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<p style="margin-top:0; margin-bottom:0">Dear Vladimir and Fieldtrip community,</p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">Apologies for my last long (and complicated) email.</p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">As it looks like for beamforming, contrasting the sources of the post-stimulus interval with a baseline is more reliable than applying the Neural Activity Index, I would like to ask some more specific questions on that:</p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0"></p>
<ol style="margin-bottom:0px; margin-top:0px">
<li>To compare two groups of participants, do I input in the <b>sourcestatistics</b> the source analysis contrast for each subject, i.e. the (sourcePost-sourcePre) ./sourcePre?</li><li>To <b>plot</b> the sources for each group, do I plot the grandaverage of the source analysis contrast, separately for each group?</li><li>During <b>preprocessing </b>of the data which are going to be used to calculate the cross-spectral density, am I supposed to do baseline subtraction as usual? (I assume yes?)</li><li>For the sourceanalysis, is it ok if the <b><span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px">post-stimulus interval is longer
than the </span>baseline</b> (e.g., 200ms and 800ms, respectively)?</li><li>I tried to plot the source contrast between post stimulus vs. baseline <b>averaged over participants</b>, but it seems there's something wrong [SEE FIGURE ATTACHED]. This is what I did:</li></ol>
<span style="font-size:12pt">% Freqanalysis using both baseline and post stimulus data:</span><br>
<div> cfg = [];</div>
<div> cfg.method = 'mtmfft';</div>
<div> cfg.output = 'powandcsd';</div>
<div> cfg.foilim = [22 22];</div>
<div> cfg.taper = 'dpss';</div>
<div> cfg.tapsmofrq = 4;</div>
<div> cfg.keeptrials = 'no';</div>
<div> cfg.keeptapers = 'no';</div>
<div> freqAll = ft_freqanalysis(cfg, dataAll);</div>
<div><br>
</div>
<div>% Beamforming:</div>
<div>
<div> cfg = [];</div>
<div> cfg.headmodel = vol1;</div>
<div> cfg.grad = sens1_aligned;</div>
<div> cfg.senstype = 'eeg';</div>
<div> cfg.grid = grid;</div>
<div> cfg.method = 'dics';</div>
<div><span style="font-size:12pt"> cfg.frequency = 22;</span></div>
<div> cfg.dics.projectnoise = 'yes';</div>
<div> cfg.dics.lambda = '5%';</div>
<div> cfg.dics.keepfilter = 'yes';</div>
<div> cfg.dics.realfilter = 'yes';</div>
<div> sourceAll = ft_sourceanalysis(cfg, freqAll);</div>
<div><span style="font-size:12pt"><br>
</span></div>
<div><span style="font-size:12pt">% place pre-computed filter in cfg to apply to each condition separately</span><br>
</div>
<div> cfg.sourcemodel.filter = sourceAll.avg.filter;</div>
<div> sourceBase_con = ft_sourceanalysis(cfg, freqBase);</div>
<div> sourcePost_con = ft_sourceanalysis(cfg, freqPost);</div>
<div><br>
</div>
<div>% contrast</div>
<div></div>
<div> sourceDiff(1,part_i) = sourcePost_con;</div>
<div> sourceDiff(1,part_i).avg.pow = (sourcePost_con.avg.pow - sourceBase_con.avg.pow) ./ sourceBase_con.avg.pow;</div>
<div><br>
</div>
<div>Then, I calculated the grand average of the sourceDiff for all participants, did sourceinterpolate and volumenormalise and plotted the result. Do you have any idea what I did wrong?</div>
<div><br>
</div>
<div>Thanks so much for all your help, looking forward to hearing your experienced insights! :) </div>
<div><br>
</div>
<div>Best wishes,</div>
<div>Ioanna</div>
<div><br>
</div>
</div>
<br>
<p></p>
</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> fieldtrip <fieldtrip-bounces@science.ru.nl> on behalf of Ioanna Zioga <i.zioga@qmul.ac.uk><br>
<b>Sent:</b> 05 May 2019 02:53:30<br>
<b>To:</b> Vladimir Litvak<br>
<b>Cc:</b> FieldTrip discussion list; M.vanEs@donders.ru.nl<br>
<b>Subject:</b> Re: [FieldTrip] beamforming pipeline & comparing sources between groups of participants?</font>
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<p style="margin-top:0; margin-bottom:0">Dear Vladimir,</p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">Thank you so much for your valuable comments!</p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">I input an inwardshift of 5 and the pixels are gone - the plots look pretty
<span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px">
now, yayy </span>:D</p>
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</p>
<p style="margin-top:0; margin-bottom:0">As I want to compare two groups of participants, I'm working on getting the source grand averages. </p>
<p style="margin-top:0; margin-bottom:0">A few remaining issues mainly on the order of the steps to follow:</p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">1) Option 1:</p>
