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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Hi Roey,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Since you do not have the subject’s anatomical MRI and are using the colin27 standard brain, you can just use the template BEM headmodel in fieldtrip/template/headmodel (see for example, <a href="http://fieldtrip.fcdonders.nl/template/headmodel">http://fieldtrip.fcdonders.nl/template/headmodel</a>) . This head model is based on the colin27 brain.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Best,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Jim<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> fieldtrip-bounces@science.ru.nl [mailto:fieldtrip-bounces@science.ru.nl] <b>On Behalf Of </b>Roey Schurr<br><b>Sent:</b> donderdag 24 juli 2014 20:50<br><b>To:</b> FieldTrip discussion list<br><b>Subject:</b> Re: [FieldTrip] MNE Source Reconstruction Sanity Check<o:p></o:p></span></p></div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>Dear Jim,<o:p></o:p></p><div><p class=MsoNormal>Thank you for drawing my attention to this problem. I have actually tried building a realistic head model using OPENMEG but encountered some compitability problems since our lab does not use Linux. This is indeed one of the most important (short) future tasks - being able to use such realistic head models.<o:p></o:p></p></div><div><p class=MsoNormal>Best,<o:p></o:p></p></div><div><p class=MsoNormal>roey<o:p></o:p></p></div></div><div><p class=MsoNormal style='margin-bottom:12.0pt'><o:p> </o:p></p><div><p class=MsoNormal>On Thu, Jul 24, 2014 at 6:34 PM, E688205 <<a href="mailto:j.herring@fcdonders.ru.nl" target="_blank">j.herring@fcdonders.ru.nl</a>> wrote:<o:p></o:p></p><div><div><div><p class=MsoNormal>Dear Roey,<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>To add to Diego's comments, since you are dealing with EEG data a single sphere headmodel is not a good idea because it does not take into account the differences in conductivity between the skull, scalp, and brain. This is not a problem for MEG but is important for EEG. Therefore it is better to use, for example, a BEM head model. <o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Best,<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Jim<o:p></o:p></p></div><div><div><div><p class=MsoNormal style='margin-bottom:12.0pt'><br>On 23 jul. 2014, at 16:38, "Lozano Soldevilla, D. (Diego)" <<a href="mailto:d.lozanosoldevilla@fcdonders.ru.nl" target="_blank">d.lozanosoldevilla@fcdonders.ru.nl</a>> wrote:<o:p></o:p></p></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><div><div><div><p class=MsoNormal><span style='color:black'>Dear Roey,<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='color:black'>In my opinion it's definitely not a good idea to compute MNE using 19 sensors. There are studies that have found a drastic localization precision from 31 to 63 electrodes and further improvements till 123:<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='color:black'><o:p> </o:p></span></p></div><p class=MsoNormal><span style='color:black'><a href="http://www.ncbi.nlm.nih.gov/pubmed/15351361" target="_blank">http://www.ncbi.nlm.nih.gov/pubmed/15351361</a> (see figure 1)<br><a href="http://www.ncbi.nlm.nih.gov/pubmed/12495765" target="_blank">http://www.ncbi.nlm.nih.gov/pubmed/12495765</a><o:p></o:p></span></p><div><p class=MsoNormal><span style='color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='color:black'>Although it's very difficult to know the "minimum" number of electrodes needed to accurately localize a given source (it depends on the strength of the source you want to localize, source reconstruction algorithm, data noise...), 19 electrodes are too low to trust the results you can get. <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='color:black'>best,<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='color:black'>Diego<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='color:black'><o:p> </o:p></span></p></div></div><div><p class=MsoNormal><span style='color:black'><o:p> </o:p></span></p><div class=MsoNormal align=center style='text-align:center'><span style='color:black'><hr size=2 width="100%" noshade style='color:black' align=center></span></div><pre style='word-wrap:break-word;white-space:pre-wrap'><span style='font-family:"Times New Roman","serif";color:black'><o:p> </o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>From roeysc at <a href="http://gmail.com" target="_blank">gmail.com</a> Mon Jul 21 11:21:32 2014<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>From: roeysc at <a href="http://gmail.com" target="_blank">gmail.com</a> (Roey Schurr)<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>Date: Mon, 21 Jul 2014 12:21:32 +0300<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>Subject: [FieldTrip] MNE Source Reconstruction Sanity Check<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>Message-ID: <<a href="mailto:CAHm4wZBRYo4fV63EL9yXaAQ_W43cHF_8J2b+rNyzd55x4aRviw@mail.gmail.com" target="_blank">CAHm4wZBRYo4fV63EL9yXaAQ_W43cHF_8J2b+rNyzd55x4aRviw@mail.gmail.com</a>><o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'><o:p> </o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>Dear fieldtrippers,<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'><o:p> </o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'><o:p> </o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'><o:p> </o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>I want to do a sanity check on mne source reconstruction.<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'><o:p> </o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>I'm working on continuous EEG recordings (19 electrodes), estimating the<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>source reconstruction activity using the *mne* (minimum norm estimate)<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>method, a *template MRI* (Colin27) and a *singlesphere* headmodel. As a<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>sanity check for the source reconstruction itself, I wanted to compare<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>conditions in which I could estimate the loci of significant changes, e.g.:<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>rest vs movement of the hand, moving the right hand vs the left hand, etc.