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Hi Marta,
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<div class="">Rather than just trying out more or less all kinds of possible solutions, I suggest to step back and think about what you want to achieve:</div>
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<div class="">You seem to want to call ft_channelrepair and use the ’spline’ method to interpolate between non-bad channels, to get a modelled signal for the bad channels.</div>
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<div class="">So far so good.</div>
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<div class="">Now, in order to use the ’spline’ method, you need to supply a geometric description of the channels, a.k.a. an elec structure, which is a matlab structure that at least should specify the 3D positions of the electrodes. This is different from
a layout, because a layout is a 2D schematic of the channel array that can be used for topographical visualization. Also, it could be that another method in ft_channelrepair does not require a set of 3D channel position, but only requires a definition of channel
neighbours (without position information). So, you either need to supply ft_channelrepair with 3D channel position information for the ’spline’ interpolation, or you should consider using a different interpolation method.</div>
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<div class="">What you should know, is that the information in the layout structure, pertaining to the channel positions, is stored in the field <name-of-the-variable>.pos, whereas in an elec structure, the channel positions should be represented as <name-of-the-variable>.chanpos,
so your attempt in adding a column of zeros is not only wrong in the sense that it would have led to a distorted spline interpolation, it is also not going to work due to a difference in fieldnames.</div>
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<div class="">Long story short, if you require ft_channelrepair to use a method that needs a sensor description, you need to pass a valid sensor description in the cfg, OR in the data argument.</div>
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<div class="">Please consult the documentation</div>
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<div class=""><a href="https://www.fieldtriptoolbox.org/faq/how_are_electrodes_magnetometers_or_gradiometers_described/" class="">https://www.fieldtriptoolbox.org/faq/how_are_electrodes_magnetometers_or_gradiometers_described/</a></div>
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<div class="">for a more detailed description of an elec-array.</div>
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<div class="">Best wishes,</div>
<div class="">Jan-Mathijs</div>
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<div class="">On 28 May 2021, at 15:59, Marta Topor via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>> wrote:</div>
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Hi Tzvetan, </div>
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Thank you for your quick response, much appreciated!</div>
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I have spent a bit of time today trying to work this out. </div>
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If I do not include the cfg.elec line, I get another error:</div>
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<span style="font-family: "Courier New", monospace;" class="">Error using ft_fetch_sens (line 202)</span><br class="">
<span style="font-family: "Courier New", monospace;" class="">no electrodes, gradiometers or optodes specified.</span><br class="">
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<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">I have checked through my code and files thoroughly and I do not have a 3D layout file. I initially created my layout file from an image and it has always been in 2D.
It seems that when I was running the code before, it worked OK with the 2D file. </span></div>
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<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">Do you have any ideas for getting around this issue? I tried adding 0s throughout the layout structure to "pretend" it was 3D but it also did not work that way. </span></div>
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<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">Thanks again and best wishes,</span></div>
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<font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>fieldtrip <<a href="mailto:fieldtrip-bounces@science.ru.nl" class="">fieldtrip-bounces@science.ru.nl</a>> on behalf of Tzvetan
Popov <<a href="mailto:tzvetan.popov@uni-konstanz.de" class="">tzvetan.popov@uni-konstanz.de</a>><br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>28 May 2021 7:37 AM<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [FieldTrip] layout file error after upgrading to the newest version</font>
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Dear Marta,
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<div class="">In your cfg.elec, a 3D description of electrodes positions is expected. Yet you have a 2D layout structure. I assume that your neighbours are also defined in this 2D plane. </div>
<div class="">Can you comment out the cfg.elec line and try again? Ft_read_sens is not supposed to work on 2D layout file, hence the error. </div>
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<div class="">Good luck,</div>
<div class="">tzvetan</div>
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<blockquote type="cite" class="">
<div class="">On 27 May 2021, at 22:24, Marta Topor <<a href="mailto:m.topor@surrey.ac.uk" class="">m.topor@surrey.ac.uk</a>> wrote:</div>
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Dear colleagues, </div>
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I came across a surprising error and I am struggling to figure it out. </div>
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<span class="" style="font-size: 12pt; font-family: Calibri, Arial, Helvetica, sans-serif;">I wrote a few scripts last year in version</span><span class="" style="font-size: 12pt; font-family: Calibri, Arial, Helvetica, sans-serif;"> </span><span class="" style="font-size: 12pt; font-family: Calibri, Arial, Helvetica, sans-serif;">fieldtrip-20200409.