<p style="margin-top:0; margin-bottom:0"></p>
<ol style="margin-bottom:0px; margin-top:0px">
<li>Calculate <span style="font-size:12pt">the individual sources</span></li><li><span style="font-size:12pt"><i>Interpolate </i>the individual sources</span></li><li><span style="font-size:12pt"><i>Do </i><i>volume normalization</i> on the individual sources</span></li><li><span style="font-size:12pt">Calculate the <b>grand average sources </b>separately for the two groups</span></li></ol>
<span style="font-size:12pt">
<p style="margin-top:0; margin-bottom:0"><span style="font-size:12pt"><br>
</span></p>
Option 2 (less time and memory demanding):</span>
<p></p>
<p style="margin-top:0; margin-bottom:0"></p>
<ol style="margin-bottom:0px; margin-top:0px">
<li>Cal<span style="font-size:12pt">culate <span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px">
the individual sources</span></span></li><li><span style="font-size:12pt"><span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px"></span>Calculate the
<b>grand average sources </b>separately for the two groups</span></li><li><span style="font-size:12pt"><i>Interpolate </i>the two grand average sources</span></li><li><span style="font-size:12pt"><i>Do </i><i>volume normalization</i> on the two grand average sources</span><br>
</li></ol>
<br>
<p></p>
<p style="margin-top:0; margin-bottom:0">2) Please find attached the plots I get from option 2. Does it look ok that the sources are quite spread out (mostly central and posterior areas)? It is delta band activity (2.5-3.5 Hz) in response to acoustic tones
(notes), so I expected something more focal, and especially temporal.</p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">3) For normalization in the calculation of the individual sources, I used the Neural Activity Index, as normalizing with the baseline interval showed no sources at all in quite a few participants. I was quite surprised
to see that. As participants were listerning to whole melodies (sequences of notes), and here I analyze the sources in response to the last note only, is it possible that the sources are contaminated because they use the same ones throughout the whole melody,
so they cancel out?</p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">Looking forward to your insights. As always, any comment/suggestion is more than welcome! </p>
<p style="margin-top:0; margin-bottom:0">I truly appreciate your time and help, it's been a great learning experience.</p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">Best,</p>
<p style="margin-top:0; margin-bottom:0">Ioanna</p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0"></p>
<p style="font-family:Calibri,Helvetica,sans-serif; font-size:16px"><span style="font-family:Helvetica,serif,EmojiFont; font-size:12px">---</span><br class="" style="font-family:Helvetica,serif,EmojiFont; font-size:12px">
<span style="font-family:Helvetica,serif,EmojiFont; font-size:12px">Ioanna Zioga</span></p>
<p style="font-family:Calibri,Helvetica,sans-serif; font-size:16px"><span style="font-family:Helvetica,serif,EmojiFont; font-size:12px"><span style="background-color:rgb(255,238,148)"></span>PhD student</span></p>
<p style="font-family:Calibri,Helvetica,sans-serif; font-size:16px"><span style="font-family:Helvetica,serif,EmojiFont; font-size:12px">School of Biological and Chemical Sciences</span></p>
<p style="font-family:Calibri,Helvetica,sans-serif; font-size:16px"><span style="font-family:Helvetica,serif,EmojiFont; font-size:12px">Queen Mary University of London</span><br>
</p>
<p style="font-family:Calibri,Helvetica,sans-serif; font-size:16px"><span style="font-family:Helvetica,serif,EmojiFont; font-size:12px"><a href="https://www.researchgate.net/profile/Ioanna_Zioga4" class="x_OWAAutoLink" id="LPlnk851471" previewremoved="true">https://www.researchgate.net/profile/Ioanna_Zioga4</a></span><br>
</p>
<p style="font-family:Calibri,Helvetica,sans-serif; font-size:16px"><span style="font-family:Helvetica,serif,EmojiFont; font-size:12px"><a href="https://www.researchgate.net/profile/Ioanna_Zioga4" class="x_OWAAutoLink" id="LPlnk972235" previewremoved="true"></a></span><a href="https://scholar.google.gr/citations?user=yPmCqmQAAAAJ&hl=en" class="x_OWAAutoLink" id="LPlnk408095" style="font-family:Arial,Helvetica,sans-serif; font-size:9pt" previewremoved="true">https://scholar.google.gr/citations?user=yPmCqmQAAAAJ&hl=en</a></p>
<p></p>
</div>
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<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Vladimir Litvak <litvak.vladimir@gmail.com><br>
