[FieldTrip] simultaneous artifact and ICA viewing in ft_databrowser

[Stan van Pelt]

For everyone's information, I have found a solution based on a post some 4
years ago related to ft_resampledata
(http://mailman.science.ru.nl/pipermail/fieldtrip/2010-September/003095.ht
ml).

To make the ICA and artifact data align, the trl-field of the ICA-data
needs to be 'resampled', as well as the artifact-samples:

 

    % i. Downsample data

    resamplefs     = 150;

    cfg            = [];

    cfg.resamplefs = resamplefs;

    cfg.detrend    = 'no';

    data150        = ft_resampledata(cfg, data);

    % 'Downsample' trial information to make trial start/end samplenrs
correspond to artifact samplenrs 

    data150.cfg.previous.trl(:,1:3) =
round(data150.cfg.previous.trl(:,1:3) * (1/fs) * resamplefs); 

    

    % ii. run ICA on downsampled data

    cfg              = [];

    cfg.method       = 'runica'; % this is the default and uses the
implementation from EEGLAB

    cfg.channel      = 'MEG';

    cfg.runica.maxsteps = 120;

    eval(['comp150',num2str(n),'= ft_componentanalysis(cfg, data150);']);

    

    % iii. plot the components for visual inspection and select bad
components

    cfg              = [];

    cfg.component    = [1:10]; % components to be plotted

    cfg.layout       = 'CTF275.lay'; % specify the layout file that should
be used for plotting

 

    % add preveiously manually defined eog and muscle artifacts, to
compare with components

    load artifact_eog_all

    load artifact_muscle_all

    cfg.artfctdef.eog.artifact=ceil(art_eog_all*(resamplefs/fs)); %
'resample' artifact data

    cfg.artfctdef.muscle.artifact=ceil(art_muscle_all*(resamplefs/fs)); %
'resample' artifact data

    

    % visual inspection

    ft_databrowser(cfg, comp150',num2str(n),');

 

    % 'Upsample' trial information again to original 

    data150.cfg.previous.trl(:,1:3) = data.cfg.trl(:,1:3);

 

Best,

Stan

 

From: fieldtrip-bounces at science.ru.nl
[mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Stan van Pelt
Sent: maandag 6 oktober 2014 9:17
To: 'FieldTrip discussion list'
Subject: [FieldTrip] simultaneous artifact and ICA viewing in
ft_databrowser

 

Dear fellow FieldTrippers,

 

For proper artifact removal, I would like to compare the (temporal)
correspondence between the ICA components of my (CTF MEG275) data and the
artifacts that I semi-automatically identified beforehand (eye blinks,
saccades, muscle tension). ft_databrowser in principle allows me to show
this, but I run into some problems that I think have to do with data
resampling. The code I use is:

 

% iii. plot the components for visual inspection and select bad components

cfg              = [];

cfg.component    = [1:10]; % components to be plotted

cfg.layout       = 'CTF275.lay'; % specify the layout file that should be
used for plotting

 

% add preveiously manually defined eog and muscle artifacts, to compare
with components 

load artifact_eog_all

load artifact_muscle_all    

cfg.artfctdef.eog.artifact=art_eog_all;

cfg.artfctdef.muscle.artifact=art_muscle_all;

    

% visual inspection

ft_databrowser(cfg, comp150);

 

The problem I have is that the artifacts are not shown at the right
moments in time during the experiment. The data that are ICA-ed are
resampled from 1200->150Hz, but I do not know how I can 'resample' the
artifact definitions, since they are defined in samples, not in time. If I
manually resample (by dividing the values by a factor 8), they are still
not displayed at the correct moments in time.

I have the impression that convert_event (fieltrip/private) could be of
use here, but I cannot figure it out correctly.

 

Best,

Stan

 

--

Stan van Pelt, PhD

Donders Institute for Brain, Cognition and Behaviour

Radboud University

Montessorilaan 3, B.01.34

6525 HR Nijmegen, the Netherlands

tel: +31 24 3616288 

 

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