<div dir="ltr">Dear Jan,<div><br></div><div>Thanks for your suggestions!</div><div><br></div><div>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). </div><div><br></div><div>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. </div><div><br></div><div><div><div dir="ltr" data-smartmail="gmail_signature"><div dir="ltr">Best,<div>Elsa Sangaran</div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">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:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
Hi Elsa,
<div><br>
</div>
<div>Have you consulted this piece of documentation?</div>
<div><br>
</div>
<div><a href="https://www.fieldtriptoolbox.org/getting_started/brainvision/" target="_blank">https://www.fieldtriptoolbox.org/getting_started/brainvision/</a></div>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>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)?</div>
<div><br>
</div>
<div><br>
</div>
<div>Best wishes,</div>
<div>Jan-Mathijs</div>
<div><br>
</div>
<div>
<div><br>
<blockquote type="cite">
<div>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:</div>
<br>
<div>
<div dir="ltr"><font face="arial, sans-serif">Dear all, </font>
<div><font face="arial, sans-serif"><br>
</font></div>
<div><font face="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. </font>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: </div>
<div><br>
</div>
<div>Script: </div>
<div>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New";color:blue">for</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""> subj = (name_subj)</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></div>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New"">
</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New";color:rgb(60,118,61)">% (re)set directory to the directory that contains the trialfun</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></div>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""> subject = subj{:};</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></div>
<p class="MsoNormal" style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New"">
</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></p>
<p class="MsoNormal" style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""> </span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></p>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New"">seg_file =[dir_raw_data_external subject
</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New";color:rgb(160,32,240)">'.seg'</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New"">];
</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New";color:rgb(60,118,61)">%Subject's .seg file, ie. 'pilot1.seg'</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></div>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New"">header_file =[dir_raw_data_external subject
</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New";color:rgb(160,32,240)">'.vhdr'</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New"">];
</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New";color:rgb(60,118,61)">%Subject's .vhdr file, ie. 'pilot1.vhdr'</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></div>
<p class="MsoNormal" style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New"">
</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></p>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New"">cfg = [];
</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></div>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New"">cfg.dataset = seg_file;</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></div>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New"">hdr = ft_read_header(header_file);</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></div>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New"">nTrials = hdr.nSamples/trial_length;</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></div>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New"">hdr.nTrials = nTrials;</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></div>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New"">hdr.nSamples = trial_length;</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></div>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New"">dat = ft_read_data(seg_file,</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New";color:rgb(160,32,240)">'header'</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New"">,
hdr); </span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></div>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New"">cfg.label = channel_labels;
</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></div>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New"">cfg.trial = squeeze(num2cell(dat,[1 2]))';</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></div>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New"">cfg.hdr = hdr;</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></div>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;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><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></div>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New"">cfg.label = cfg.hdr.label;</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></div>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New"">cfg.trialinfo = [];</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></div>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New"">cfg.sampleinfo = [0 300];
</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></div>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New"">cfg.fsample = 250;</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></div>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New"">data_raw = cfg;</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></div>
<p class="MsoNormal" style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""> </span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></p>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New";color:rgb(60,118,61)">% make variables for header and eeg file</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></div>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New";color:rgb(60,118,61)">% headerfile = [dir_raw_data_external subject '.vhdr'];</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></div>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New";color:rgb(60,118,61)">% segfile = [dir_raw_data_external subject '.seg'];</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></div>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="DE" style="font-size:10pt;font-family:"Courier New";color:rgb(60,118,61)">%