<b>Sent:</b> 04 May 2019 14:57:06<br>
<b>To:</b> Ioanna Zioga<br>
<b>Cc:</b> FieldTrip discussion list; M.vanEs@donders.ru.nl<br>
<b>Subject:</b> Re: [FieldTrip] beamforming pipeline & comparing sources between groups of participants?</font>
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<div dir="ltr">Dear Ioanna,</div>
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</div>
<div dir="ltr">Indeed you are now closer to something sensible than before.</div>
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1) Does anyone have any idea why do the plots look so digitized? I used cfg.grid.resolution = 7 (units are mm). Is there any chance there is an incompatibility between my headmodel and the MRI template?</div>
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</div>
<div>Those pixels are the points of BEM failure. You used negative inwardshift which expands the grid rather than shrinks it. Make it positive and play with the value until those pixels are gone.</div>
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<span style="font-size:11pt">2) Is one contrasting method enough, i.e.: If I contrast the sources in the post-stimulus time window compared to a baseline, do I also need to do cfg.normalize in the calculation of the leadfield or calculate the Neural Activity
Index?</span><br>
</div>
</div>
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<div><br>
</div>
<div>If you want to get a single image that will look informative you can do those things. But if you want to do stats you should get raw images with depth bias and compare them statistically and then something sensible should come out in the statistical results
if you’ve done everything correctly.</div>
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<span style="font-size:11pt"><span style="font-family:sans-serif; font-size:14.6667px">3) Is it ok to compute the volume condution model in SPM, </span><span style="font-family:sans-serif; font-size:14.6667px">then use that to calculate the leadfield in fieldtrip,
and </span><span style="font-family:sans-serif; font-size:14.6667px">then </span><span style="font-family:sans-serif; font-size:14.6667px">use</span><span style="font-family:sans-serif; font-size:14.6667px"> a template MRI to just </span><span style="font-family:sans-serif; font-size:14.6667px">do
the visualization of the sources (see pipeline below)?</span><br>
</span></div>
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<div><br>
</div>
<div>It should be OK if the coordinate systems are handled correctly.</div>
<div>If you keep everything in MNI-aligned coordinates in mm the output should match the template image.</div>
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4) <span style="font-family:sans-serif; font-size:14.6667px">Do I need to do cfg.reducerank when calculating the leadfield</span><span style="font-family:sans-serif; font-size:14.6667px">?</span></div>
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<div><br>
</div>
No, for EEG you don’t. I’m not sure what the default is but you can set it to 3.
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Here I'm adding my code, in case anyone could have a look and spot any mistakes/make suggestions! That would be extremely helpful.</div>
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<div>In principle it shouldn’t be necessary to do additional alignment in FT if you’ve already coregistered your volume and sensors in SPM and your grid was generated based on that same vol.</div>
<div><br>
</div>
<div>Best,</div>
<div><br>
</div>
<div>Vladimir </div>
<div><br>
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Maybe it can also be of help to people who want to do the same analysis in the future.</div>
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After using SPM to create a volume conduction model in SPM, <span style="font-size:11pt">I moved to fieldtrip:</span></div>
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<span style="font-size:11pt"><br>
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<div>% Convert volume conduction model and electrodes from SPM</div>
<div>volsens = spm_eeg_inv_get_vol_sens(D, 1, 'MNI-aligned', 'inv', 'EEG');</div>
<div>vol1 = volsens.EEG.vol;</div>
<div>sens1 = volsens.EEG.sens;</div>
<div><br>
</div>
<div>% Calculate the cross-spectral density matrix of my EEG data, EEGft (after re-referencing to common average)</div>
<div>cfg = [];</div>
<div>cfg.method = 'mtmfft';</div>
<div>cfg.output = 'powandcsd';</div>
<div>cfg.foilim = [22 22];</div>
<div>cfg.taper = 'dpss';</div>
<div>cfg.tapsmofrq = 10;</div>