<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>I have about 60 seconds of recording for each condition.<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'><o:p> </o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'><o:p> </o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'><o:p> </o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>What I did was:<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'><o:p> </o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>1) Segment the recording of each condition into many "trials" of 2 seconds<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>each.<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'><o:p> </o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>2) For each trial, average the activity in each of the 90 ROIs of the aal<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>atlas (I excluded the cerebellum from the source reconstruction).<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'><o:p> </o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'><o:p> </o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'><o:p> </o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>I was wondering what comparison would be best in this case. Since this is<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>not Evoked Responses data, I find it hard to find relevant ideas, and would<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>like to hear your thoughts.<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'><o:p> </o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'><o:p> </o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'><o:p> </o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>1) I did a frequency analysis (mtmfft) in conventional bands of interest<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>and ran ft_freqstatistics on the resulting structures (using ttest2 and the<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>bonferoni correction for the multiple comparison problem). This gave some<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>results, however for most conditions they are not very encouraging (the<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>ROIs that showed significant differences were not close to those that I<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>have assumed).<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'><o:p> </o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'><o:p> </o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'><o:p> </o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>*QUESTION 1*: do you think this is a proper method? Note that I did not use<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>a frequency based source reconstruction in the first place, because I'm<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>ultimately interested in the time course in the source space.<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'><o:p> </o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'><o:p> </o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'><o:p> </o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>2) I was wondering if a cluster based permutation test is impossible to use<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>here, since this is a continuous recording, so clustering according to time<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>adjacency seems irrelevant.<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'><o:p> </o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'><o:p> </o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'><o:p> </o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>*QUESTION 2*: is it possible to use a cluster based statistical test here?<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>If so, it could be better than a-priori averaging the source activity in<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>the atlas ROIs, which could mask some of the effects, if they are located<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>in a small area.<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'><o:p> </o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'><o:p> </o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'><o:p> </o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>3) Another possibility is looking at the data itself. Unfortunately I<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>encountered some problems using ft_sourcemovie, though this is a subject<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>for a different thread.<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'><o:p> </o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'><o:p> </o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'><o:p> </o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>Any thoughts and advice are highly appreciated!<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'><o:p> </o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>Thank you for taking the time,<o:p></o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'><o:p> </o:p></span></pre><pre><span style='font-family:"Times New Roman","serif";color:black'>roey<o:p></o:p></span></pre></div></div></div></blockquote></div></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><p class=MsoNormal>_______________________________________________<o:p></o:p></p><div><p class=MsoNormal><br>fieldtrip mailing list<br><a href="mailto:fieldtrip@donders.ru.nl" target="_blank">fieldtrip@donders.ru.nl</a><br><a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip" target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><o:p></o:p></p></div></div></blockquote></div></div><p class=MsoNormal><br>_______________________________________________<br>fieldtrip mailing list<br><a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br><a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip" target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><o:p></o:p></p></div><p class=MsoNormal><o:p> </o:p></p></div></div></body></html>