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Checking that inner skull surface is inside outer skull surface...[failed]</div>
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Surface inner skull is not completely inside surface outer skull(sum of solid angles = 8.85217e-16 * 4*PI).</div>
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Could't create the geometry file</div>
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<div>Hello All,</div>
<div>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?</div>
<div>Isaiah </div>
On Aug 4, 2014, at 2:35 PM, Denis-Alexander Engemann <<a href="mailto:denis.engemann@gmail.com">denis.engemann@gmail.com</a>> wrote:<br>
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<div dir="ltr">Isahiah,
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<div>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.</div>
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<div class="gmail_extra"><br>
<div class="gmail_quote">On Mon, Aug 4, 2014 at 11:30 PM, Isaiah C. Smith <span dir="ltr">
<<a href="mailto:Isaiah.C.Smith.17@dartmouth.edu" target="_blank">Isaiah.C.Smith.17@dartmouth.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thanks so much for the help but sorry,<br>
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?</blockquote>
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<div>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.</div>
<div>Hope these vague remarks help ...</div>
<div> </div>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex; position: static; z-index: auto;">
<span class="HOEnZb"><font color="#888888">Isaiah<br>
</font></span>
<div class="im HOEnZb">On Aug 4, 2014, at 2:11 PM, Alexandre Gramfort <<a href="mailto:alexandre.gramfort@telecom-paristech.fr">alexandre.gramfort@telecom-paristech.fr</a>> wrote:<br>
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<div class="HOEnZb">
<div class="h5">>> # Make high resolution head surface<br>
>> HEAD_FNAME=${SUBJECTS_DIR}/${SUBJECT}/bem/${SUBJECT}-head.fif<br>
>> if [ ! -f ${HEAD_FNAME} ];<br>
>> then<br>
>> mkheadsurf -s ${SUBJECT}<br>
>> mne_surf2bem --surf ${SUBJECTS_DIR}/${SUBJECT}/surf/lh.seghead --id 4<br>
>> --check --fif ${HEAD_FNAME}<br>
>> fi<br>
>><br>
>> # Setup BEM<br>
>><br>
>> to create the head surface. Or do I have to create the boundaries?<br>
><br>
> this sets up the head surface for coregistration with mne_analyze.<br>
> It will not be used for forward modeling but just to create the -trans.fif file.<br>
><br>
> Try what denis suggests if this does not succeed for you.<br>
><br>
> Alex<br>
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