[Mne_analysis] Geometry Creation Problem

[Alexandre Gramfort]

indeed it seems like a segmentation problem.
have a look to the surfaces with freeview and check the quality of the
freesurfer reconstruction before going further

Alex

On Mon, Aug 4, 2014 at 11:57 PM, Isaiah C. Smith
<Isaiah.C.Smith.17 at dartmouth.edu> wrote:
> 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> 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> 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> 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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