<div>cfg.keeptrials = 'no';</div>
<div>cfg.keeptapers = 'no';</div>
<div>cfg.toi = 0.6;</div>
<div>cfg.t_ftimwin = 0.4;</div>
<div>freq = ft_freqanalysis(cfg, EEGft);</div>
<div><br>
</div>
<div>% Convert all units to mm</div>
<div>sens1 = ft_convert_units(sens1, 'mm');</div>
<div>vol1 = ft_convert_units(vol1, 'mm');</div>
<div><br>
</div>
<div>% Plot brain, skull, and scalp [SEE FIGURE VOL_COND_MODEL ATTACHED]</div>
<div>figure; ft_plot_mesh(vol1.bnd(1), 'facecolor',[0.4 0.6 0.4], 'facealpha', 0.9, 'edgecolor', [1 1 1], 'edgealpha', 0.05); rotate3d on</div>
<div>hold on; ft_plot_mesh(vol1.bnd(2),'edgecolor','none','facealpha',0.4);</div>
<div>hold on; ft_plot_mesh(vol1.bnd(3),'edgecolor','none','facecolor',[0.2 0.2 0.2],'facealpha',0.3);</div>
<div><br>
</div>
<div>% Interactively aligned electrodes to head surface</div>
<div>cfg = [];</div>
<div>cfg.method = 'interactive';</div>
<div>cfg.elec = sens1;</div>
<div>cfg.headshape = vol1.bnd(3); % scalp</div>
<div>sens1_aligned = ft_electroderealign(cfg);</div>
<div><br>
</div>
<div>% plot scalp & sensors [SEE FIGURE ELEC_ALIGN ATTACHED]</div>
<div>figure; ft_plot_mesh(vol1.bnd,'edgecolor','none','facealpha',0.8,'facecolor',[0.6 0.6 0.8])</div>
<div>hold on; ft_plot_sens(sens1_aligned,'elecsize',30);</div>
<div>alpha 0.7; <span style="font-size:11pt">rotate3d on</span></div>
<div><br>
</div>
<div>% Calculate leadfield</div>
<div>
<div>cfg = [];</div>
<div>cfg.grid.resolution = 7;</div>
<div>cfg.inwardshift = -7;</div>
<div><span style="font-size:11pt">cfg.unit = 'mm';</span><br>
</div>
<div>cfg.headmodel = vol1;</div>
<div>cfg.grad = sens1_aligned;</div>
<div>cfg.elec = sens1_aligned;</div>
<div>cfg.senstype = 'eeg';</div>
<div></div>
<div>grid = ft_prepare_leadfield(cfg, freq);</div>
<div><br>
</div>
<div>% plot leadfield and headmodel [SEE FIGURE LEADFIELD ATTACHED]</div>
<div>figure; hold on; ft_plot_mesh(grid.pos(grid.inside,:));</div>
<div>hold on; ft_plot_mesh(vol1.bnd(1));</div>
<div><br>
</div>
<div>% Beamforming</div>
<div>cfg = [];</div>
<div>cfg.headmodel = vol1;</div>
<div>cfg.grad = sens1_aligned;</div>
<div>cfg.senstype = 'eeg';</div>
<div>cfg.grid = grid;</div>
<div>cfg.method = 'dics';</div>
<div>cfg.frequency = [22 22];</div>
<div>cfg.dics.projectnoise = 'yes';</div>
<div>cfg.dics.lambda = '5%';</div>
<div>cfg.dics.keepfilter = 'yes';</div>
<div>cfg.dics.realfilter = 'yes';</div>
<div>sourceA = ft_sourceanalysis(cfg, freq);</div>
<div><br>
</div>
% Plot results on an MRI template</div>
<div>
<div>load standard_mri;</div>
<div></div>
<div><br>
</div>
% Interpolated sourceA to MRI</div>
<div>
<div>cfg = [];</div>
<div>cfg.parameter = 'pow';</div>
<div>sourceAint = ft_sourceinterpolate(cfg, sourceA, mri);</div>
<div><br>
</div>
<div>% Plot source [SEE FIGURE SOURCEANALYSIS ATTACHED]</div>
<div>cfg = [];</div>
<div>cfg.method = 'slice';</div>
<div>cfg.funparameter = 'pow';</div>
<div>cfg.maskparameter = cfg.funparameter;</div>
<div>cfg.funcolorlim = [0.0 2479475.3054];</div>
<div>cfg.opacitylim = [0.0 1.2];</div>
<div>cfg.opacitymap = 'rampup';</div>
<div>ft_sourceplot(cfg, sourceAint);</div>
<div><br>
</div>
</div>
<div>Please feel free to make any comments/suggestions on the above code and questions!</div>
Any insight is extremely appreciated! </div>
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<br>
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I think I'm getting there.. and luckily I'm -still- excited about it <span>😊</span></div>
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<span><br>
</span></div>
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Thank you all so much in advance, have a great weekend! <br>
<br>
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Best, <br>
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Ioanna <br>
<br>
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<div id="x_x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> fieldtrip <<a href="mailto:fieldtrip-bounces@science.ru.nl" id="LPlnk871958" class="OWAAutoLink" previewremoved="true">fieldtrip-bounces@science.ru.nl</a>>
on behalf of Es, M.W.J. van (Mats) <<a href="mailto:M.vanEs@donders.ru.nl" id="LPlnk394336" class="OWAAutoLink" previewremoved="true">M.vanEs@donders.ru.nl</a>><br>
<b>Sent:</b> Thursday, May 2, 2019 11:03:39 AM<br>
<b>To:</b> FieldTrip discussion list<br>
<b>Subject:</b> Re: [FieldTrip] beamforming pipeline & comparing sources between groups of participants?</font>
<div> </div>
</div>
<div>
<div class="x_x_WordSection1">
