<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><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 style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);" class=""><div class="">Hi Eric,</div><div class=""><br class=""></div><div class="">Absolutely! This week I will prepare the updated instructions, make them understandable, and follow the MNE contributing guide. </div><div class=""><br class=""></div><div class="">Kind regards,</div><div class="">Ricardo. </div><div class=""><br class=""></div></div><div><br class=""><blockquote type="cite" class=""><div class="">El 27 oct 2020, a las 6:56, Eric Larson <<a href="mailto:larson.eric.d@gmail.com" class="">larson.eric.d@gmail.com</a>> escribió:</div><br class="Apple-interchange-newline"><div class=""><p class=""><span style="padding: 3px 10px; border-radius: 5px; color: #ffffff; font-weight: bold; display: inline-block; background-color: #ff0000;" class=""> External Email - Use Caution </span></p><div class=""><br class="webkit-block-placeholder"></div><div dir="ltr" class="">Hey Ricardo,<div class=""><br class=""></div><div class="">This is great information! Would you be up for making a Pull Request on GitHub to modify this tutorial with updated instructions?</div><div class=""><br class=""></div><div class=""><a href="https://github.com/mne-tools/mne-python/blob/master/tutorials/source-modeling/plot_fix_bem_in_blender.py" class="">https://github.com/mne-tools/mne-python/blob/master/tutorials/source-modeling/plot_fix_bem_in_blender.py</a></div><div class=""><br class=""></div><div class="">This is what gets rendered to create the HTML tutorial.</div><div class=""><br class=""></div><div class="">Eric</div><div class=""><br class=""></div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Oct 27, 2020 at 2:15 AM Ricardo Licona <<a href="mailto:ricklicona@me.com" class="">ricklicona@me.com</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="overflow-wrap: break-word;" class=""><p class=""><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)" class=""> External Email - Use Caution </span></p><div class=""><br class="webkit-block-placeholder"></div><div style="color:rgb(14,16,26);margin-top:0pt;margin-bottom:0pt" class=""><div style="margin-top:0pt;margin-bottom:0pt" class=""><span style="margin-top:0pt;margin-bottom:0pt" class="">Dear all,</span></div><div style="margin-top:0pt;margin-bottom:0pt" class=""><br class=""></div><div style="margin-top:0pt;margin-bottom:0pt" class=""><span style="margin-top:0pt;margin-bottom:0pt" class="">I solved the problem for Subject 09. In the Blender edit images that I sent you, there are no intersections (I analyzed the plot in detail); for this case, I only modified the outer skin. However, when I changed the outer skull solely, the problem finished. I exclusively employed mne.viz.plot_bem, although also I would consider Eric's options. </span></div><div style="margin-top:0pt;margin-bottom:0pt" class=""><br class=""></div><div style="margin-top:0pt;margin-bottom:0pt" class=""><span style="margin-top:0pt;margin-bottom:0pt" class="">For new users, I recommend make little modifications in Blender, then check the BEM plots (mne.viz.plot_bem) and save the plots. The idea is that you detect step by step, which parts of the surfaces to modify and eliminate the intersections between the surfaces. Here is the original tutorial: <a href="https://mne.tools/stable/auto_tutorials/source-modeling/plot_fix_bem_in_blender.html#sphx-glr-auto-tutorials-source-modeling-plot-fix-bem-in-blender-py" target="_blank" class="">https://mne.tools/stable/auto_tutorials/source-modeling/plot_fix_bem_in_blender.html#sphx-glr-auto-tutorials-source-modeling-plot-fix-bem-in-blender-py</a>. </span></div><div style="margin-top:0pt;margin-bottom:0pt" class=""><br class=""></div><div style="margin-top:0pt;margin-bottom:0pt" class=""><span style="margin-top:0pt;margin-bottom:0pt" class="">Only the next keyboard keys are necessaries in Blender: </span></div><ul style="margin-top:0pt;margin-bottom:0pt" class=""><li style="margin-top:0pt;margin-bottom:0pt;list-style-type:disc" class=""><span style="margin-top:0pt;margin-bottom:0pt" class="">TAB: To change to EDIT mode</span></li><li