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<p class="MsoNormal"><span lang="EN-US">Hi Brian,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">In general I woulrd recommend that you comment or reply to posts in the FieldTrip list on the list instead of sending mails directly to people so that issues that are solved are visible to everybody.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">As to the issue at hand, I haven’t heard from anybody and regretfully forgot to ask Mr. Schoffelen at the last conference I met him.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">My solution to this was to implement the algorithm by myself according to the description given in the paper by Hipp et al. I could offer to send you the code, it should be easy to integrate with a reasonable amount of
Matlab skills. Naturally I will not be able to offer any guarantees that the code is correct, but the results look reasonable enough to me.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Go to <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><a href="http://dropcanvas.com/1xfe7/1">http://dropcanvas.com/1xfe7/1</a><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">for a plot of the grand average seed-based connectivity from the left somatosensory cortex (MNI = [- 40, - 30, 50]) to all other voxels within the Beta band for a group of 22 healthy subjects. The paradigm is 5 minutes
eyes-closed resting-state.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Son<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Von: Brian Scally [RPG] [<a href="mailto:psbs@leeds.ac.uk">mailto:psbs@leeds.ac.uk</a>]
<o:p></o:p></span></p>
<p class="MsoNormal">Gesendet: Donnerstag, 27. Juli 2017 15:54<o:p></o:p></p>
<p class="MsoNormal">An: Ta Dinh, Son <<a href="mailto:son.ta.dinh@tum.de">son.ta.dinh@tum.de</a>><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">Betreff: Fieldtrip powcorr_ortho issue<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Dear Son Ta Dinh,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Hope you are well. I came across a post you made on the Fieldtrip mailing list about the powcorr_ortho function for ft_connectivity analysis. I am essentially getting the same results - random connectivity patterns. I
wondered if you had heard from anyone about this issue or managed to resolve it?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">All the best,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Brian Scally<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">PhD Student,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">School of Psychology,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">University of Leeds<o:p></o:p></span></p>
<p class="MsoNormal"><a href="mailto:b.scally@leeds.ac.uk">b.scally@leeds.ac.uk</a><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span style="mso-fareast-language:DE">Von:</span></b><span style="mso-fareast-language:DE">
<a href="mailto:fieldtrip-bounces@science.ru.nl">fieldtrip-bounces@science.ru.nl</a> [<a href="mailto:fieldtrip-bounces@science.ru.nl">mailto:fieldtrip-bounces@science.ru.nl</a>]
<b>Im Auftrag von </b>Ta Dinh, Son<br>
<b>Gesendet:</b> Donnerstag, 13. </span><span lang="EN-US" style="mso-fareast-language:DE">April 2017 14:58<br>
<b>An:</b> <a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a><br>
<b>Betreff:</b> [FieldTrip] Functional connectivity analysis with powcorr_ortho<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Dear FieldTrip list,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I am trying to do a functional connectivity analysis using the power envelope correlation introduced by Hipp et al. (Nat Neuroscience 2012) as implemented in the ft_connectivity_powcorr_ortho function. My data consists
of 5 minutes of eyes-closed resting-state data and my schematic pipeline is as follows:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<ol style="margin-top:0cm" start="1" type="1">
<li class="MsoNormal" style="margin-left:0cm;mso-list:l0 level1 lfo3"><span lang="EN-US">I use LCMV beamforming to source reconstruct my bandpassed and preprocessed data<o:p></o:p></span></li><li class="MsoNormal" style="margin-left:0cm;mso-list:l0 level1 lfo3"><span lang="EN-US">Using the resulting spatial filter I get a projected time series for every voxel (virtual channel)<o:p></o:p></span></li><li class="MsoNormal" style="margin-left:0cm;mso-list:l0 level1 lfo3"><span lang="EN-US">I do a frequency analysis on these time series<o:p></o:p></span></li><li class="MsoNormal" style="margin-left:0cm;mso-list:l0 level1 lfo3"><span lang="EN-US">The results of this frequency analysis (the Fourier coefficients) are used for the connectivity analysis using powcorr_ortho<o:p></o:p></span></li></ol>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">To check the results of this analysis, I plotted the results of a seed-based connectivity analysis with a voxel in the left visual cortex (-20, -80, 20) as seed. In the alpha band, I expect to see a strong local connectivity
pattern in the occipital region extending partially into the contralateral hemisphere, similar to what Siems et al. NeuroImage 2016 find. However, I get a basically random connectivity pattern. When using this pipeline with the debiased weighted phase lag
index, I get exactly what I am expecting.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I looked into the source code of the ft_connectivity_powcorr_ortho function and saw a few disconcerting comments (Fix-Me’s and the like) and now I am wondering whether my pipeline is simply not suited to the connectivity
analysis with powcorr_ortho as implemented in FieldTrip or if the function is simply not fully implemented yet. Has anyone used it successfully before?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I use the following FieldTrip (pseudo-) code:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">%% LCMV source reconstruction<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">cfg = [];<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">cfg.method = ‘lcmv’;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">cfg.keeptrials = ‘yes’;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">cfg.elec = elec; <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">cfg.grid = lf; % regular grid of 1 cm resolution<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">cfg.headmodel = vol % standard_bem.mat<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">cfg.lcmv.keepfilter = ‘yes’;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">cfg.lcmv.lambda = ‘5%’;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">cfg.lcmv.projectnoise = ‘yes’;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">source = ft_sourceanalysis(cfg, tlock_data);<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">%% pseudo-code for the computation of the virtual channel time series<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">virtChan_data = tlock_data;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">virtChan_data.label = [source.pos(:, 1), source.pos(:,2), source.pos(:,3)];<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">virtChan_data.trial = source.avg.filter * tlock_data.trial;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">%% frequency analysis of the virtual channels<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">cfg = [];<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">cfg.method = ‘mtmfft’;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">cfg.output = ‘fourier’;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">cfg.keeptrials = ‘yes’;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">cfg.foi = 10; % alpha band<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">cfg.taper = ‘hanning’ % I originally used 3 tapers but source code in ft_connectivity_powcorr_ortho implies that multitaper is not compatible<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">virtFreq = ft_freqanalysis(cfg, virtChan_data);<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">%% connectivity analysis<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">cfg = [];<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">cfg.method = ‘powcorr_ortho’;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">conn = ft_connectivityanalysis(cfg,virtFreq);<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Any suggestions and/or comments would be immensely helpful! Thanks in advance.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Son<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman",serif;color:#888888;mso-fareast-language:DE">Son Ta Dinh, M.Sc.</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman",serif;color:#888888;mso-fareast-language:DE"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman",serif;color:#888888;mso-fareast-language:DE">PhD student in Human Pain Research</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman",serif;color:#888888;mso-fareast-language:DE"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:"Times New Roman",serif;color:#888888;mso-fareast-language:DE">Klinikum rechts der Isar</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:#888888;mso-fareast-language:DE"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:"Times New Roman",serif;color:#888888;mso-fareast-language:DE">Technische Universität München<br>
Munich, Germany<br>
Phone: </span><a href="tel:%2B49%2089%204140%207664" target="_blank"><span style="font-size:7.5pt;font-family:"Times New Roman",serif;color:blue;mso-fareast-language:DE">+49 89 4140 7664</span></a><span style="font-size:7.5pt;font-family:"Times New Roman",serif;color:#888888;mso-fareast-language:DE"><br>
</span><a href="http://www.painlabmunich.de/" target="_blank"><span style="font-size:7.5pt;font-family:"Times New Roman",serif;color:blue;mso-fareast-language:DE">http://www.painlabmunich.de/</span></a><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:#888888;mso-fareast-language:DE"><o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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