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<p class="MsoNormal">Hi Elsa, hi Jan-Mathijs, hi all,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Just to let you know, I have pulled a request for the getting started page, so the topic will probably be over soon. I shared possible code for translating BrainVision data into a FieldTrip structure. I hope it helps. Thanks for suggesting
this.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Cheers !<o:p></o:p></p>
<p class="MsoNormal">Eva<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div style="mso-element:para-border-div;border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal" style="border:none;padding:0cm"><b>De : </b><a href="mailto:fieldtrip@science.ru.nl">Schoffelen, J.M. (Jan Mathijs) via fieldtrip</a><br>
<b>Envoyé le :</b>lundi 20 septembre 2021 18:20<br>
<b>À : </b><a href="mailto:fieldtrip@science.ru.nl">FieldTrip discussion list</a><br>
<b>Cc : </b><a href="mailto:janmathijs.schoffelen@donders.ru.nl">Schoffelen, J.M. (Jan Mathijs)</a><br>
<b>Objet :</b>Re: [FieldTrip] Exporting preprocessed data from BVA to Fieldtrip</p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Dear Elsa, <o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Thanks for letting us know, and I am glad that you seem up and running by now. <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Please consider critically evaluating the online documentation. If it’s just plain wrong it should be fixed. If you have a slightly different (but apparently more robust) route to success I’d recommend to consider adding this as a new piece
of documentation to the getting started page, so that future users might optimally benefit from your (and your colleague’s) endeavours.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Best wishes,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Jan-Mathijs<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal">On 20 Sep 2021, at 17:53, Elsa Sangaran <<a href="mailto:elsangaran@gmail.com">elsangaran@gmail.com</a>> wrote:<o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal">Dear Jan, <o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Thanks for your suggestions!<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Yes, I have consulted the Fieldtrip website before to find out how to export the data. What I used initially for the filename for output was the '.seg' extension as mentioned in the website. However, another Fieldtrip user who faced a similar
problem as mine, suggested using '.dat' extension instead, and this solved the issue that I was having when exporting the data from BVA (I don't get the warning/error messages anymore). <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Thanks for the comments regarding the segmented data - this was helpful! The modified script that I am now using which was provided by another Fieldtrip user (thanks Eva!) to read in the segmented data, seems to work well. I used ft_definetrial
instead of both the ft_read_data and ft_define_trial and removed the ft_redefinetrial. <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal">Best, <o:p></o:p></p>
<div>
<p class="MsoNormal">Elsa Sangaran<o:p></o:p></p>
</div>
</div>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal">On Fri, 17 Sept 2021 at 16:45, Schoffelen, J.M. (Jan Mathijs) via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl" target="_blank">fieldtrip@science.ru.nl</a>> wrote:<o:p></o:p></p>
</div>
<blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm">
<div>
<p class="MsoNormal">Hi Elsa, <o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Have you consulted this piece of documentation?<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><a href="https://urldefense.com/v3/__https:/www.fieldtriptoolbox.org/getting_started/brainvision/__;!!HJOPV4FYYWzcc1jazlU!sjEGljT2DLVAgyLVIV9J38cMwLO2dtj5aoOHELJTW99Id7QovsCWoWwrBpZtj_Fe573RzFo1XMGPTzQ$" target="_blank">https://www.fieldtriptoolbox.org/getting_started/brainvision/</a><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">It is not clear to me why you use a mix of low-level functionality (ft_read_data) and high level functionality (ft_definetrial), in combination with exported already epoched data to try to achieve what you want to achieve.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">If you already have segmented data, why would you need to epoch your data once more (as suggested by your intention to call ft_definetrial, followed by ft_redefinetrial)?<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Best wishes,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Jan-Mathijs<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<div>
<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal">On 17 Sep 2021, at 15:16, Elsa Sangaran via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl" target="_blank">fieldtrip@science.ru.nl</a>> wrote:<o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">Dear all, </span>
<o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">I am having some trouble with the exported data (averages of different conditions in my experiment) which I preprocessed on Brain Vision Analyzer. </span>I used the generic data export option
on BVA, which generated 3 files (.seg, .vhdr, .vmrk), which I then imported to Fieldtrip. When reading in the exported data, I get the following error messages and warnings: <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Script: <o:p></o:p></p>
</div>
<div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:blue">for</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New""> subj = (name_subj)</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New"">
<span style="color:#3C763D">% (re)set directory to the directory that contains the trialfun</span></span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New""> subject = subj{:};</span><o:p></o:p></p>
</div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New"">
</span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New""> </span></p>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New"">seg_file =[dir_raw_data_external subject
<span style="color:#A020F0">'.seg'</span>]; <span style="color:#3C763D">
%Subject's .seg file, ie. 'pilot1.seg'</span></span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New"">header_file =[dir_raw_data_external subject
<span style="color:#A020F0">'.vhdr'</span>]; <span style="color:#3C763D">
%Subject's .vhdr file, ie. 'pilot1.vhdr'</span></span><o:p></o:p></p>
</div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New"">
</span></p>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New"">cfg = [];
</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New"">cfg.dataset = seg_file;</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New"">hdr = ft_read_header(header_file);</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New"">nTrials = hdr.nSamples/trial_length;</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New"">hdr.nTrials = nTrials;</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New"">hdr.nSamples = trial_length;</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New"">dat = ft_read_data(seg_file,<span style="color:#A020F0">'header'</span>, hdr);