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">Dear Ioanna,</span></p>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"> </span></p>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">Indeed, these types of analysis are exciting, but complex! I have some suggestions for you. They might not solve your problem per se, but at least it should give you
some insight in your analysis.</span></p>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"> </span></p>
<p style="text-indent:-18pt; margin:0cm 0cm 0.0001pt 36pt; font-size:12pt; font-family:"Times New Roman",serif">
<span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"><span style="">1)<span style="font:7.0pt "Times New Roman"">
</span></span></span><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">As Vladimir suggested, make sure your headmodel and sourcemodel align and are of the same unit. Also, it might be better to look at source contrasts
due to the center of the head bias (see </span><a href="http://www.fieldtriptoolbox.org/tutorial/beamformer/#source-analysis-without-contrasting-condition" id="LPlnk138030" class="x_x_OWAAutoLink" style="color:rgb(5,99,193); text-decoration:underline" previewremoved="true"><span lang="EN-US">http://www.fieldtriptoolbox.org/tutorial/beamformer/#source-analysis-without-contrasting-condition</span></a><span lang="EN-US">)</span><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"></span></p>
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<div id="LPTitle_15568225739410.7422404587285318" style="top:0px; color:rgb(0,120,215); font-weight:400; font-size:21px; font-family:wf_segoe-ui_light,"Segoe UI Light","Segoe WP Light","Segoe UI","Segoe WP",Tahoma,Arial,sans-serif; line-height:21px">
<a id="LPUrlAnchor_15568225739420.9398969280200229" href="http://www.fieldtriptoolbox.org/tutorial/beamformer/#source-analysis-without-contrasting-condition" target="_blank" style="text-decoration:none">Localizing oscillatory sources using beamformer techniques
- FieldTrip toolbox</a></div>
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<a href="http://www.fieldtriptoolbox.org" id="LPlnk546921" class="OWAAutoLink" previewremoved="true">www.fieldtriptoolbox.org</a></div>
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Tags: tutorial meg freq source headmodel mri plot meg-language Localizing oscillatory sources using beamformer techniques Introduction. In this tutorial we will continue working on the dataset described in the preprocessing tutorials. Below we will repeat code
to select the trials and preprocess the data as described in the first tutorials (trigger based trial selection, visual artifact ...</div>
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<br>
<p style="text-indent:-18pt; margin:0cm 0cm 0.0001pt 36pt; font-size:12pt; font-family:"Times New Roman",serif">
<span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"><span style="">-<span style="font:7.0pt "Times New Roman"">
</span></span></span><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">Your frequency analysis looks correct. Since dics sourceanalysis is done on a single frequency, you can use smoothing to still encompass an entire
frequency range. </span></p>
<p style="text-indent:-18pt; margin:0cm 0cm 0.0001pt 36pt; font-size:12pt; font-family:"Times New Roman",serif">
<span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"><span style="">-<span style="font:7.0pt "Times New Roman"">
</span></span></span><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">This means that in the sourceanalysis you don’t have to specify the [12 32] but could enter the center frequency: [22 22], since the estimate
at this frequency encompasses the entire range. </span></p>
<p style="text-indent:-18pt; margin:0cm 0cm 0.0001pt 36pt; font-size:12pt; font-family:"Times New Roman",serif">
<span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"><span style="">-<span style="font:7.0pt "Times New Roman"">
</span></span></span><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">In your sourceanalysis you don’t have to specify cfg.latency. Your frequency estimate is based on this window already. The cfg.latency option is
used when your frequency data is time-resolved (cfg.method = ‘mtmconvol’/’wavelet’ in ft_freqanalysis).</span></p>
<p style="text-indent:-18pt; margin:0cm 0cm 0.0001pt 36pt; font-size:12pt; font-family:"Times New Roman",serif">
<span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"><span style="">-<span style="font:7.0pt "Times New Roman"">
</span></span></span><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">In your frequency analysis, there’s no need to keep trial information for sourceanalysis. As default, sourceanalysis will average over trials anyway.
