<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Dear all,<div class=""><br class=""></div><div class="">I am wondering, was my question unclear, or maybe no one is using Neuralynx data?</div><div class="">I can think of ways to avoid these two problems, but I would prefer to find a proper solution if possible. </div><div class=""><br class=""></div><div class="">Thanks in advance,</div><div class=""><br class=""><div class="">
<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; "><div class="">Florian Gerard-Mercier</div><div class=""><br class=""></div></span><br class="Apple-interchange-newline">
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<br class=""><div><blockquote type="cite" class=""><div class="">On 14 Oct, 2016, at 3:08 PM, Florian Gerard-Mercier <<a href="mailto:florian@brain.riken.jp" class="">florian@brain.riken.jp</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Dear community,<div class=""><br class=""></div><div class=""><br class=""></div><div class="">My name is Florian Gerard-Mercier and I work in Keiji Tanaka’s laboratory in Riken BSI, Japan.</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">I am new to Fieldtrip.</div><div class="">My goal is to do a simple analysis of ECoG data in response to electrical stimulation (all in monkey cortex). To this effect I followed the TMS-EEG tutorial (since the issues are almost identical).</div><div class="">The recording system is Neuralynx.</div><div class=""><br class=""></div><div class="">I have encountered 2 problems which I don’t believe are related.</div><div class="">I have basically followed the tutorials to the letter so except if I mention otherwise, the cfg, etc. are standard.</div><div class=""><br class=""></div><div class=""><u class=""><b class="">1) Fsample discrepancy between data and header.</b></u></div><div class="">When I load Neuralynx data, I get warnings that the sample rate is actually half that in the header, and is thus being corrected (note, 16129 instead of 32258Hz).</div><div class="">This is no problem, until I get the final results where I noticed that my 50Hz noise is now represented as lasting 40ms for each cycle (= twice longer than it actually is).</div><div class="">Navigating in the workspace, I noticed that even though cfg.Fs is 16129 as expected, somehow the data outputted by ft_preprocessing has a field fsample equal to half that number (8064.5).</div><div class="">This later gives many conflicts such as: if I force data.fsample to be 16129, I have the correct time axis in the end, but now my trial duration is only half that which I want…</div><div class="">Any idea on how to solve this issue? I haven’t found any previous ticket on this Fsample discrepancy issue.</div><div class="">I do not know either how much trust I have to put in that warning and correction of the sampling rate in the first place.</div><div class=""><br class=""></div><div class=""><u class=""><b class="">2) 50Hz line noise filtering</b></u></div><div class="">The previous point makes it so that if I filter 50Hz, of course nothing happens. But even if I filter 25Hz (or 50Hz with the Fsample corrected back to 16129), the attenuation is far too small (whether I use padding or not). I did look up the similar problems that had been submitted to this list in the past, but didn’t find any satisfactory fix.</div><div class="">To give an idea:</div><div class=""><div class="">cfg = [];</div><div class="">cfg.Fsample = 1000; % I downsampled the data in the meantime as said in the tuto</div><div class="">cfg.bsfilter = 'yes';</div><div class="">cfg.bsfiltord = 2; % somehow I have an error that the filtering doesn’t work every time I try to run it with an order >2</div><div class="">cfg.bsfreq = [49.9 50.1];</div><div class="">filtDat = ft_preprocessing(cfg, data_lite);</div><div class=""><br class=""></div><div class=""><div class="">cfgbrowse = []; cfgbrowse.viewmode = 'butterfly';</div><div class="">ft_databrowser(cfgbrowse, dat_lite /// filtDat); % screenshots of both below</div></div><div class=""><br class=""></div><div class="">changes this</div><div class=""><span id="cid:A61F9FBF-4C22-4418-BF33-2A7E0474BE79@bnf.brain.riken.jp"><data_lite.jpeg></span></div><div class=""><br class=""></div><div class="">into that</div><div class=""><br class=""></div><div class=""><span id="cid:D9CEB025-4841-41D7-AEA6-DB89088A2C37@bnf.brain.riken.jp"><filtDat.jpeg></span></div><div class=""><br class="webkit-block-placeholder"></div><div class="">{Note also the issue with Fsample: here I have a time axis that corresponds to my 50Hz noise, but the duration of the trial is reduced from [-0.05, 0.45] by a factor of 2.}</div><div class=""><br class=""></div><div class="">This is in stark contrast to what happens if I use the bandstop filter directly on the raw data:</div><div class=""><div style="margin: 0px; line-height: normal;" class="">dat = ft_read_data(dataset_dir);</div></div><div class=""><div style="margin: 0px; line-height: normal;" class="">dat_filt = ft_preproc_bandstopfilter(dat, 16129, [49.9 50.1], 2);</div></div><div class="">changes this</div><div class=""><span id="cid:4FF67112-09FC-4A3B-A444-C64EB817293E@bnf.brain.riken.jp"><RawData.jpeg></span></div><div class=""><br class=""></div><div class="">into that</div><div class=""><br class=""></div><div class=""><span id="cid:DAD0B9D2-A389-4AC0-AF4F-D22BC8CC53AF@bnf.brain.riken.jp"><RawData_after_filter.jpeg></span></div><div class=""><br class=""></div><div class="">Which should be perfect for my simple purposes. (Here I just did a simple Matlab plot, so the x axis numbering is not actual time)</div><div class=""><br class=""></div><div class="">Of course, I tried to feed that filtered data into the preprocessing pipeline by doing </div><div class=""><div style="margin: 0px; line-height: normal;" class="">cfg = ft_rejectartifact(cfg_artifact); %cfg_artifact is defined as in the tutorial, it is to reject the electrical stimulation artifacts. The problem should not stem from here.</div></div><div class=""><div style="margin: 0px; line-height: normal;" class="">data_artifact_rejected = ft_preprocessing(cfg, dat_filt);</div></div><div class="">But I get the error that dat_filt is not raw or comp data.</div><div class=""><br class=""></div><div class="">I have read that it is recommended to do the line noise filtering after the trial segmentation and stimulation artefact removal, but 1) it doesn’t seem to work well, 2) I don’t really understand why, given that my artefacts are nowhere near the 50Hz frequency.</div><div class=""><br class=""></div><div class="">So for this point:</div><div class="">- how to make the (recommended) 50Hz post processing work?</div><div class="">- or more simply, how could I feed prefiltered data to ft_preprocessing?</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">Thank you very much for your consideration and I look forward to your help.</div><div class=""><br class=""></div><div class="">All the best,</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">
<span class="Apple-style-span" style="border-collapse: separate; font-variant-ligatures: normal; font-variant-position: normal; font-variant-numeric: normal; font-variant-alternates: normal; font-variant-east-asian: normal; line-height: normal; border-spacing: 0px;"><div class="">Florian</div></span>
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