[Mne_analysis] Geometry Creation Problem

[dgw]

Hi Isaiah,

This post probably best fits the MNE list (it takes a bit to track
down which problem relates to which list, but generally, mne_...
commands relate to the MNE list and FreeSurfer commands relate to the
freesurfer list). You are likely getting the error (only visualizing
the surfaces will show this is the reason: the easiest way is with
freeview), because the inner skull surface is crossing the outer skull
surface. MNE checks this because the BEM mathematics don't work when
this happens (they must be concentric). There are many different
potential solutions to this problem, so the easiest way to solve this
problem is to figure out what type of data you are working with (EEG,
MEG, MEEG?; what kind of MR data do you have available for this
participant?) What are you trying to do? We can figure out from that
the easiest/best way to solve this issue.

HTH,
D

P.S. Have you run through the tutorial first (this may help you see
how all the pieces fit together)?

On Mon, Aug 4, 2014 at 5:57 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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