(trial information is only required if you use some kind of resampling procedure (like cfg.jackknife, cfg.bootstrap etc). (If you’d want to do single-trial analysis, you could multiply the spatial filter (from sourceanalysis) with channel-level single-trial
frequency estimates. )</span></p>
<p style="text-indent:-18pt; margin:0cm 0cm 0.0001pt 36pt; font-size:12pt; font-family:"Times New Roman",serif">
<span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"><span style="">2)<span style="font:7.0pt "Times New Roman"">
</span></span></span><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">Yes, you should do sourceanalysis separately for every participant.</span></p>
<p style="text-indent:-18pt; margin:0cm 0cm 0.0001pt 36pt; font-size:12pt; font-family:"Times New Roman",serif">
<span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"><span style="">3)<span style="font:7.0pt "Times New Roman"">
</span></span></span><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">Take a look at ft_sourcegrandaverage</span></p>
<p style="text-indent:-18pt; margin:0cm 0cm 0.0001pt 36pt; font-size:12pt; font-family:"Times New Roman",serif">
<span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"><span style="">4)<span style="font:7.0pt "Times New Roman"">
</span></span></span><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">Very good question, without a straightforward answer.
</span></p>
<p style="text-indent:-18pt; margin:0cm 0cm 0.0001pt 36pt; font-size:12pt; font-family:"Times New Roman",serif">
<span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"><span style="">-<span style="font:7.0pt "Times New Roman"">
</span></span></span><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">If you’ve already found a statistically significant effect at the channel level, there’s no need to do statistics at the source level anymore;
you’ve already rejected the null-hypothesis. You use source analysis only to visualize and interpret the data.</span></p>
<p style="text-indent:-18pt; margin:0cm 0cm 0.0001pt 36pt; font-size:12pt; font-family:"Times New Roman",serif">
<span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"><span style="">-<span style="font:7.0pt "Times New Roman"">
</span></span></span><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">If you think you can gain statistical sensitivity by going to the source level, you should think of some way to reduce the dimensionality of your
data. If you would statistically test power at every grid point, you will probably lose any effect when doing multiple comparison correction. For example, you might know (from the literature) that if there would be an effect, it will most likely be in a specific
ROI. Then you could choose to average power in this ROI and test this between groups.</span></p>
<p style="margin:0cm 0cm 0.0001pt 36pt; font-size:12pt; font-family:"Times New Roman",serif">
<span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">Alternatively, you could define your own ROI based on for example the induced power effect over all subjects: find out which region has the highest power increase (i.e.
from baseline) in this task in general (thus irrespective of condition). Use this region the then test differences between conditions.</span></p>
<p style="margin:0cm 0cm 0.0001pt 36pt; font-size:12pt; font-family:"Times New Roman",serif">
<span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"> </span></p>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">Hope this helps!</span></p>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"> </span></p>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">All the best,</span></p>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">Mats</span></p>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"> </span></p>
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<i><span style="font-size:10.5pt; font-family:"Arial",sans-serif; color:#333333">PhD candidate</span></i><span style="font-size:10.5pt; font-family:"Arial",sans-serif; color:#333333"></span></p>
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<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span style="font-size:10.5pt; font-family:"Arial",sans-serif; color:#333333">Dynamic Connectivity</span></p>
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<b><span lang="EN-US" style="font-size:10.5pt; font-family:"Arial",sans-serif; color:#333333">Donders Institute for Brain,
</span></b></p>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<b><span lang="EN-US" style="font-size:10.5pt; font-family:"Arial",sans-serif; color:#333333">Cognition and Behaviour</span></b></p>
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<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span style="font-size:10.5pt; font-family:"Arial",sans-serif; color:#BE311A">e:</span></p>
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<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span style="font-size:10.5pt; font-family:"Arial",sans-serif; color:#333333"><a href="mailto:m.vanes@donders.ru.nl" id="LPlnk176367" class="x_x_OWAAutoLink" style="color:rgb(5,99,193); text-decoration:underline" previewremoved="true"><span style="color:#1DA1DB">m.vanes@donders.ru.nl</span></a></span></p>
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<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span style="font-size:10.5pt; font-family:"Arial",sans-serif; color:#BE311A">a:</span></p>
