[Mne_analysis] Geometry Creation Problem

Tue Aug 5 09:00:46 EDT 2014

On Tue, Aug 5, 2014 at 12:41 AM, Isaiah C. Smith
<Isaiah.C.Smith.17 at dartmouth.edu> wrote:
> 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.

What type of MR data do you have? Do you have any Multi-Echo FLASH
data available (this is strongly recommended for EEG data)? As I
described in my previous post: the issue is that the the
inner_skull_surf and outer_skull_surf cross, which violates an
assumption in the BEM calculations (I recommend you take a look so you
can see where and how severe the crossing is). The best
troubleshooting options will depend on your answers to the above
questions, but if you don't have any more MRI data available for this
participant, then I will suggest you try the following: change the
names of the BEM surfaces (the ones you listed above). Then try some
of the other options with mne_make_watershed_bem (first I would try
using the -atlas option; then you can play around with the -preflood
number (this is a percentage), though I am not terribly familiar with
it's use). There are more options, but I would start with those.

HTH,
D

> 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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