style="margin-top:0pt;margin-bottom:0pt;list-style-type:disc" class=""><span style="margin-top:0pt;margin-bottom:0pt" class="">C: To get a 'circle form' and select the parts that you want to change</span></li><li style="margin-top:0pt;margin-bottom:0pt;list-style-type:disc" class=""><span style="margin-top:0pt;margin-bottom:0pt" class="">G: To enlarge or reduce the pieces set (elemental)</span></li></ul><div style="margin-top:0pt;margin-bottom:0pt" class=""><br class=""></div><div style="margin-top:0pt;margin-bottom:0pt" class=""><span style="margin-top:0pt;margin-bottom:0pt" class="">Here the plot and other important files (download:<a href="https://correoipn-my.sharepoint.com/:f:/g/personal/jliconam1700_alumno_ipn_mx/ElKGzCPCRXtNorraicEzoDsBPkjYyqD5RbBB-NMHmCZ9EA?e=8gstBV" target="_blank" class=""> https://correoipn-my.sharepoint.com/:f:/g/personal/jliconam1700_alumno_ipn_mx/ElKGzCPCRXtNorraicEzoDsBPkjYyqD5RbBB-NMHmCZ9EA?e=8gstBV</a>):</span></div><ul style="margin-top:0pt;margin-bottom:0pt" class=""><li style="margin-top:0pt;margin-bottom:0pt;list-style-type:disc" class=""><span style="margin-top:0pt;margin-bottom:0pt" class="">Graph with outer skull changed</span></li><li style="margin-top:0pt;margin-bottom:0pt;list-style-type:disc" class=""><span style="margin-top:0pt;margin-bottom:0pt" class="">Blender image of the region changed</span></li><li style="margin-top:0pt;margin-bottom:0pt;list-style-type:disc" class=""><span style="margin-top:0pt;margin-bottom:0pt" class="">Outer skull .surf file</span></li><li style="margin-top:0pt;margin-bottom:0pt;list-style-type:disc" class=""><span style="margin-top:0pt;margin-bottom:0pt" class="">Outer skull fixed .obj file</span></li></ul><div style="margin-top:0pt;margin-bottom:0pt" class=""><br class=""></div><div style="margin-top:0pt;margin-bottom:0pt" class=""><span style="margin-top:0pt;margin-bottom:0pt" class="">OS: Mac Os X (Catalina 10.15.7)</span></div><div style="margin-top:0pt;margin-bottom:0pt" class=""><span style="margin-top:0pt;margin-bottom:0pt" class="">MNE: 0.21.0</span></div><div style="margin-top:0pt;margin-bottom:0pt" class=""><span style="margin-top:0pt;margin-bottom:0pt" class="">FreeSurfer: 6.0 (due to some problems with the recent versions and Mac Os X)</span></div><div style="margin-top:0pt;margin-bottom:0pt" class=""><br class=""></div><div style="margin-top:0pt;margin-bottom:0pt" class=""><span style="margin-top:0pt;margin-bottom:0pt" class="">Thanks for all.</span></div><div style="margin-top:0pt;margin-bottom:0pt" class=""><br class=""></div><div style="margin-top:0pt;margin-bottom:0pt" class=""><span style="margin-top:0pt;margin-bottom:0pt" class="">Best, </span></div><div style="margin-top:0pt;margin-bottom:0pt" class=""><span style="margin-top:0pt;margin-bottom:0pt" class="">Ricardo. </span></div><div style="margin-top:0pt;margin-bottom:0pt" class=""><br class=""></div><div style="margin-top:0pt;margin-bottom:0pt" class=""><br class=""></div><p style="margin-top:0pt;margin-bottom:0pt" class=""></p></div><div style="color:rgb(14,16,26);margin-top:0pt;margin-bottom:0pt" class=""><br class=""></div><p style="color:rgb(14,16,26);margin-top:0pt;margin-bottom:0pt" class=""></p><div class=""><br class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">El 26 oct 2020, a las 9:49, Eric Larson <<a href="mailto:larson.eric.d@gmail.com" target="_blank" class="">larson.eric.d@gmail.com</a>> escribió:</div><br class=""><div class=""><p class=""><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)" class=""> External Email - Use Caution </span></p><div class=""><br class=""></div><div dir="ltr" class="">The first image did not come through. But in the second (corrected) one, in the lower left plot you can see the outer skull (yellow) surface come very close to the outer skin (peach) surface. `plot_bem` by default only shows some slices -- if you use mne Report to render the bem with `decim=1` you'll get an interactive slider where you can see all slices. There are probably some slices for which they do intersect. You can also plot them in 3D using `plot_alignment` with the `surfaces` argument, or use FreeView -- or there is probably a way to view them in Blender to see where they intersect.