<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">Hi Eric,<div><br></div><div>thanks this help. Only one question for my understanding. <i>Is</i> the brainmask.mgz used by the watershed algorithm at all ? </div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Il giorno lun 27 apr 2020 alle ore 22:45 Eric Larson <<a href="mailto:larson.eric.d@gmail.com">larson.eric.d@gmail.com</a>> ha scritto:<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">You can run FreeSurfer in discrete steps and correct the brainmask.mgz at the right point in the processing (probably at the end of -autorecon1). See:<div><br></div><div><a href="https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable" target="_blank">https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable</a></div><div><br></div><div>See also "going farther back" here:</div><div><br></div><div><a href="https://mne.tools/dev/overview/faq.html#my-watershed-bem-meshes-look-incorrect" target="_blank">https://mne.tools/dev/overview/faq.html#my-watershed-bem-meshes-look-incorrect</a><br><div><br></div><div>Alternatively, if you don't want to mess with FreeSurfer, you could try dealing with the coordinate frames and such. Usually looking at the output of `plot_alignment` with the subject/src/trans/bem set properly (and also plot_bem) will tell you if the forward calculation will do what you want it to do. See for example:</div><div><br></div><div><a href="https://mne.tools/dev/auto_tutorials/source-modeling/plot_forward.html" target="_blank">https://mne.tools/dev/auto_tutorials/source-modeling/plot_forward.html</a></div><div><br></div><div>Eric</div><div><br></div><div><br></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Apr 27, 2020 at 4:39 PM Edoardo Pinzuti <<a href="mailto:edoardo.pinzuti@gmail.com" target="_blank">edoardo.pinzuti@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">The only problem is that the FreeSurfer skullstripping and other segmentation steps do not work well (maybe due to a not so good T1) and it required manual correction. On the other hand, I have the corrected brain mask. Could be one solution to run FreeSurfer with this brainmask? <div><br></div><div>Thanks a lot </div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Il giorno lun 27 apr 2020 alle ore 22:23 Alexandre Gramfort <<a href="mailto:alexandre.gramfort@inria.fr" target="_blank">alexandre.gramfort@inria.fr</a>> ha scritto:<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">I would redo the segmentation as it will be just a few hours of CPU time<div>and you're sure not to mess it up with coord frames etc.<br><div><br></div><div>my 2c</div><div>Alex</div><div><br></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Apr 27, 2020 at 6:17 PM Edoardo Pinzuti <<a href="mailto:edoardo.pinzuti@gmail.com" target="_blank">edoardo.pinzuti@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">Dear MNE experts,<div><br></div><div>I have already done a year ago the segmentation and the BEM models in fiedltrip. Is there a way to import them in MNE without starting from the segmentation again ?</div><div><br></div><div>Thanks</div></div>
_______________________________________________<br>
Mne_analysis mailing list<br>
<a href="mailto:Mne_analysis@nmr.mgh.harvard.edu" target="_blank">Mne_analysis@nmr.mgh.harvard.edu</a><br>
<a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" rel="noreferrer" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a></blockquote></div>
_______________________________________________<br>
Mne_analysis mailing list<br>
<a href="mailto:Mne_analysis@nmr.mgh.harvard.edu" target="_blank">Mne_analysis@nmr.mgh.harvard.edu</a><br>
<a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" rel="noreferrer" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a></blockquote></div>
_______________________________________________<br>
Mne_analysis mailing list<br>
<a href="mailto:Mne_analysis@nmr.mgh.harvard.edu" target="_blank">Mne_analysis@nmr.mgh.harvard.edu</a><br>
<a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" rel="noreferrer" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a></blockquote></div>
_______________________________________________<br>
Mne_analysis mailing list<br>
<a href="mailto:Mne_analysis@nmr.mgh.harvard.edu" target="_blank">Mne_analysis@nmr.mgh.harvard.edu</a><br>
<a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" rel="noreferrer" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a></blockquote></div>