<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 dir="ltr">Have you looked at `brainmask.mgz` to see if it's correct? I suspect that it is not.</div><div dir="ltr"><br></div><div dir="ltr">MNE's `mne watershed_bem` is just <a href="https://github.com/mne-tools/mne-python/blob/maint/0.17/mne/bem.py#L1082-L1105">a convenience wrapper</a> for `mri_watershed` in Freesurfer. Thus you can try running `mri_watershed` directly with different options to see what helps. Typically the `-atlas` / `-gcaatlas` options are useful, as is the `-h` (what we rename `--preflood` in MNE) option. Sometimes tweaking these can help.<div><br></div><div>However, sometimes this is not enough to make things work, and you'll need to dig into why Freesurfer is not working properly -- probably starting with where it fails first. You can see what Freesurfer's recon_all actually does, in order, <a href="https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable">here</a>. In your case, if you had done `recon_all -autorecon1`, it would have run just up through the skull stripping step, which should have been enough to reproduce the problem if your brainmask.mgz is indeed wrong. You can try <a href="https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11658.html">manually setting the control points and/or using -gentle</a>. You can look at the talairach transformation to see if it's not quite right, and if it's not, <a href="https://surfer.nmr.mgh.harvard.edu/fswiki/Edits">adjust it manually</a>. But before trying those, one thing I have found helpful is to have an expert options `xopts.txt` file containing the line:</div><div></div><div class="markdown-here-wrapper" style=""><pre style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;font-size:1em;line-height:1.2em;margin:1.2em 0px"><code style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;margin:0px 0.15em;padding:0px 0.3em;white-space:pre-wrap;border:1px solid rgb(234,234,234);background-color:rgb(248,248,248);border-radius:3px;display:inline;white-space:pre;overflow:auto;border-radius:3px;border:1px solid rgb(204,204,204);padding:0.5em 0.7em;display:block!important">mri_normalize -mprage -b 20 -n 5
</code></pre><div title="MDH:PGRpdj5gYGA8L2Rpdj48ZGl2PjxkaXY+bXJpX25vcm1hbGl6ZSAtbXByYWdlIC1iIDIwIC1uIDU8
L2Rpdj48L2Rpdj48ZGl2PmBgYDwvZGl2PjxkaXY+PC9kaXY+" style="height:0;width:0;max-height:0;max-width:0;overflow:hidden;font-size:0em;padding:0;margin:0"></div></div><div>I would actually try that in a clean directory with `recon_all -autorecon1 -xopts xopts.txt` first to see if it magically fixes your `brainmask.mgz`, and resort to manual control point setting and/or talairach adjustment only if necessary.</div><div><br></div><div>Once everything looks good at the end of `-autorecon1`, you can try running the `mne watershed_bem` command to see if the output is good. Once it is (and once brainmask.mgz is correct), you can then proceed with `recon_all -autorecon2` and `recon_all -autorecon3` to complete your `recon_all` run.<br></div><div><br></div><div>Those are all the tips I can think of offhand. If you need further assistance, try to isolate your problem to a single Freesurfer command (e.g., "`recon_all -autorecon1` fails to produce `brainmask.mgz` properly") and post further questions to the Freesurfer listserv, since that's where the skull-stripping and watershed experts are more likely to reside. But please do let us know if you find a solution in the end.</div><div><br></div><div>HTH,</div><div>Eric</div><div><br></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Feb 4, 2019 at 5:15 AM Broman Emilia <<a href="mailto:emilia.broman@aalto.fi">emilia.broman@aalto.fi</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>
Hi, <br>
<br>
I have been using mne_watershed_bem to generate BEM surfaces from T1 images. For 9 subjects (out of 50) the inner skull surface excludes the cerebellum. I found an old thread from 2014 where you suggested using the gcatlas option and changing the preflood number. I have tried playing with these, but the results are still quite bad. Do you have any new ideas on how to deal with this problem? <br>
<br>
Thanks,<br>
Emilia <br>
<br>
_______________________________________________<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><br>
</blockquote></div>