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<span style="font-size:10.5pt; font-family:"Arial",sans-serif; color:#333333">Kapittelweg 29, 6525 EN Nijmegen</span></p>
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<span style="font-size:10.5pt; font-family:"Arial",sans-serif; color:#BE311A">p:
</span><span style="font-size:10.5pt; font-family:"Arial",sans-serif; color:#BE311A"></span></p>
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<span style="font-size:10.5pt; font-family:"Arial",sans-serif; color:#333333; background:white">+31(0)24 36 68291</span><span style="font-size:10.5pt; font-family:"Arial",sans-serif; color:#333333"></span></p>
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<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"> </span></p>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"> </span></p>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"> </span></p>
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<span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"> </span></p>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"> </span></p>
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<b><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif"> Ioanna Zioga <<a href="mailto:i.zioga@qmul.ac.uk" id="LPlnk731550" class="OWAAutoLink" previewremoved="true">i.zioga@qmul.ac.uk</a>>
<br>
<b>Sent:</b> woensdag 1 mei 2019 16:48<br>
<b>To:</b> <a href="mailto:litvak.vladimir@gmail.com" id="LPlnk418176" class="OWAAutoLink" previewremoved="true">
litvak.vladimir@gmail.com</a><br>
<b>Cc:</b> <a href="mailto:fieldtrip@science.ru.nl" id="LPlnk907764" class="OWAAutoLink" previewremoved="true">
fieldtrip@science.ru.nl</a><br>
<b>Subject:</b> [FieldTrip] beamforming pipeline & comparing sources between groups of participants?</span></p>
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<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
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<div id="x_x_divtagdefaultwrapper">
<p><span style="font-family:"Calibri",sans-serif; color:black">Dear Vladimir,</span></p>
<p><span style="font-family:"Calibri",sans-serif; color:black"> </span></p>
<p><span style="font-family:"Calibri",sans-serif; color:black">For anyone interested, I used SPM to make a template head model which I'm going to use to do beamforming in FT.</span></p>
<p><span style="font-family:"Calibri",sans-serif; color:black">I have queries with regards to the source analysis pipeline I'm using in FT, as the results I get don't seem right.</span></p>
<p><span style="font-family:"Calibri",sans-serif; color:black"> </span></p>
<p><span style="font-family:"Calibri",sans-serif; color:black">Vladimir, following our previous email exchange (and thanks to your suggestions), I have now managed to compute the lead field matrix in FT (by removing eeglab and fieldtrip directories from the
path, and adding spm's).</span></p>
<p><span style="font-family:"Calibri",sans-serif; color:black"> </span></p>
<p><span style="font-family:"Calibri",sans-serif; color:black">I want to contrast the sources of two groups of participants (high- vs. low-learners) in two frequency bands (low: 2.5-4.5 Hz; high: 12-32 Hz), from 0.20-1 sec post stimulus onset.</span></p>
<p><span style="font-family:"Calibri",sans-serif; color:black"> </span></p>
<p><span style="font-family:"Calibri",sans-serif; color:black">Here is my pipeline:</span></p>
<p><span style="font-family:"Calibri",sans-serif; color:black"> </span></p>
<p><span style="font-family:"Calibri",sans-serif; color:black">% Calculate the cross spectral density matrix (e.g., for the 12-32 Hz frequency band)</span></p>
<div>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span style="font-family:"Calibri",sans-serif; color:black">cfg = [];</span></p>
</div>
<div>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span style="font-family:"Calibri",sans-serif; color:black">cfg.method = 'mtmfft';</span></p>
</div>
<div>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span style="font-family:"Calibri",sans-serif; color:black">cfg.output = 'powandcsd';</span></p>
</div>
<div>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span style="font-family:"Calibri",sans-serif; color:black">cfg.foilim = [22 22];</span></p>
</div>
<div>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span style="font-family:"Calibri",sans-serif; color:black">cfg.taper = 'dpss';</span></p>
</div>
<div>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span style="font-family:"Calibri",sans-serif; color:black">cfg.tapsmofrq = 10;</span></p>
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<div>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span style="font-family:"Calibri",sans-serif; color:black">cfg.keeptrials = 'yes';</span></p>
</div>
<div>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span style="font-family:"Calibri",sans-serif; color:black">cfg.keeptapers = 'no';</span></p>
</div>
<div>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span style="font-family:"Calibri",sans-serif; color:black">cfg.toi = 0.6;</span></p>
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<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span style="font-family:"Calibri",sans-serif; color:black">cfg.t_ftimwin = 0.4;</span></p>
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<div>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span style="font-family:"Calibri",sans-serif; color:black">freq = ft_freqanalysis(cfg, EEGft);</span></p>
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<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span style="font-family:"Calibri",sans-serif; color:black"> </span></p>