<div class=""><br class=""></div><div class="">Could you slightly expand downward (and smooth -- it's quite jagged) the outer skin surface in blender?<div class=""><br class=""></div><div class="">Eric</div><div class=""><br class=""></div></div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sun, Oct 25, 2020 at 2:36 PM Ricardo Licona <<a href="mailto:ricklicona@me.com" target="_blank" class="">ricklicona@me.com</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class=""><p class=""><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)" class=""> External Email - Use Caution </span></p><div class=""><br class=""></div>Dear all,<div class=""><br class=""></div><div class=""><div class="">I had problems with BEM surfaces of FreeSurfer, thus I tried to correct them with the software Blender. After manual editing, according to plots, the intersections between the outer skull and outer skin disappear. However, when I run my Python script to create the 3-layer BEM model (conductivity = (0.3, 0.006, 0.3)), I have the same error message: “FAILED to create 3-layer BEM for sub009: Surface outer skull is not completely inside surface outer skin.”</div></div><div class=""><br class=""></div><div class="">I am using the ds117 dataset. </div><div class=""><br class=""></div><div class="">Plots (subject 9):</div><div class=""><br class=""></div><div class="">* Original plot without edit:<a href="https://correoipn-my.sharepoint.com/:i:/g/personal/jliconam1700_alumno_ipn_mx/Ee725N_sYlhHtVMvMVDq7UABDrd6yjCwE9unGYMVVj3UvQ?e=co8vb4" target="_blank" class=""><font color="red" class=""><b class="">MailScanner has detected a possible fraud attempt from "correoipn-my.sharepoint.com" claiming to be</b></font> https://correoipn-my.sharepoint.com/:i:/g/personal/jliconam1700_alumno_ipn_mx/Ee725N_sYlhHtVMvMVDq7UABDrd6yjCwE9unGYMVVj3UvQ?e=co8vb4</a></div><div class=""><br class=""></div><div class="">* Plot after Blender edit: <a href="https://correoipn-my.sharepoint.com/:i:/g/personal/jliconam1700_alumno_ipn_mx/EQjGk_LZgyNItO-sJ8dYLZgB9a6W1HfqzqtiIEZYy6dlQA?e=KAlbM4" target="_blank" class="">https://correoipn-my.sharepoint.com/:i:/g/personal/jliconam1700_alumno_ipn_mx/EQjGk_LZgyNItO-sJ8dYLZgB9a6W1HfqzqtiIEZYy6dlQA?e=KAlbM4</a></div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">Any advice? </div><div class=""><br class=""></div><div class=""><span class="">OS: Mac Os X (Catalina 10.15.7)</span><br class=""><span class="">MNE: 0.21.0</span><br class=""><span class="">FreeSurfer: 6.0 (due to some problems with the recent versions and Mac Os X)</span></div><div class=""><span class=""><br class=""></span></div><div class=""><span class="">Best,</span></div><div class=""><font class=""><span class="">Ricardo. </span></font></div></div>_______________________________________________<br class="">
Mne_analysis mailing list<br class="">
<a href="mailto:Mne_analysis@nmr.mgh.harvard.edu" target="_blank" class="">Mne_analysis@nmr.mgh.harvard.edu</a><br class="">
<a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" rel="noreferrer" target="_blank" class="">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a></blockquote></div>
_______________________________________________<br class="">Mne_analysis mailing list<br class=""><a href="mailto:Mne_analysis@nmr.mgh.harvard.edu" target="_blank" class="">Mne_analysis@nmr.mgh.harvard.edu</a><br class=""><a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" target="_blank" class="">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a></div></blockquote></div><br class=""></div></div>_______________________________________________<br class="">
Mne_analysis mailing list<br class="">
<a href="mailto:Mne_analysis@nmr.mgh.harvard.edu" target="_blank" class="">Mne_analysis@nmr.mgh.harvard.edu</a><br class="">
<a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" rel="noreferrer" target="_blank" class="">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a></blockquote></div>
_______________________________________________<br class="">Mne_analysis mailing list<br class=""><a href="mailto:Mne_analysis@nmr.mgh.harvard.edu" class="">Mne_analysis@nmr.mgh.harvard.edu</a><br class="">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</div></blockquote></div><br class=""></body></html>