</span><span lang="DE" style="font-size:10pt;font-family:"Courier New""></span></div>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="DE" style="font-size:10pt;font-family:"Courier New";color:rgb(60,118,61)">% cfg = [];</span><span lang="DE" style="font-size:10pt;font-family:"Courier New""></span></div>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="DE" style="font-size:10pt;font-family:"Courier New";color:rgb(60,118,61)">% cfg.headerfile = headerfile;</span><span lang="DE" style="font-size:10pt;font-family:"Courier New""></span></div>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New";color:rgb(60,118,61)">% cfg.dataset = segfile;</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></div>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New";color:rgb(60,118,61)">% data_raw = ft_preprocessing(cfg);</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></div>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New";color:rgb(60,118,61)">%
</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></div>
<p class="MsoNormal" style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""> </span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></p>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New";color:rgb(60,118,61)">%cfg.trialdef.eventtype = 'string'</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></div>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New";color:rgb(60,118,61)">%cfg.trialdef.eventvalue = number, string or list with numbers or strings</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></div>
<p class="MsoNormal" style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New"">
</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></p>
<p class="MsoNormal" style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New"">
</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></p>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""> cfg = [];</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></div>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""> cfg.trialdef.prestim = 0.2;</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></div>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""> cfg.trialdef.poststim = 1;</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></div>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""> cfg.trialdef.eventtype =
</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New";color:rgb(160,32,240)">'Time 0'</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New"">;</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></div>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""> cfg.trialdef.eventvalue =
</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New";color:rgb(160,32,240)">''</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New"">;</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></div>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""> cfg.trialdef.triallength = 1.2;</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></div>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""> cfg.trialdef.ntrials = 1;</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></div>
<p class="MsoNormal" style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New"">
</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></p>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""> cfg.headerfile = header_file;</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></div>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""> cfg.datafile = seg_file;</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></div>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""> cfg_deftrial = ft_definetrial(cfg);</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></div>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""> data_segmented = ft_redefinetrial(cfg_deftrial, data_raw);</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></div>
<p class="MsoNormal" style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
</p>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New";color:blue">end</span><span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""></span></div>
<div style="margin:0cm;line-height:normal;font-size:11pt;font-family:Calibri,sans-serif">
<span lang="EN-GB" style="font-size:10pt;font-family:"Courier New""><br>
</span></div>
<div style="margin:0cm;line-height:normal"><font face="arial, sans-serif"><span lang="EN-GB">For </span><span>ft_definetrial, I get the following warnings:</span></font></div>
<div style="margin:0cm 0cm 8pt;line-height:107%"><br>
</div>
<ul>
<li><span lang="EN-GB"><font face="arial, sans-serif">Warning: could not determine dimord of "dataset"</font></span></li><li><span lang="EN-GB"><font face="arial, sans-serif">Warning: inconsistent sampleinfo</font></span></li><li><span lang="EN-GB"><font face="arial, sans-serif">Warning: inconsistent trialinfo</font></span></li></ul>
<div><br>
</div>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%"><span lang="EN-GB"><font face="arial, sans-serif">For ft_redefinetrial, I get the following warnings: </font></span></p>
<div style="margin:0cm 0cm 8pt;line-height:107%"><br>
</div>
<ul>
<li><span lang="EN-GB"><font face="arial, sans-serif">Warning: the data does not contain sampleinfo
</font></span></li><li><span lang="EN-GB"><font face="arial, sans-serif">Warning: reconstructing sampleinfo by assuming that the trials are consecutive segments of a continuous recording</font></span></li></ul>
<div><br>
</div>
<div style="margin:0cm 0cm 8pt;line-height:107%"><span lang="EN-GB"><font face="arial, sans-serif"></font></span><br>
</div>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%"><span style="font-family:arial,sans-serif;color:rgb(17,17,17)">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:0cm 0cm 8pt;line-height:107%"><span style="color:rgb(17,17,17);font-family:arial,sans-serif">Thank you in advance for your help.</span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%"><span style="color:rgb(17,17,17);font-family:arial,sans-serif"><br>
</span></p>
</div>
<div>
<div dir="ltr">
<div dir="ltr"><font face="arial, sans-serif">Best,</font>
<div><font face="arial, sans-serif">Elsa Sangaran</font></div>
</div>
</div>
</div>
</div>
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