[FieldTrip] RE : Exporting preprocessed data from BVA to Fieldtrip
Eva Masson
eva.masson at hotmail.fr
Mon Sep 20 20:12:53 CEST 2021
Hi Elsa, hi Jan-Mathijs, hi all,
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.
Cheers !
Eva
De : Schoffelen, J.M. (Jan Mathijs) via fieldtrip<mailto:fieldtrip at science.ru.nl>
Envoyé le :lundi 20 septembre 2021 18:20
À : FieldTrip discussion list<mailto:fieldtrip at science.ru.nl>
Cc : Schoffelen, J.M. (Jan Mathijs)<mailto:janmathijs.schoffelen at donders.ru.nl>
Objet :Re: [FieldTrip] Exporting preprocessed data from BVA to Fieldtrip
Dear Elsa,
Thanks for letting us know, and I am glad that you seem up and running by now.
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.
Best wishes,
Jan-Mathijs
On 20 Sep 2021, at 17:53, Elsa Sangaran <elsangaran at gmail.com<mailto:elsangaran at gmail.com>> wrote:
Dear Jan,
Thanks for your suggestions!
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).
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.
Best,
Elsa Sangaran
On Fri, 17 Sept 2021 at 16:45, Schoffelen, J.M. (Jan Mathijs) via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:
Hi Elsa,
Have you consulted this piece of documentation?
https://www.fieldtriptoolbox.org/getting_started/brainvision/<https://urldefense.com/v3/__https:/www.fieldtriptoolbox.org/getting_started/brainvision/__;!!HJOPV4FYYWzcc1jazlU!sjEGljT2DLVAgyLVIV9J38cMwLO2dtj5aoOHELJTW99Id7QovsCWoWwrBpZtj_Fe573RzFo1XMGPTzQ$>
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.
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)?
Best wishes,
Jan-Mathijs
On 17 Sep 2021, at 15:16, Elsa Sangaran via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:
Dear all,
I am having some trouble with the exported data (averages of different conditions in my experiment) which I preprocessed on Brain Vision Analyzer. 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:
Script:
for subj = (name_subj)
% (re)set directory to the directory that contains the trialfun
subject = subj{:};
seg_file =[dir_raw_data_external subject '.seg']; %Subject's .seg file, ie. 'pilot1.seg'
header_file =[dir_raw_data_external subject '.vhdr']; %Subject's .vhdr file, ie. 'pilot1.vhdr'
cfg = [];
cfg.dataset = seg_file;
hdr = ft_read_header(header_file);
nTrials = hdr.nSamples/trial_length;
hdr.nTrials = nTrials;
hdr.nSamples = trial_length;
dat = ft_read_data(seg_file,'header', hdr);
cfg.label = channel_labels;
cfg.trial = squeeze(num2cell(dat,[1 2]))';
cfg.hdr = hdr;
cfg.time = repmat({[time_start:(time_end-time_start)/trial_length:time_end-(time_end-time_start)/trial_length]},1,nTrials);
cfg.label = cfg.hdr.label;
cfg.trialinfo = [];
cfg.sampleinfo = [0 300];
cfg.fsample = 250;
data_raw = cfg;
% make variables for header and eeg file
% headerfile = [dir_raw_data_external subject '.vhdr'];
% segfile = [dir_raw_data_external subject '.seg'];
%
% cfg = [];
% cfg.headerfile = headerfile;
% cfg.dataset = segfile;
% data_raw = ft_preprocessing(cfg);
%
%cfg.trialdef.eventtype = 'string'
%cfg.trialdef.eventvalue = number, string or list with numbers or strings
cfg = [];
cfg.trialdef.prestim = 0.2;
cfg.trialdef.poststim = 1;
cfg.trialdef.eventtype = 'Time 0';
cfg.trialdef.eventvalue = '';
cfg.trialdef.triallength = 1.2;
cfg.trialdef.ntrials = 1;
cfg.headerfile = header_file;
cfg.datafile = seg_file;
cfg_deftrial = ft_definetrial(cfg);
data_segmented = ft_redefinetrial(cfg_deftrial, data_raw);
end
For ft_definetrial, I get the following warnings:
* Warning: could not determine dimord of "dataset"
* Warning: inconsistent sampleinfo
* Warning: inconsistent trialinfo
For ft_redefinetrial, I get the following warnings:
* Warning: the data does not contain sampleinfo
* Warning: reconstructing sampleinfo by assuming that the trials are consecutive segments of a continuous recording
I appreciate your advice and guidance on how to go about this as I am still new to using Fieldtrip.
Thank you in advance for your help.
Best,
Elsa Sangaran
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