<div dir="ltr">Dear Tzvetan<div><br></div><div>I get your point. I am only using that gradiometers. However, in the text which i copied into the previous email it is stated that ft_combineplanar is used for '<span style="color:rgb(0,0,0);font-family:Calibri,Geneva,Arial,Verdana,sans-serif;font-size:15px;line-height:22.5px;text-align:justify">plotting the two different gradiometers together'. They mention gradiometers specifically. Also when running the code it is clear that the gradiometers not the magnetometers are combined. This is the resulting matrix when running the tutorial :</span></div><div><span style="color:rgb(0,0,0);font-family:Calibri,Geneva,Arial,Verdana,sans-serif;font-size:15px;line-height:22.5px;text-align:justify"><img src="cid:ii_152559cdd686e8b2" alt="Inline-Bild 1" width="472" height="380" style="margin-right: 0px;"><br></span></div><div><span style="color:rgb(0,0,0);font-family:Calibri,Geneva,Arial,Verdana,sans-serif;font-size:15px;line-height:22.5px;text-align:justify"><br></span></div><div style="text-align:justify"><font color="#000000" face="Calibri, Geneva, Arial, Verdana, sans-serif"><span style="font-size:15px;line-height:22.5px">With this in mind, can you clarify why the toturial only uses magnetometers? As i understand it , it uses gradiometers. </span></font></div><div style="text-align:justify"><font color="#000000" face="Calibri, Geneva, Arial, Verdana, sans-serif"><span style="font-size:15px;line-height:22.5px"><br></span></font></div><div style="text-align:justify"><font color="#000000" face="Calibri, Geneva, Arial, Verdana, sans-serif"><span style="font-size:15px;line-height:22.5px">Thank you a lot</span></font></div><div style="text-align:justify"><font color="#000000" face="Calibri, Geneva, Arial, Verdana, sans-serif"><span style="font-size:15px;line-height:22.5px">Victoria</span></font></div><div><br></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">2016-01-18 12:59 GMT+00:00 Tzvetan Popov <span dir="ltr"><<a href="mailto:tzvetan.popov@uni-konstanz.de" target="_blank">tzvetan.popov@uni-konstanz.de</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hi Victoria,<div>well if you work with the magnetometers yes. Maybe I misunderstood your previous posts. Yet this configuration from your post below cfg.channel = 'MEGGRAD’; results in time-frequency representation of power on the planar gradiometers only. In that case neither ft_megplanar nor ft_combineplanar are appropriate since the data stems from planar gradiometers. The tutorial you mentioned deals only with the magnetometers thus ft_megplanar and ft_combineplanar are used.</div><div><br></div><div>best</div><span class="HOEnZb"><font color="#888888"><div>tzvetan</div></font></span><div><div class="h5"><div> <div><blockquote type="cite"><div dir="ltr">Dear Tzvetan<div><br></div><div>Are you sure about that in the tutorial <a href="http://www.fieldtriptoolbox.org/tutorial/natmeg/preprocessing" target="_blank">http://www.fieldtriptoolbox.org/tutorial/natmeg/preprocessing</a> neuromag data is used and ft_combineplanar is used to combine the gradiometers. This is a paragraph from this tutorial:</div><div><br></div><div><p style="padding:0px;margin:0px 0px 1em;font-size:15px;line-height:22.5px;font-family:Calibri,Geneva,Arial,Verdana,sans-serif;text-align:justify">In fact, we are now plotting the two different gradiometers together. You can see the channel locations being in pairs, one above the other. They are in reality, however, at the same location but oriented differently - radially and axially <em style="padding:0px;margin:0px">with respect to the surface of the helmet</em>. They can thereby pick up both radial orientations of the magnetic fields. To use them properly for the purpose of plotting, we should therefor combine them first, adding their fields.</p><pre style="padding:0.5em;margin-top:0px;margin-bottom:1em;font-size:12px;border:1px dashed rgb(204,204,204);overflow:hidden;font-family:Consolas,'Andale Mono',Menlo,Monaco,monospace;white-space:pre-wrap;width:640px;text-align:justify;background-color:rgb(247,249,250)">TFR_left_MEG_comb = ft_combineplanar<span style="padding:0px;margin:0px;color:rgb(102,204,102)">(</span><span style="padding:0px;margin:0px;color:rgb(102,204,102)">[</span><span style="padding:0px;margin:0px;color:rgb(102,204,102)">]</span>,TFR_left_MEG<span style="padding:0px;margin:0px;color:rgb(102,204,102)">)</span>;
