:19 2011 nvert = 131982 ntri = 263960
>        Triangle and vertex normals and neighboring triangles...[done]
>        Vertex neighbors...[done]
>        Distances between neighboring vertices...[61440 distances done]
> Mapping lh im14 -> ico (5) ...[done]
> Source space vertex moved from 55033 to 55034 because of double occupation.
> Source space vertex moved from 55033 to 55023 because of double occupation.
> Source space vertex moved from 131819 to 53897 because of double occupation.
> Source space vertex moved from 53897 to 53907 because of double occupation.
> Source space vertex moved from 56212 to 57359 because of double occupation.
> Source space vertex moved from 55024 to 57341 because of double occupation.
> vertex 55023 is in the map multiple times.
> Cannot continue
> Source space creation failed
> Temporary files removed.
>
> As this has never happend before and I do not have a lot of experience with neither freesurfer nor MNE, I do not know where to look for the source of error. Could please someone help me finding a solution? Thank you very much.
> Sincerely,
> Maria Felber
>
>
> --
> Maria J. Felber, PhD Student
> Max Planck Institute for Human Cognitive and Brain Sciences
> Stephanstraße 1A
> 04103 Leipzig, Germany
> Phone:  +49 341 9940-2465/2522
>
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-- 
Maria J. Felber, PhD Student
Max Planck Institute for Human Cognitive and Brain Sciences
Stephanstraße 1A 
04103 Leipzig, Germany
Phone:  +49 341 9940-2465/2522

-- 
Maria J. Felber, PhD Student
Max Planck Institute for Human Cognitive and Brain Sciences
Stephanstraße 1A 
04103 Leipzig, Germany
Phone:  +49 341 9940-2465/2522