<p><span style="padding: 3px 10px; border-radius: 5px; color: #ffffff; font-weight: bold; display: inline-block; background-color: #ff0000;"> External Email - Use Caution </span></p><p></p><div dir="ltr"><div>Depending on how your segmentation looks, the simplest solution might be to run mri_expand in Freesurfer on the inner skull surface with a small negative value.</div><div><br></div><div>Be sure to check the quality of the BEM afterwards.</div><div><br></div><div>Mainak<br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Nov 19, 2019 at 2:03 PM Eric Larson <<a href="mailto:larson.eric.d@gmail.com">larson.eric.d@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><p><span style="padding:3px 10px;border-radius:5px;color:rgb(255,255,255);font-weight:bold;display:inline-block;background-color:rgb(255,0,0)"> External Email - Use Caution </span></p><p></p><div dir="ltr">There are many options for computing the watershed bem, MNE only exposes some of them. You can try to fix it using Freesurfer commands. Check the archive for ideas here, such as:<div><br></div><div><a href="https://mail.nmr.mgh.harvard.edu/pipermail//mne_analysis/2019-April/005805.html" target="_blank">https://mail.nmr.mgh.harvard.edu/pipermail//mne_analysis/2019-April/005805.html</a><div><div><br></div><div>Eric</div><div><br></div></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Nov 19, 2019 at 7:13 AM Mina Jamshidi <<a href="mailto:jamshidi@cbs.mpg.de" target="_blank">jamshidi@cbs.mpg.de</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"> External Email - Use Caution <br>
<br>
Dear All,<br>
<br>
what is the remedy when there is the following error for bem calculation (with mne watershed_bem)?<br>
Surface inner skull is not completely inside surface outer skull<br>
<br>
Best,<br>
Mina<br>
P.S. I plot the sufaces using mne.viz.plot_bem and see that the inner skull is not inside in outer skull surface.<br>
<br>
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