TFR_right_MEG_comb = ft_combineplanar<span style="padding:0px;margin:0px;color:rgb(102,204,102)">(</span><span style="padding:0px;margin:0px;color:rgb(102,204,102)">[</span><span style="padding:0px;margin:0px;color:rgb(102,204,102)">]</span>,TFR_right_MEG<span style="padding:0px;margin:0px;color:rgb(102,204,102)">)</span>;
cfg = <span style="padding:0px;margin:0px;color:rgb(102,204,102)">[</span><span style="padding:0px;margin:0px;color:rgb(102,204,102)">]</span>;
cfg.<span style="padding:0px;margin:0px;color:rgb(0,102,0)">baseline</span> = <span style="padding:0px;margin:0px;color:rgb(102,204,102)">[</span>-<span style="padding:0px;margin:0px;color:rgb(204,102,204)">0.5</span> -<span style="padding:0px;margin:0px;color:rgb(204,102,204)">0.1</span><span style="padding:0px;margin:0px;color:rgb(102,204,102)">]</span>;
cfg.<span style="padding:0px;margin:0px;color:rgb(0,102,0)">baselinetype</span> = <span style="padding:0px;margin:0px;color:rgb(128,128,128);font-style:italic">'absolute'</span>;
cfg.<a href="http://www.mathworks.com/access/helpdesk/help/techdoc/ref/xlim.html" title="" style="padding:0px;margin:0px;color:rgb(0,136,204);text-decoration:none" target="_blank"><span style="padding:0px;margin:0px;font-weight:bold">xlim</span></a> = <span style="padding:0px;margin:0px;color:rgb(102,204,102)">[</span><span style="padding:0px;margin:0px;color:rgb(204,102,204)">0.4</span> <span style="padding:0px;margin:0px;color:rgb(204,102,204)">0.8</span><span style="padding:0px;margin:0px;color:rgb(102,204,102)">]</span>;
cfg.<a href="http://www.mathworks.com/access/helpdesk/help/techdoc/ref/ylim.html" title="" style="padding:0px;margin:0px;color:rgb(0,136,204);text-decoration:none" target="_blank"><span style="padding:0px;margin:0px;font-weight:bold">ylim</span></a> = <span style="padding:0px;margin:0px;color:rgb(102,204,102)">[</span><span style="padding:0px;margin:0px;color:rgb(204,102,204)">15</span> <span style="padding:0px;margin:0px;color:rgb(204,102,204)">25</span><span style="padding:0px;margin:0px;color:rgb(102,204,102)">]</span>;
cfg.<a href="http://www.mathworks.com/access/helpdesk/help/techdoc/ref/zlim.html" title="" style="padding:0px;margin:0px;color:rgb(0,136,204);text-decoration:none" target="_blank"><span style="padding:0px;margin:0px;font-weight:bold">zlim</span></a> = <span style="padding:0px;margin:0px;color:rgb(102,204,102)">[</span>-4e-24 4e-24<span style="padding:0px;margin:0px;color:rgb(102,204,102)">]</span>;
cfg.<span style="padding:0px;margin:0px;color:rgb(0,102,0)">marker</span> = <span style="padding:0px;margin:0px;color:rgb(128,128,128);font-style:italic">'on'</span>;
cfg.<span style="padding:0px;margin:0px;color:rgb(0,102,0)">layout</span> = <span style="padding:0px;margin:0px;color:rgb(128,128,128);font-style:italic">'neuromag306cmb.lay'</span>;
<a href="http://www.mathworks.com/access/helpdesk/help/techdoc/ref/figure.html" title="" style="padding:0px;margin:0px;color:rgb(0,136,204);text-decoration:none" target="_blank"><span style="padding:0px;margin:0px;font-weight:bold">figure</span></a>;
ft_topoplotTFR<span style="padding:0px;margin:0px;color:rgb(102,204,102)">(</span>cfg, TFR_left_MEG_comb<span style="padding:0px;margin:0px;color:rgb(102,204,102)">)</span>;