They all worked fine, last time I worked with those scripts in that version was January 2021. I had to take care of a few other tasks since then, so the project was on pause. I had my work laptop upgraded in the meantime which meant I had to upgrade to the
newest Fieldtrip version.</span><br class="">
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<span class="" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; display: inline !important;">I started working on that same project again, in version fieldtrip-20210525, and noticed layout file issues when interpolating channels. </span></div>
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<span class="" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; display: inline !important;">For a bit of background, I am using the Mobita water-based 32 EEG electrode system. I created my own layout file in the previous Fieldtrip
version which worked without any issues in all scripts.</span></div>
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<span class="" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; display: inline !important;">I now have an error using the ft_channelrepair() funtion and I think it relates to the ft_read_sens() funtion. </span></div>
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<span class="" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; display: inline !important;"><b class="">The cfg I used: </b></span></div>
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<span class="" style="font-family: "Courier New", monospace; font-size: 12pt;">cfg = [];</span><br class="">
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<div class=""><span class="" style="font-family: "Courier New", monospace; font-size: 12pt;">cfg.method = 'spline';</span></div>
<div class=""><span class="" style="font-family: "Courier New", monospace; font-size: 12pt;">cfg.neighbours = neighbours_EEG;</span></div>
<div class=""><span class="" style="font-family: "Courier New", monospace; font-size: 12pt;">cfg.badchannel = badchannels_train;</span></div>
<div class=""><span class="" style="font-family: "Courier New", monospace; font-size: 12pt;">cfg.senstype = 'EEG';</span></div>
</span><span class="" style="font-family: "Courier New", monospace; font-size: 12pt; display: inline !important;">cfg.elec = layout_file;</span><span class="" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; display: inline !important;"><br class="">
</span></div>
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<span class="" style="font-family: "Courier New", monospace; font-size: 12pt; display: inline !important;">mydata_interpolated_train = ft_channelrepair(cfg, mydata_artrm_train);</span><span class="" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; display: inline !important;"><br class="">
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<div class=""><b class="">The layout file fields are:</b></div>
<div class=""><span class="" style="font-family: "Courier New", monospace;">pos: [34×2 double]</span>
<div class=""><span class="" style="font-family: "Courier New", monospace;">label: {34×1 cell}</span></div>
<div class=""><span class="" style="font-family: "Courier New", monospace;">width: [34×1 double]</span></div>
<div class=""><span class="" style="font-family: "Courier New", monospace;">height: [34×1 double]</span></div>
<div class=""><span class="" style="font-family: "Courier New", monospace;">outline: {1×4 cell}</span></div>
<div class=""><span class="" style="font-family: "Courier New", monospace;">mask: {[101×2 double]}</span></div>
<span class="" style="font-family: "Courier New", monospace;">cfg: [1×1 struct]</span><br class="">
</div>
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<div class="">But I can only see these fields if I use the function importdata(). When I use the function ft_read_sens() and when I try to interpolate channels, I get the following error:</div>
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<div class=""><b class="">Error message:</b></div>
<div class=""><span class="" style="font-family: "Courier New", monospace; font-size: 12pt;">Unrecognized function or variable 'lab'.</span>
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<div class=""><span class="" style="font-family: "Courier New", monospace; font-size: 12pt;">Error in channelposition (line 352)</span></div>
<div class=""><span class="" style="font-family: "Courier New", monospace; font-size: 12pt;">n = size(lab,2);</span></div>
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<div class=""><span class="" style="font-family: "Courier New", monospace; font-size: 12pt;">Error in ft_datatype_sens (line 438)</span></div>
<div class=""><span class="" style="font-family: "Courier New", monospace; font-size: 12pt;"> [chanpos, chanori, lab] = channelposition(sens);</span></div>
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<div class=""><span class="" style="font-family: "Courier New", monospace; font-size: 12pt;">Error in ft_datatype_sens (line 240)</span></div>
<div class=""><span class="" style="font-family: "Courier New", monospace; font-size: 12pt;"> sens = ft_datatype_sens(sens, new_argin{:});</span></div>
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<div class=""><span class="" style="font-family: "Courier New", monospace; font-size: 12pt;">Error in ft_datatype_sens (line 207)</span></div>
<div class=""><span class="" style="font-family: "Courier New", monospace; font-size: 12pt;"> sens = ft_datatype_sens(sens, new_argin{:});</span></div>
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<div class=""><span class="" style="font-family: "Courier New", monospace; font-size: 12pt;">Error in ft_datatype_sens (line 180)</span></div>
<div class=""><span class="" style="font-family: "Courier New", monospace; font-size: 12pt;"> sens = ft_datatype_sens(sens, new_argin{:});</span></div>
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<div class=""><span class="" style="font-family: "Courier New", monospace; font-size: 12pt;">Error in ft_read_sens (line 539)</span></div>
<div class=""><span class="" style="font-family: "Courier New", monospace; font-size: 12pt;">sens = ft_datatype_sens(sens);</span></div>
<span class="" style="font-size: 12pt;"> </span><br class="">
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<span class="" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">There are no errors when I plot the channels using the following code though and it all looks absolutely fine:</span></div>
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<span class="" style="font-family: "Courier New", monospace; font-size: 12pt;">cfg = [];</span>
<div class=""><span class="" style="font-family: "Courier New", monospace; font-size: 12pt;">cfg.layout = layout_m; %layout_m is imported from the layout_file using the importdata() function</span></div>
<div class=""><span class="" style="font-family: "Courier New", monospace; font-size: 12pt;">cfg.channel = 'eeg';</span></div>
<span class="" style="font-family: "Courier New", monospace; font-size: 12pt;">ft_layoutplot(cfg, mydata_artrm_train);</span><br class="">
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<span class="" style="font-family: Calibri, Helvetica, sans-serif; font-size: 12pt;">Any ideas what could be the issue here and how I could get it solved? </span></div>
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<span class="" style="font-family: Calibri, Helvetica, sans-serif; font-size: 12pt;">Thanks for your help in advance!</span></div>
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<div class="" style="margin-top: 0px; margin-bottom: 0px;"><span class="" style="font-family: "Calibri Light", "Helvetica Light", sans-serif;">_________________________</span></div>
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<div class="" style="margin-top: 0px; margin-bottom: 0px;"><span class="" style="font-family: "Calibri Light", "Helvetica Light", sans-serif;">Marta Topor</span></div>
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<div class="" style="margin-top: 0px; margin-bottom: 0px;"><span class="" style="font-family: "Calibri Light", "Helvetica Light", sans-serif;">School of Psychology</span></div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><span class="" style="font-family: "Calibri Light", "Helvetica Light", sans-serif;">University of Surrey </span></div>
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<span class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none; float: none; display: inline !important;">fieldtrip
mailing list</span><br class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none;">
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