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<span style="">Hi there.</span><o:p class="ContentPasted0" style="font-family: inherit; font-size: inherit; font-style: inherit; font-variant-ligatures: inherit; font-variant-caps: inherit; font-weight: inherit;"> </o:p><br>
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<span style="mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin"><o:p class="ContentPasted0"> </o:p></span></p>
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<span style="mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin" class="ContentPasted0">I am a masters student, new to FieldTrip, currently using the toolbox for the first time to undertake preprocessing, ICA, artifact rejection and statistical analysis
of EEG data. I recently reached the end of my pipeline – successfully performing each of these stages and producing results from my analysis – when I decided to go back and re-try the process again, to try to make further improvements now that I had gotten
some successful practice. <o:p class="ContentPasted0"> </o:p></span></p>
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<span style="mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin"><o:p class="ContentPasted0"> </o:p></span></p>
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<span style="mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin" class="ContentPasted0">After my first successful run of the pipeline, the files and folders that I had been calling in the script weren’t ideally organised, so I reorganised/tidied the
folders and files in the MatLab working directory that I had been using, and made sure to update the paths being called in the pipeline script. It is worth noting here that nothing else in the original pipeline script was yet changed and nothing was removed
from any of the original working directory – files and folders were just re-organised into more relevant folders and sub-folders.<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin"><o:p class="ContentPasted0"> </o:p></span></p>
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<span style="mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin" class="ContentPasted0">Now, when trying to run the very first preprocessing stage of my pipeline again – defining the trials from the events in my raw BDF data with ft_definetrial, I
get an error.<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin"><o:p class="ContentPasted0"> </o:p></span></p>
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<span style="mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin" class="ContentPasted0">Here is the code that I am trying to run:<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin"><o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin" class="ContentPasted0">>> cfg = [];<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin" class="ContentPasted0"><span style="mso-spacerun:yes" class="ContentPasted0"> </span>cfg.dataset = 'al001.bdf'; % Initialise Biosemi Data File.<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin"><o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin" class="ContentPasted0"><span style="mso-spacerun:yes" class="ContentPasted0"> </span>%% Baseline correct.<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin" class="ContentPasted0">cfg.preproc.demean = 'yes'; % Subtract window mean from each point.<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin" class="ContentPasted0">cfg.baselinewindow = [-0.2 0]; % Use window recommended by Steven Luck.<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin"><o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin" class="ContentPasted0">%% De-trend.<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin" class="ContentPasted0">cfg.detrend = 'yes'; % Remove baseline drift.<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin"><o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin" class="ContentPasted0">%% Band-pass filter.<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin" class="ContentPasted0">cfg.bpfilter = 'yes';<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin" class="ContentPasted0">cfg.bpfreq = [0.1 30]; % Use range specified.<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin" class="ContentPasted0">cfg.bpfilttype = 'fir'; % Use FIR filter.<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin"><o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin" class="ContentPasted0">%% Notch (band-stop) filter.<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin" class="ContentPasted0">cfg.bsfreq = [7 8]; % Remove SSVEP of 7.52Hz.<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin"><o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin" class="ContentPasted0">%% Re-reference.<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin" class="ContentPasted0">cfg.reref = 'yes';<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin" class="ContentPasted0">cfg.refmethod = 'avg'; % Use average.<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin"><o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin" class="ContentPasted0">cfg.channel = {'Fp1', 'AF3', 'F7', 'F3', 'FC1', 'FC5', 'T7', 'C3', 'CP1', 'CP5', 'P7', 'P3', 'Pz', 'PO3', 'O1', 'Oz', 'O2', 'Po4', 'P4', 'P8',
