[Mne_analysis] Geometry Creation Problem

[Isaiah C. Smith]

Thank you, D,
What I am trying to do is created the volume conduction models using the MR images that I have. Eventually, I need to use these to find the lead field matrix, and then create a source model as well. I was told that this was a segmentation issue resulting from the freesurfer use (recon-all). I have been going through the tutorials and using the cookbook and was able to see the individual outer_skull_surf, outer_scalp_surf, inner_skull_surf, and brain_surf in XQuartz. The data that we are working with is EEG. 
Isaiah
On Aug 4, 2014, at 7:45 PM, dgw <dgwakeman at gmail.com> wrote:

> 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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