[FieldTrip] Jump artifacts not detected

Schoffelen, J.M. (Jan Mathijs) jan.schoffelen at donders.ru.nl
Thu Jul 9 09:21:36 CEST 2015

Hi Mats,

This sometimes happens, and is the consequence of the fact that the specific algorithmic parameters applied prior to Z-scoring the data are intended to increase the sensitivity to the particular type of artifact at hand, but it does not give a guarantee that all artifact are sufficiently amplified. One reason for this is in your particular case that the jump is not big enough in relation to the total number of samples that are used, causing the Z-value to be sub-threshold.
Either way, if the ‘muscle’ algorithm picks up this jump it’s not a problem, is it?  Either way, the ‘interactive’ mode allows you to play around with the threshold, and to reject/accept individual snippets of data, irrespective of whether the threshold is or is not exceeded.
Out of curiosity, why are you using an ‘old’ version of the code? I suggest that if you have experienced problems with the development version of the code, you team up with one of the knowledgeable people in the group to get it sorted out. If you stick to using static code, you may not benefit from improvements to the development version that may happen in the future.


PS: for efficiency you may want to consider to present screen dumps in your e-mail rather than pointing to a mat-file, because it’ll save time for people who are willing to look into your problem.

Jan-Mathijs Schoffelen, MD PhD, Senior researcher

Max Planck Institute for Psycholinguistics
Donders Centre for Cognitive Neuroimaging

E-mail: j.schoffelen at donders.ru.nl<mailto:j.schoffelen at donders.ru.nl>
Telephone: +31-24-3614793


On Jul 8, 2015, at 10:15 PM, Es, M.W.J. van (Mats) <M.vanEs at donders.ru.nl<mailto:M.vanEs at donders.ru.nl>> wrote:

Hi everyone,

I am currently preprocessing my MEG data (removing artifacts). The strange thing is that when looking for jump artifacts I don't find any, but when looking for muscle artifacts I do find jump artifacts. See the code below. Here you can find 5 trials of my data, where in the second trial there is a jump artifact (according to muscle artifact detection): http://dropcanvas.com/yp0d0

%% detect jump artifacts
cfg = [];

% channel selection, cutoff and padding
cfg.artfctdef.zvalue.channel    = 'MEG';
cfg.artfctdef.zvalue.cutoff     = 20; % artifact threshold
cfg.artfctdef.zvalue.trlpadding = 0;
cfg.artfctdef.zvalue.artpadding = 0;
cfg.artfctdef.zvalue.fltpadding = 0;

% algorithmic parameters
cfg.artfctdef.zvalue.cumulative    = 'yes';
cfg.artfctdef.zvalue.medianfilter  = 'yes';
cfg.artfctdef.zvalue.medianfiltord = 9;
cfg.artfctdef.zvalue.absdiff       = 'yes';

% make the process interactive
cfg.artfctdef.zvalue.interactive = 'yes';

[~, artifact_jump] = ft_artifact_zvalue_old(cfg, data_short);

%% Detect muscle artifacts
cfg            = [];

% channel selection, cutoff and padding
cfg.artfctdef.zvalue.channel = 'MEG';
cfg.artfctdef.zvalue.cutoff      = 4; % artifact threshold
cfg.artfctdef.zvalue.trlpadding  = 0; % pad at both sides of trial till it is ... seconds.
cfg.artfctdef.zvalue.fltpadding  = 0;
cfg.artfctdef.zvalue.artpadding  = 0.2; % take 0.2s padding of an artifact (of the part that is above threshold)

% algorithmic parameters
cfg.artfctdef.zvalue.bpfilter    = 'yes';
cfg.artfctdef.zvalue.bpfreq      = [110 140];
cfg.artfctdef.zvalue.bpfiltord   = 9;
cfg.artfctdef.zvalue.bpfilttype  = 'but';
cfg.artfctdef.zvalue.hilbert     = 'yes';
cfg.artfctdef.zvalue.boxcar      = 0.2;

% make the process interactive
cfg.artfctdef.zvalue.interactive = 'yes';

[~, artifact_muscle] = ft_artifact_zvalue_old(cfg, data_short);

Another thing is that when I only look for jump artifacts in the channel from where I know a jump is present, it actually is detected (try specifying cfg.artfctdef.zvalue.channel    = 'MLF32';)

I am using matlab2013a on the mentat cluster and I use the latest version of FieldTrip. Any help on detecting these jump artifacts is greatly appreciated.

Mats van Es
fieldtrip mailing list
fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>

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