<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Leo,<div><br></div><div>May I add to Lilla's comments that the reconstructed headmodel looks quite bad to me. This suggests that the automatic anatomical segmentation did not work well. The most likely cause is that the coordinate system which you specified for the anatomical image in the input was incorrect (e.g. specifying 'spm', while it should have been 'ctf' or so), or that the transformation matrix mapping from voxels to head coordinates was not correct.</div><div><br></div><div>Best,</div><div>Jan-Mathijs</div><div><br></div><div><br><div><div>On Sep 30, 2013, at 9:53 AM, <a href="mailto:lilla.magyari@mpi.nl">lilla.magyari@mpi.nl</a> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hello Leo and Stephen,<br><br>yes, it is unfortunate, that there is still a problem with the MNE<br>tutorial. I think the main problem is the integration of the pipeline with<br>Freesurfer which requires a more careful look on the script.<br>I could not find the attached image from Leo. If the sourcespace and the<br>volume conduction models are not well-aligned because one of them is too<br>small compared to the other, then it will probably help if you convert the<br>units.<br>In Fieldtrip, the handling of the units of the volume conduction model has<br>changed, which means that they are not automatically converted to 'cm'<br>anymore.<br>Lilla<br><br><br><blockquote type="cite">Hello Leo,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">This looks like the same problem I was having a few months ago, and there<br></blockquote><blockquote type="cite">should be some messages on the list about it. I am not able to look at my<br></blockquote><blockquote type="cite">data and scripts right now, but if I remember correctly (you can check the<br></blockquote><blockquote type="cite">lists for more) the problem had to do with the transformation matrix, and<br></blockquote><blockquote type="cite">ft_convert_units. In my case, during the "volume conduction model" step of<br></blockquote><blockquote type="cite">the tutorial (the last step before you can plot the vol and sourcespace<br></blockquote><blockquote type="cite">together), I had to add an extra<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">vol = ft_convert_units(vol, 'cm')<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">before ft_transform_geometry. I don't remember if this alone will solve<br></blockquote><blockquote type="cite">the<br></blockquote><blockquote type="cite">problem (unfortunately the the situation is kind of complicated right now,<br></blockquote><blockquote type="cite">there is also a different version of the minimum norms tutorial that is<br></blockquote><blockquote type="cite">still in development--see the previous messages for links--and I think my<br></blockquote><blockquote type="cite">processing pipeline ended up being a mixture of the two to get things<br></blockquote><blockquote type="cite">working. Which means that it's hard to track where exactly I solved the<br></blockquote><blockquote type="cite">problem.)<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Best,<br></blockquote><blockquote type="cite">Steve<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Message: 1<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Date: Sat, 28 Sep 2013 15:25:32 +0200<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">From: Zizlsperger Leopold <<a href="mailto:zizlsperger@gmail.com">zizlsperger@gmail.com</a>><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">To: <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Subject: [FieldTrip] EEG Source reconstruction: sourcespace and the<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> volume conductor misaligned<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Message-ID: <<a href="mailto:06D14B0C-655A-4EF2-A69A-B735DBDBC504@gmail.com">06D14B0C-655A-4EF2-A69A-B735DBDBC504@gmail.com</a>><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Content-Type: text/plain; charset="iso-8859-1"<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Hi all,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">I am following the instructions in the "Source reconstruction of<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">event-related fields using minimum-norm estimate" tutorial closely to do<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">a<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">source-analysis of EEG data using the example MRI. As I am following the<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">tutorial almost unchanged I am not including the script here.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">When I re-align the volume conduction model to the sourcespace they are<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">not aligned very well, see screenshot attached. I remember a similar<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">question in the mailing list a while ago but cannot find it...<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Is there a way to interactively realign volume conduction model and<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">sourcespace? Re-doing the fiducials did not change the aligment<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">considerably. Also, my volume conduction model looks weird...<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">I used ft_determine_coordsys on both the vol and the sourcespace, see<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">screenshots attached, too.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Would be nice if you could point me in the right direction.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Thanks in advance.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Leo<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">----<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Dr. med. Leopold Zizlsperger<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Klinik f?r Neurologie<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Uniklinik RWTH Aachen<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Pauwelsstrasse 30<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">52074 Aachen<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Tel: +49 241 80 35465<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><a href="mailto:lzizlsperger@ukaachen.de">lzizlsperger@ukaachen.de</a><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Leopold Zizlsperger, MD<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Department of Neurology<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">RWTH Aachen University<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Pauwelsstrasse 30<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">52074 Aachen, Germany<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Tel: +49 241 80 35465<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><a href="mailto:lzizlsperger@ukaachen.de">lzizlsperger@ukaachen.de</a><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">-------------- next part --------------<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">An HTML attachment was scrubbed...<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">URL: <<br></blockquote></blockquote><blockquote 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type="cite">------------------------------<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">_______________________________________________<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">fieldtrip mailing list<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">End of fieldtrip Digest, Vol 34, Issue 28<br></blockquote></blockquote><blockquote type="cite"><blockquote 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"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Jan-Mathijs Schoffelen, MD PhD </div><div><br></div><div>Donders Institute for Brain, Cognition and Behaviour, <br>Centre for Cognitive Neuroimaging,<br>Radboud University Nijmegen, The Netherlands</div><div><br></div><div>Max Planck Institute for Psycholinguistics,</div><div>Nijmegen, The Netherlands</div><div><br></div><div><a href="mailto:J.Schoffelen@donders.ru.nl">J.Schoffelen@donders.ru.nl</a></div><div>Telephone: +31-24-3614793</div><div><br></div><div><a href="http://www.hettaligebrein.nl">http://www.hettaligebrein.nl</a></div></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span></span>
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