[FieldTrip] ft_rejectvisual function gives errors in 2020 fieldtrip versions

Tue Jun 2 11:37:01 CEST 2020

Dear Helena,

Thanks for providing some more details. Indeed, the error occurs (as I suspected) because you explicitly define the cfg.ylim to have only a single element. This is incorrect because the code expects a 2-element vector (e.g. [-60 60]) once this parameter is defined as a numeric variable. I suspect that things will run through fine for you if you either omit cfg.ylim altogether, or specify it as ‘maxmin’, or specify a 2-element vector. I saw that this parameter is not documented in the help-section of the function, and I suspect there might be more undocumented options. Please feel free to update the documentation section of the function in order to avoid similar future problems with other users, and send us a PR through github.
Thanks for noticing!

Best wishes,
Jan-Mathijs

On 2 Jun 2020, at 11:16, Helena Pereira <hri.pereira at campus.fct.unl.pt<mailto:hri.pereira at campus.fct.unl.pt>> wrote:

Dear Jan-Mathijs,

Thank you for your e-mail.

I am using data from the output of ICA (.mat data). Here is my cfg for visual artifact:

cgf = [];
cfg.preproc.demean = 'yes';
cfg.prepoc.baselinewindow  = [-0.2 0];
data_process=ft_preprocessing(cfg,data_process );

cgf = [];
cfg.method   = 'trial';
cfg.ylim =  60;
visual_cleaned = ft_rejectvisual(cfg,data_process);

cgf = [];
cfg.method   = 'channel';
cfg.alim =  50 ; %why this value?
%cfg.eogscale = 5e-8;
vc_data = ft_rejectvisual(cfg,visual_cleaned);

For ICA:
cfg = [];
%cfg.channel = 1:64;
cfg.method = 'runica';
cfg.demean = 'yes';
ica_cleaned = ft_componentanalysis(cfg, vc_data);

% %Save ICA data
outfile=strcat(save_dir,'/',infile,'_', sti,'.mat')
save(outfile, 'ica_cleaned', '-v7.3')

Before ICA, I did the following processing steps:
cfg = [];
cfg.dataset=infile;   % infile: data.seg
cfg.trialfun = 'ft_trialfun_general'; % this is the default
cfg.trialdef.eventtype  = 'Stimulus'; %Event type: e.g. Stimulus, response, STATUS
cfg.trialdef.eventvalue = {stimulus};

cfg.trialdef.prestim    = 2; %latency in seconds
cfg.trialdef.poststim   = 2; %latency in seconds
cfg=ft_definetrial(cfg);

% Processing AOC, AMC and MC data
cfg.channel = [1:69]; %discard channels not used
cfg.preproc.reref = 'yes';
cfg.preproc.refchannel = {'M1' 'M2'}; %avg mastoids
cfg.continuous = 'no';
cfg.preproc.detrend = 'no';
%Baseline correction
cfg.preproc.demean = 'yes';
cfg.prepoc.baselinewindow  = [-0.2 0];
%Filtering
cfg.preproc.lpfilter = 'yes';
cfg.preproc.hpfilter = 'yes';
cfg.preproc.lpfreq = 100;
cfg.preproc.hpfreq = 1;
data_process=ft_preprocessing(cfg);

Can the error be associated with the fact that I am using non-continuous data?

I am using BrainVision Format, that is, .seg, .vmrk and vhdr data.

Thank you,
Stay safe,
Helena Pereira

Schoffelen, J.M. (Jan Mathijs) <jan.schoffelen at donders.ru.nl<mailto:jan.schoffelen at donders.ru.nl>> escreveu no dia terça, 2/06/2020 à(s) 09:28:
Hi Helena,

ft_rejectvisual is not deprecated. As a matter of fact, there has been some recent updates to this function, to make its behavior more robust. Since these changes have passed our internal tests, the new version has made it into the release version. Unfortunately, this seems to cause you some problems. As of yet, it is not clear whether this now is a genuine bug, or a feature of an inconsistency in your data, which only surfaces now. In order to be able to confirm your problem, you’d need to give a bit more detail about what you have been doing. Important details to include are some characteristics of the data, and a specification of the cfg that you used as an input to ft_rejectvisual. Also, you couuld try and diagnose the problem a bit more yourself by using the matlab debugger, which you can use to investigate why the variable info.cfg.ylim seems to have an unexpected number of elements (as the error message suggests).

Best wishes,

Jan-Mathijs

On 1 Jun 2020, at 20:51, Helena Pereira <hri.pereira at campus.fct.unl.pt<mailto:hri.pereira at campus.fct.unl.pt>> wrote:

Dear all,

I am analysing data from EEG subjects. To remove artifacts, I used a code that was computed using the ft_rejectvisual function of 20191019 fieldtrip version. However, when the fieldtrip was uptaded to the 20200521, this error appeared:

Index exceeds the number of array elements (1).

Error in rejectvisual_trial>redraw (line 274)
  ymax = info.cfg.ylim(2);

Error in rejectvisual_trial (line 96)
  redraw(h);

Error in ft_rejectvisual (line 230)
    [chansel, trlsel, cfg] = rejectvisual_trial(cfg,
    tmpdata);

Is ft_rejectvisual function deprecated? How can I solve this error? The version 20191019 is no longer available at the FTP server, but I know it works well because I tested the code with that old version.

Thanks in advance,
Best regards,
Helena Pereira

_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
https://doi.org/10.1371/journal.pcbi.1002202

_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
https://doi.org/10.1371/journal.pcbi.1002202
_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
https://doi.org/10.1371/journal.pcbi.1002202

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20200602/13a00df9/attachment.htm>