<div>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span style="font-family:"Calibri",sans-serif; color:black">% Source analysis using DICS beamformer</span></p>
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<div>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span style="font-family:"Calibri",sans-serif; color:black">cfg = [];</span></p>
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<div>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span style="font-family:"Calibri",sans-serif; color:black">cfg.headmodel = vol1;</span></p>
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<div>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span style="font-family:"Calibri",sans-serif; color:black">cfg.grad = sens1;</span></p>
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<div>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span style="font-family:"Calibri",sans-serif; color:black">cfg.senstype = 'eeg';</span></p>
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<div>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span style="font-family:"Calibri",sans-serif; color:black">cfg.grid = grid;</span></p>
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<div>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span style="font-family:"Calibri",sans-serif; color:black">cfg.method = 'dics';</span></p>
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<div>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span style="font-family:"Calibri",sans-serif; color:black">cfg.frequency = [12 32];</span></p>
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<div>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span style="font-family:"Calibri",sans-serif; color:black">cfg.latency = [0.2 1];</span></p>
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<div>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span style="font-family:"Calibri",sans-serif; color:black">cfg.dics.projectnoise = 'yes';</span></p>
</div>
<div>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span style="font-family:"Calibri",sans-serif; color:black">cfg.dics.lambda = 0;</span></p>
</div>
<div>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span style="font-family:"Calibri",sans-serif; color:black">cfg.dics.keepfilter = 'yes';</span></p>
</div>
<div>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span style="font-family:"Calibri",sans-serif; color:black">cfg.dics.realfilter = 'yes';</span></p>
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<div>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span style="font-family:"Calibri",sans-serif; color:black">sourceA = ft_sourceanalysis(cfg, freq);</span></p>
</div>
<div>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span style="font-family:"Calibri",sans-serif; color:black"> </span></p>
</div>
<div>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span style="font-family:"Calibri",sans-serif; color:black">% Plot sources</span></p>
</div>
<div>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span style="font-family:"Calibri",sans-serif; color:black">cfg = [];</span></p>
</div>
<div>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span style="font-family:"Calibri",sans-serif; color:black">cfg.method = 'slice';</span></p>
</div>
<div>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span style="font-family:"Calibri",sans-serif; color:black">cfg.funparameter = 'pow';</span></p>
</div>
<div>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span style="font-family:"Calibri",sans-serif; color:black">ft_sourceplot(cfg, sourceA);</span></p>
</div>
<div>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span style="font-family:"Calibri",sans-serif; color:black"> </span></p>
</div>
<p style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span style="font-family:"Calibri",sans-serif; color:black">=> The source plots look weird though - they scale from 0 to x10^45, and are totally black.
</span></p>
<p><span style="font-family:"Calibri",sans-serif; color:black"> </span></p>
<p><span style="font-family:"Calibri",sans-serif; color:black">1) Am I doing something wrong in the freqanalysis or the sourceanalysis?</span></p>
<p><span style="font-family:"Calibri",sans-serif; color:black">2) Do I need to do the ft_sourceanalysis separately for each participant?</span></p>
<p><span style="font-family:"Calibri",sans-serif; color:black">3) Is there a way to average the results of the source analysis over groups of participants?</span></p>
<p><span style="font-family:"Calibri",sans-serif; color:black">4) Could you give any direction/resource on how to statistically compare the sources of different groups?</span></p>
<p><span style="font-family:"Calibri",sans-serif; color:black"> </span></p>
<p><span style="font-family:"Calibri",sans-serif; color:black">As you all know this is a very exciting but also not trivial analysis.. so I'd be extremely grateful for any help at this point, it'd be very much appreciated! Thanks so much in advance!</span></p>
<p><span style="font-family:"Calibri",sans-serif; color:black"> </span></p>
<p><span style="font-family:"Calibri",sans-serif; color:black">Best,</span></p>
<p><span style="font-family:"Calibri",sans-serif; color:black">Ioanna</span></p>
<p><span style="font-family:"Calibri",sans-serif; color:black"> </span></p>
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<div dir="ltr"><leadfield.png></div>
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