<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Carina,<div><div><div><br><blockquote type="cite"><div>1.) I know that I can calculate the appropriate model order and window length with the bsmart toolbox. But from the documentation I somehow do not get the format of data I should use for this calculation. <br>When I enter the time-frequency data (which I want to use to estimate granger causality) (size: 2 x 2 x freq x time points), it doesn't work.<br></div></blockquote><div><br></div><div>The 'it doesn't work' statement is typically not enough for us to diagnose where the problem lies (at least at which step it goes wrong). At the moment I can only assume that you use an outdated version of FieldTrip, because when I try to do TF-resolved Granger using AR-models it works. It is good that you pasted the script below, but an error message may be informative too.</div><div><br></div><blockquote type="cite"><div>Any advise? I have a sampling rate of 1000. What sort of time window and maximal model order would make sense do you think?<br></div></blockquote><div><br></div><div>I think that the time window is rather short: I'd rather go for 0.4 or 0.5 to begin with, but this is an empirical question. Also, shifting the windows one time step at a time does not really make sense to me, 0.01 or even 0.05 is much more memory friendly. For the model order: higher one. Some people seem to get nice results when taking a relatively high model order. Of course, for a high model order you also need longer time-windows.</div><div><br></div><blockquote type="cite"><div>2)I would like to keep the time domain analyzing my data. What do you think would be an appropriate sliding time window using the 'ft_mvaranalysis' function? And what does it mean exactly? By choosing the model order, I am already determining the maximal time lag between the two functions. Are the values then estimated for the whole time window?<br></div></blockquote><div><br></div><div>No. The time window determines the length of the data segment which is used to fit an AR-model (of order X) of the data at time point Y (as defined in your toi)</div><br><blockquote type="cite"><div>3)What do you think about statistics? Would it makes sense to use the non-parametric cluster approach to shuffle within patients and do a group analysis that way?<br></div></blockquote><div><br></div><div>This depends on your experimental question and you null-hypothesis.</div><div><br></div><div>Best,</div><div>Jan-Mathijs</div><div><br></div><blockquote type="cite"><div><br>Thank you so much in advance!<br>Best,<br>Carina<br><br><br>As a summary,I am doing following steps with field trip:<br><br><br>cfg = [];<br>cfg.dftfilter ='yes'<br>prep_cond1{subj} = ft_preprocessing(cfg, data);<br><br><br>cfg = [];<br>cfg.order = 5;<br>cfg.toolbox = 'bsmart';<br>cfg.t_ftimwin = 0.05<br>cfg.toi = -1:0.001:3.5;<br>mdata_cond1{subj}= ft_mvaranalysis(cfg, prep_cond1{subj});<br><br><br>cfg = [];<br>cfg.method = 'mvar';<br>cfg.foi = 4:100;<br>cond1_freq{subj}= ft_freqanalysis_mvar(cfg,mdata_cond1{subj});<br><br><br>cfg = [];<br>cfg.method = 'granger';<br>cond1_granger{subj} = ft_connectivityanalysis(cfg, cond1_freq{subj});<br><br>_______________________________________________<br>fieldtrip mailing list<br><a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>http://mailman.science.ru.nl/mailman/listinfo/fieldtrip<br></div></blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; 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; font-size: medium; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; 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; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; 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; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; 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; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; 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; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><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></span></div></span></div></span></div></span></div></span></span>
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