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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Times",serif;color:#1F497D;mso-fareast-language:EN-US">Dear Jan-Mathijs, dear Stephen,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Times",serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Times",serif;color:#1F497D;mso-fareast-language:EN-US">thank you for your answers! Indeed changing the input variables in ft_read_header, line 1762 to 0 and 0 solved the issue. Now
it works just fine and returns the header struct perfectly!<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Times",serif;color:#1F497D;mso-fareast-language:EN-US">Concerning the PR: sure why not. A silly change might just be an appropriate starting point for a coding rookie MD like me
</span><span lang="EN-GB" style="font-size:11.0pt;font-family:Wingdings;color:#1F497D;mso-fareast-language:EN-US">J</span><span lang="EN-GB" style="font-size:11.0pt;font-family:"Times",serif;color:#1F497D;mso-fareast-language:EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Times",serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Times",serif;color:#1F497D;mso-fareast-language:EN-US">As a side note, in my version it was located in line 1762 as well, not 1792.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Times",serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Times",serif;color:#1F497D;mso-fareast-language:EN-US">Thanks again to you both!<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Times",serif;color:#1F497D;mso-fareast-language:EN-US">Best wishes,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Times",serif;color:#1F497D;mso-fareast-language:EN-US">Johannes<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Times",serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri",sans-serif;color:#1F3864">Dr. med. Johannes Lang<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri",sans-serif;color:#1F3864">Universität Erlangen<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri",sans-serif;color:#1F3864">Neurologische Klinik</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri",sans-serif;color:#1F3864">Epilepsiezentrum<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri",sans-serif;color:#1F3864">Schwabachanlage 6<br>
91054 Erlangen<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri",sans-serif;color:#1F3864"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri",sans-serif;color:#1F3864">+49 (0)9131/85-33001<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Times",serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Times",serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif">Von:</span></b><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> fieldtrip <fieldtrip-bounces@science.ru.nl>
<b>Im Auftrag von </b>Stephen Whitmarsh<br>
<b>Gesendet:</b> Mittwoch, 1. Juli 2020 17:49<br>
<b>An:</b> FieldTrip discussion list <fieldtrip@science.ru.nl><br>
<b>Betreff:</b> Re: [FieldTrip] error using ft_read_header func<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB">Dear Jan and J-M,<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB">Since I was lurking, let me chime in for a second;<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB">1) ft_read_header works as it is now works for me.<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB">2) I replaced the 1 with a 0 as JM suggested, with same behaviour, so it won't break it. Although it's on line 1792 instead of 1762, I assume a typo by JM. I won't take your chance of having yoru first FieldTrip commit
though :-) <o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB">3) I have encountered this error before, but probably when reading corrupt data. I have to say, .ncs files have given me a headache when dealing with missing data (indicated by missing timestamps).<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB">4) I tried it on a clean, fresh, Fieldtrip pull, without external neuralynx libraries. However, we do use those provided by Neuralynx (download info when you use ft_read_header), which
<i>greatly </i>speeds up loading data.<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB">5) I have had weirdly 'stuck' mex files, with unclear errors, which only restarting my computer fixed. Seriously, at least give it a shot. I wouldn't be surprised if that would work.<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB">Let me know if I can help in another way.<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB">Cheers,<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB">Stephen<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB">Op wo 1 jul. 2020 om 17:14 schreef Schoffelen, J.M. (Jan Mathijs) <<a href="mailto:jan.schoffelen@donders.ru.nl">jan.schoffelen@donders.ru.nl</a>>:<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB">Dear Johannes, <o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB">Welcome to the community! I am not so familiar with this fileformat, but looking in the code it seems that this is a genuine bug. I am wondering whether this has ever worked at all.<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB">Long story short, in reading the header, it seems, as per line 177 in read_neuralynx_ncs, that both begrecord AND endrecord need to be defined as 0. However, in ft_read_header, line 1762, read_neuralynx_ncs is called
with 1 and 0 as input arguments, rather than (what I would expect) 0 and 0. Perhaps other people might chime in here to confirm, particularly those who are reading along and who work with this fileformat themselves, but I would say that this is incorrect.<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB">Could you try in your own code, to change the ‘1’ on line 1762 in ft_read_header into a ‘0’, and confirm that reading in of the header information then works for you?<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB">If so, then feel free to make a PR on github for this. I know it’s a silly change, which I could easily do myself, but in the spirit of ‘we’re all in it together’ I don’t want to take the opportunity away from you :). <o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB">Of course I am just kidding, but also partly serious: if you make the suggested change in a pull request, then this improvement of the codebase will be forever in www-space associated with you (and who knows what the
effect of this will be on your professional career, and on the grand scheme of things). This last remark is just a gentle nudge to everybody who is reading along. Oh, and did I already raise the argument that a medical degree does not forbid you to write code?<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB">Best wishes,<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB">Jan-Mathijs<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="color:black">J.M.Schoffelen, MD PhD<br>
Associate PI, VIDI-fellow - PI, language in interaction<br>
Telephone: +31-24-3614793<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="color:black">Physical location: room 00.028<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span lang="EN-GB" style="color:black">Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB"><br>
<br>
<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB">On 1 Jul 2020, at 16:23, Lang, Johannes <<a href="mailto:Johannes.Lang@uk-erlangen.de" target="_blank">Johannes.Lang@uk-erlangen.de</a>> wrote:<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB">Dear all,</span><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB"> </span><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB">I’m new to the community and keep running into an error using the ft_read_header function.</span><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB"> </span><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB">The way I understood the documentation</span><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB"> </span><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB">hdr = ft_read_header(‘filename’)</span><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB"> </span><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB">should read the header information into an array.</span><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB">However, I keep running into an error</span><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB"> </span><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB">Error using read_neuralynx_ncs (line 182)</span><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB">cannot read beyond the last record</span><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB"> </span><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB">Error in ft_read_header (line 1762)</span><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB"> ncs = read_neuralynx_ncs(filename, 1, 0);</span><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB"> </span><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB">Not sure why this is. Has anyone had the same issue before?</span><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB">Thanks in advance.</span><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB"> </span><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB">Kind regards,</span><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB"> </span><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB">Johannes Lang</span><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.5pt;font-family:"Helvetica",sans-serif">_______________________________________________<br>
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</span><span lang="EN-GB"><a href="https://doi.org/10.1371/journal.pcbi.1002202" target="_blank"><span style="font-size:10.5pt;font-family:"Helvetica",sans-serif;color:#954F72">https://doi.org/10.1371/journal.pcbi.1002202</span></a><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB">_______________________________________________<br>
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