</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New"">cfg.label = channel_labels;
</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New"">cfg.trial = squeeze(num2cell(dat,[1 2]))';</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New"">cfg.hdr = hdr;</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New"">cfg.time = repmat({[time_start:(time_end-time_start)/trial_length:time_end-(time_end-time_start)/trial_length]},1,nTrials);</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New"">cfg.label = cfg.hdr.label;</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New"">cfg.trialinfo = [];</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New"">cfg.sampleinfo = [0 300];
</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New"">cfg.fsample = 250;</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New"">data_raw = cfg;</span><o:p></o:p></p>
</div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New""> </span></p>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:#3C763D">% make variables for header and eeg file</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:#3C763D">% headerfile = [dir_raw_data_external subject '.vhdr'];</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:#3C763D">% segfile = [dir_raw_data_external subject '.seg'];</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="DE" style="font-size:10.0pt;font-family:"Courier New";color:#3C763D">%
</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="DE" style="font-size:10.0pt;font-family:"Courier New";color:#3C763D">% cfg = [];</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="DE" style="font-size:10.0pt;font-family:"Courier New";color:#3C763D">% cfg.headerfile = headerfile;</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:#3C763D">% cfg.dataset = segfile;</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:#3C763D">% data_raw = ft_preprocessing(cfg);</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:#3C763D">%
</span><o:p></o:p></p>
</div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New""> </span></p>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:#3C763D">%cfg.trialdef.eventtype = 'string'</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:#3C763D">%cfg.trialdef.eventvalue = number, string or list with numbers or strings</span><o:p></o:p></p>
</div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New"">
</span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New"">
</span></p>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New""> cfg = [];</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New""> cfg.trialdef.prestim = 0.2;</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New""> cfg.trialdef.poststim = 1;</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New""> cfg.trialdef.eventtype =
<span style="color:#A020F0">'Time 0'</span>;</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New""> cfg.trialdef.eventvalue =
<span style="color:#A020F0">''</span>;</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New""> cfg.trialdef.triallength = 1.2;</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New""> cfg.trialdef.ntrials = 1;</span><o:p></o:p></p>
</div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New"">
</span></p>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New""> cfg.headerfile = header_file;</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New""> cfg.datafile = seg_file;</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New""> cfg_deftrial = ft_definetrial(cfg);</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New""> data_segmented = ft_redefinetrial(cfg_deftrial, data_raw);</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Courier New";color:blue">end</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-family:"Arial",sans-serif">For </span><span style="font-family:"Arial",sans-serif">ft_definetrial, I get the following warnings:</span><o:p></o:p></p>
</div>
<div style="margin-bottom:8.0pt">
<p class="MsoNormal" style="line-height:106%"><o:p> </o:p></p>
</div>
<ul type="disc">
<li class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo1">
<span lang="EN-GB" style="font-family:"Arial",sans-serif">Warning: could not determine dimord of "dataset"</span><o:p></o:p></li><li class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo1">
<span lang="EN-GB" style="font-family:"Arial",sans-serif">Warning: inconsistent sampleinfo</span><o:p></o:p></li><li class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo1">
<span lang="EN-GB" style="font-family:"Arial",sans-serif">Warning: inconsistent trialinfo</span><o:p></o:p></li></ul>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:106%"><span lang="EN-GB" style="font-family:"Arial",sans-serif">For ft_redefinetrial, I get the following warnings: </span></p>
<div style="margin-bottom:8.0pt">
<p class="MsoNormal" style="line-height:106%"><o:p> </o:p></p>
</div>
<ul type="disc">
<li class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level1 lfo2">
<span lang="EN-GB" style="font-family:"Arial",sans-serif">Warning: the data does not contain sampleinfo
</span><o:p></o:p></li><li class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level1 lfo2">
<span lang="EN-GB" style="font-family:"Arial",sans-serif">Warning: reconstructing sampleinfo by assuming that the trials are consecutive segments of a continuous recording</span><o:p></o:p></li></ul>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div style="margin-bottom:8.0pt">
<p class="MsoNormal" style="line-height:106%"><o:p> </o:p></p>
</div>
<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:106%"><span style="font-family:"Arial",sans-serif;color:#111111">I appreciate your advice and guidance on how to go about this as I am still new to using Fieldtrip. </span></p>
<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:106%"><span style="font-family:"Arial",sans-serif;color:#111111">Thank you in advance for your help.</span></p>
<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:106%"><o:p> </o:p></p>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">Best,</span> <o:p>
</o:p></p>
<div>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">Elsa Sangaran</span><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
<p class="MsoNormal">_______________________________________________<br>
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<o:p></o:p></p>
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</blockquote>
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<p class="MsoNormal"><o:p> </o:p></p>
</div>
</div>
<p class="MsoNormal">_______________________________________________<br>
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<a href="https://urldefense.com/v3/__https:/doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!sjEGljT2DLVAgyLVIV9J38cMwLO2dtj5aoOHELJTW99Id7QovsCWoWwrBpZtj_Fe573RzFo1x2zRVIE$" target="_blank">https://doi.org/10.1371/journal.pcbi.1002202</a><o:p></o:p></p>
</blockquote>
</div>
</div>
</blockquote>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
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