'CP6', 'CP2', 'C4', 'T8', 'FC6', 'FC2', 'F4', 'F8', 'AF4', 'Fp2', 'Fz', 'Cz', 'A1', 'A2', 'LEOG', 'REOG', 'UEOG', 'DEOG', 'EXG7', 'EXG8'};<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin" class="ContentPasted0">cfg.refchannel = {'T7', 'T8'}; % Use average of mastoids.<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin"><o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin" class="ContentPasted0">%% Segment.<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin" class="ContentPasted0">cfg.trialdef.eventtype = 'STATUS'; % Events are marked as type 'STATUS'.<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin" class="ContentPasted0">cfg.trialdef.eventvalue = 111:170; % Select these events of interest.<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin" class="ContentPasted0">cfg.trialdef.prestim = 0.5; % Specify time before events to include.<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin" class="ContentPasted0">cfg.trialdef.poststim = 1.5; % Specify time after events to include.<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin"><o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin" class="ContentPasted0">cfg = ft_definetrial(cfg); % Define trials in data to segment into.<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin"><o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin" class="ContentPasted0">trials = cfg.trl; % Save trials definition as variable.<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin"><o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin" class="ContentPasted0">%% Apply pre-processing.<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin" class="ContentPasted0">data = ft_preprocessing(cfg);<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin"><o:p class="ContentPasted0"> </o:p></span></p>
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<span style="mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin"><o:p class="ContentPasted0"> </o:p></span></p>
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<span style="mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin" class="ContentPasted0">Here is the error that I am receiving:<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas"><o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas" class="ContentPasted0">evaluating trial function 'ft_trialfun_general'<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas" class="ContentPasted0">reading the header from 'al001.bdf'<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas"><o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas" class="ContentPasted0">reading the events from 'al001.bdf'<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas" class="ContentPasted0">error opening file: al001.bdf<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas" class="ContentPasted0">One or more output arguments not assigned during<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas" class="ContentPasted0">call to "read_24bit".<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas"><o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas" class="ContentPasted0">Error in read_biosemi_bdf>readLowLevel (line 283)<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas" class="ContentPasted0"><span style="mso-spacerun:yes" class="ContentPasted0">
</span>buf = read_24bit(filename, offset, numwords);<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas"><o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas" class="ContentPasted0">Error in read_biosemi_bdf (line 254)<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas" class="ContentPasted0"><span style="mso-spacerun:yes" class="ContentPasted0">
</span>buf = readLowLevel(filename, offset, epochlength); % see below in subfunction<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas"><o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas" class="ContentPasted0">Error in ft_read_data (line 430)<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas" class="ContentPasted0"><span style="mso-spacerun:yes" class="ContentPasted0">
</span>dat = read_biosemi_bdf(filename, hdr, begsample, endsample, chanindx);<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas"><o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas" class="ContentPasted0">Error in ft_read_event (line 416)<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas" class="ContentPasted0"><span style="mso-spacerun:yes" class="ContentPasted0">
</span>sdata = ft_read_data(filename, 'header', hdr, 'dataformat', dataformat, 'begsample', begsample, 'endsample', endsample, 'chanindx', schan);<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas"><o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas" class="ContentPasted0">Error in ft_trialfun_general (line 116)<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas" class="ContentPasted0"><span style="mso-spacerun:yes" class="ContentPasted0">
</span>event = ft_read_event(cfg.headerfile, eventopt{:});<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="font-family:Consolas" class="ContentPasted0">Error in ft_definetrial (line 198)<o:p class="ContentPasted0"> </o:p></span></p>
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</span>[trl, event] = feval(cfg.trialfun, cfg);<o:p class="ContentPasted0"> </o:p></span></p>
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Given that the paths are all being called correctly, and this same code that I am using was successful in reading these same files, earlier, in the successful run of the pipeline, I cannot explain why this error in reading the events is occurring. Is there
any way that the reorganisation of the MatLab path could have created an issue with the BDF events being read? Or is there another explanation for this error, given that the issue must not reside within the previously successful code or data files, themselves?<o:p class="ContentPasted0"> </o:p></p>
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I’d really appreciate any insight that the FieldTrip community can provide.<o:p class="ContentPasted0"> </o:p></p>
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Thanks.<o:p class="ContentPasted0"> </o:p></p>
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Oscar Anderson</p>
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