[Mne_analysis] Geometry Creation Problem

[Isaiah C. Smith]

Checking that inner skull surface is inside outer skull surface...[failed]
Surface inner skull is not completely inside surface outer skull(sum of solid angles = 8.85217e-16 * 4*PI).
Could't create the geometry file

Hello All,
This is the error message that I keep getting when trying to create the file. What this a segmentation problem? How would I fix it?
Isaiah
On Aug 4, 2014, at 2:35 PM, Denis-Alexander Engemann <denis.engemann at gmail.com<mailto:denis.engemann at gmail.com>> wrote:

Isahiah,

if you prefer Matlab you can also use `mne_make_scalp_surfaces` which is a shell script that calls Matlab and is provided by MNE-C.



On Mon, Aug 4, 2014 at 11:30 PM, Isaiah C. Smith <Isaiah.C.Smith.17 at dartmouth.edu<mailto:Isaiah.C.Smith.17 at dartmouth.edu>> wrote:
Thanks so much for the help but sorry,
I looked at the Python, but I am not really familiar with the format and having a hard time determining how to implement it. The lab I am working in primarily uses MATLAB. Is there a way to form models in MATLAB or the terminal along the same lines as the python attachment? And does the creation of a brain model follow the same procedures as the scalp and skull?

All is absed on your freesurfer segmentation, in that regard things are similar. The brain model (source space + forward solution) of course are not generated the same way as the head model.
Hope these vague remarks help ...

Isaiah
On Aug 4, 2014, at 2:11 PM, Alexandre Gramfort <alexandre.gramfort at telecom-paristech.fr<mailto:alexandre.gramfort at telecom-paristech.fr>> wrote:

>> # Make high resolution head surface
>> HEAD_FNAME=${SUBJECTS_DIR}/${SUBJECT}/bem/${SUBJECT}-head.fif
>> if [ ! -f ${HEAD_FNAME} ];
>> then
>>    mkheadsurf -s ${SUBJECT}
>>    mne_surf2bem --surf ${SUBJECTS_DIR}/${SUBJECT}/surf/lh.seghead --id 4
>> --check --fif ${HEAD_FNAME}
>> fi
>>
>> # Setup BEM
>>
>> to create the head surface. Or do I have to create the boundaries?
>
> this sets up the head surface for coregistration with mne_analyze.
> It will not be used for forward modeling but just to create the -trans.fif file.
>
> Try what denis suggests if this does not succeed for you.
>
> Alex
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