<a href="http://www.mathworks.com/access/helpdesk/help/techdoc/ref/print.html" title="" style="padding:0px;margin:0px;color:rgb(0,136,204);text-decoration:none" target="_blank"><span style="padding:0px;margin:0px;font-weight:bold">print</span></a> -dpng natmeg_freq13.<span style="padding:0px;margin:0px;color:rgb(0,102,0)">png</span></pre></div><div>Thus, it should be possible to use ft_combineplanar for neuromag data.</div><div>What do you think?</div><div><br></div><div>Cheers</div><div>Victoria</div></div><div class="gmail_extra"><br><div class="gmail_quote">2016-01-16 18:00 GMT+00:00 Tzvetan Popov <span dir="ltr"><<a href="mailto:tzvetan.popov@uni-konstanz.de" target="_blank">tzvetan.popov@uni-konstanz.de</a>></span>:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div style="word-wrap:break-word"><div>Dear Victoria,</div><div>you should remove the ft_combineplanar step from your analysis pipeline. This function takes input from ft_megplanar. The latter is applied only to magnetometers or axial gradiometers. </div><div><br></div><div>best</div><div>tzvetan</div><div> <br><br><blockquote type="cite"><div><div><div dir="ltr"><div>Hi !</div><div><br></div><div>I am working with a neuromag system and want to do cluster based permutation tests with time frequency data. However, before running the stats i would like to check the clusters which are formed by ft_prepare_neighbours. Thus i use ft_neighbourplot. When looking at the plot and clicking on the channels i would expect to see something like :</div><div><i><br></i></div><div><div><i>Selected channel MEG1032+1033, which has 7 neighbours: MEG0622+0623, MEG1012+1013, MEG1022+1023, MEG1042+1043, MEG1112+1113, MEG1122+1123, MEG1242+1243</i></div><div><i>Selected channel MEG0742+0743, which has 7 neighbours: MEG0432+0433, MEG0712+0713, MEG0722+0723, MEG0732+0733, MEG1822+1823, MEG1832+1833, MEG2242+2243<br></i></div></div><div><br></div><div>however what i see is:</div><div><br></div><div><div><i>Selected channel MEG0741, which has 0 neighbours: </i></div><div><i>Selected channel MEG0731, which has 0 neighbours: </i></div><div><i>Selected channel MEG0742+0743, which has 7 neighbours: MEG0432+0433, MEG0712+0713, MEG0722+0723, MEG0732+0733, MEG1822+1823, MEG1832+1833, MEG2242+2243</i></div><div><i>Selected channel MEG0711, which has 0 neighbours: </i></div><div><i>Selected channel MEG0741, which has 0 neighbours: </i></div></div><div><br></div><div>It is absolutely random when the correct output occurs. When clicking on a particular channel it would randomly show me the following results:</div><div><br></div><div><div><i>Selected channel MEG1032+1033, which has 7 neighbours: MEG0622+0623, MEG1012+1013, MEG1022+1023, MEG1042+1043, MEG1112+1113, MEG1122+1123, MEG1242+1243</i></div><div><br></div><div>or</div><div><br></div><div><i>Selected channel MEG1031, which has 0 neighbours: </i></div></div><div><br></div><div>Do you have any suggestions why this happen? Are the channels not grouped correctly?</div><div><br></div><div>Below is the code starting from the time-frequency analysis of the data.</div><div><br></div><div>Thank you very much</div><div>Victoria</div><div><br></div><div>cfg = [];</div><div>cfg.output = 'pow';</div><div>cfg.channel = 'MEGGRAD';</div><div>cfg.method = 'mtmconvol';</div><div>cfg.taper = 'hanning';</div><div>cfg.foi = [2:2:30];</div><div>%cfg.keeptrials = 'yes'; for stats keep trials</div><div>cfg.t_ftimwin = ones(length(cfg.foi),1).*0.5; % length of time window = 0.5 sec</div><div>cfg.toi = [-1.3:0.05:1]; </div><div>cfg.keeptrials = 'yes';</div><div>FreqCon = ft_freqanalysis(cfg, Con_clean);</div><div>FreqIncon = ft_freqanalysis(cfg, Incon_clean);</div><div><br></div><div>%combine planar</div><div>cfg = [];</div><div>cfg.method ='sum';</div><div>ComCon = ft_combineplanar(cfg,FreqCon);</div><div>ComIncon = ft_combineplanar(cfg, FreqIncon);</div><div><br></div><div><div>% plot neighbours</div><div>cfg=[];</div><div>cfg.method = 'triangulation';</div><div>cfg.layout = 'neuromag306cmb.lay';</div><div>ft_neighbourplot(cfg,ComCon)</div></div></div></div></div>
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