[Mne_analysis] Fwd: Source space cration failed

[Dan G Wakeman]

Hi Maria,

This was a known problem, and I strongly doubt it is related to your freesurfer reconstruction. It is caused by some safety checks run by MNE. The easy way to avoid it is to use a larger decimation i.e. ico 5. In my experience, you cannot use an ico decimation above a fifth order icosahedron.  Alternatively, you can use the full range i.e. 1mm and up of the "--spacing" option.

HTH
D
On 2011 Nov 23, at 06:08 , Maria Felber wrote:

> 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
> 
> _______________________________________________
> Mne_analysis mailing list
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