[FieldTrip] Errors with downsampling and artifact rejection
Gaëlle Leys
gaelle.leys at kuleuven.be
Mon Jun 22 16:47:00 CEST 2020
Dear Stephen,
I have included the data structures and cfg's involved in the functions.
1) A. data structure for resampling data (raw data after reading it in):
data_eeg =
struct with fields:
hdr: [1×1 struct]
label: {129×1 cell}
time: {[1×245726 double]}
trial: {[129×245726 double]}
fsample: 1000
sampleinfo: [1 245726]
elec: [1×1 struct]
cfg: [1×1 struct]
1) B. cfg for resampling data (I’m using all the default options for resampling):
Cfg=[];
[data_eeg] = ft_resampledata(cfg, data_eeg); % defaults are all OK
2) A. data structure for artifact rejection (my data already epoched):
data_eeg =
struct with fields:
hdr: [1×1 struct]
label: {129×1 cell}
time: {1×108 cell}
trial: {1×108 cell}
fsample: 1000
sampleinfo: [108×2 double]
elec: [1×1 struct]
cfg: [1×1 struct]
2) B. cfg for artifact rejection (taken from the automatic artifact rejection example):
% jump
cfg = [];
cfg.trl = trl;
cfg.datafile = '100_1_20200305.mff';
cfg.headerfile = '100_1_20200305.mff';
cfg.continuous = 'yes';
% channel selection, cutoff and padding
cfg.artfctdef.zvalue.channel = 'EEG';
cfg.artfctdef.zvalue.cutoff = 20;
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';
[cfg, artifact_jump] = ft_artifact_zvalue(cfg); %plot error and error using zeros
%[cfg, artifact_jump] = ft_artifact_zvalue(cfg, data_eeg); %no plot error, but each trial has the same graph, also error using zeros
Kind regards,
Gaëlle Leys
-----Original Message-----
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Today's Topics:
1. Errors with downsampling and artifact rejection (Gaëlle Leys)
2. Re: Errors with downsampling and artifact rejection
(Stephen Whitmarsh)
3. MNI coordinates for the EEG easycap-M1 layout
(SILVA PEREIRA, SILVANA)
----------------------------------------------------------------------
Message: 1
Date: Fri, 19 Jun 2020 12:48:26 +0000
From: Gaëlle Leys <gaelle.leys at kuleuven.be>
To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
Subject: [FieldTrip] Errors with downsampling and artifact rejection
Message-ID:
<ccb89b4d31af42d3b4cd22485438f4ef at ICTS-S-EXMBX17.luna.kuleuven.be>
Content-Type: text/plain; charset="iso-8859-1"
Dear Fieldtrip community,
I have recently started with Fieldtrip for my EEG data processing and I am encountering some problems which I can't seem to resolve.
I'm working with mff files from an EGI EEG system. I have no problem reading in and preprocessing the data. However, when trying to downsample and setup the automatic artifact removal, I'm getting some errors.
1) When trying to downsample with the default options, these are the errors that I get:
Error using resample>getSamples (line 357) The number of elements of Tx must match the number of rows of X when X is a matrix
Error in resample>nonUniformResample (line 123) [x, tx] = getSamples(varargin{1:2});
Error in resample (line 116)
[varargout{1:max(1,nargout)}] = nonUniformResample(method,varargin{:});
Error in ft_resampledata (line 228)
newdat = transpose(resample(transpose(olddat),fsres,fsorig));
I have tried downsampling before filtering, after filtering, on continuous data, or already segmented data. None of these things seem to resolve the error.
2) When trying to set up the automatic artifact removal process and choosing yes for the interactive plot, I get a plotting error:
Error using plot
Vectors must be the same length.
Error in ft_artifact_zvalue>redraw_cb (line 973)
plot(opt.h1, xval, yval, 'linestyle', '-', 'color', 'b', 'displayname', 'data');
Error in ft_artifact_zvalue (line 512)
redraw_cb(h);
I've noticed that the xval and yval are different numbers, which of course doesn't allow plotting. It seems like the xval changes according to the epoch length, however the yval remains the same and equals the amount of samples in my continuous data.
3) When choosing no for the interactive plot, I also get an error:
Error using zeros
Size inputs must be integers.
Error in ft_artifact_zvalue (line 568)
dum = zeros(1,max(opt.trl(:,2)));
I've been looking into the functions and where it goes wrong, but I can't seem to pinpoint what exactly is causing these issues. Anyone here that can help or provide me some tips?
Thanks in advance!
Kind regards,
Gaëlle Leys
Research Associate
Brain & Cognition
Tiensestraat 102 box 3714
3000 Leuven
Room PSI 02.33
tel. +32 16 37 61 98
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Message: 2
Date: Fri, 19 Jun 2020 15:08:21 +0200
From: Stephen Whitmarsh <stephen.whitmarsh at gmail.com>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] Errors with downsampling and artifact
rejection
Message-ID:
<CAFrxm=w44QZ0C7xB4cpsqdy0D0ou5UcpHNM-q3bjyaqwwJxRwg at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Dear Gaëlle,
To understand the problem it would be helpful to have 1) description of the data structures going in ft_resampledata (just type in command line and copy-paste the output) and the artefact detection function you are using, and 2) the configuration (cfg) you are using for those functions.
Cheers,
Stephen
Op vr 19 jun. 2020 om 14:56 schreef Gaëlle Leys <gaelle.leys at kuleuven.be>:
> Dear Fieldtrip community,
>
>
>
> I have recently started with Fieldtrip for my EEG data processing and
> I am encountering some problems which I can’t seem to resolve.
>
> I’m working with mff files from an EGI EEG system. I have no problem
> reading in and preprocessing the data. However, when trying to
> downsample and setup the automatic artifact removal, I’m getting some errors.
>
>
>
> 1) When trying to downsample with the default options, these are the
> errors that I get:
>
> Error using resample>getSamples (line 357)
>
> The number of elements of Tx must match the number of rows of X when X
> is a matrix
>
>
>
> Error in resample>nonUniformResample (line 123)
>
> [x, tx] = getSamples(varargin{1:2});
>
>
>
> Error in resample (line 116)
>
> [varargout{1:max(1,nargout)}] =
> nonUniformResample(method,varargin{:});
>
>
>
> Error in ft_resampledata (line 228)
>
> newdat = transpose(resample(transpose(olddat),fsres,fsorig));
>
>
>
> I have tried downsampling before filtering, after
> filtering, on continuous data, or already segmented data. None of
> these things seem to resolve the error.
>
>
>
> 2) When trying to set up the automatic artifact removal process and
> choosing yes for the interactive plot, I get a plotting error:
>
> Error using plot
>
> Vectors must be the same length.
>
>
>
> Error in ft_artifact_zvalue>redraw_cb (line 973)
>
> plot(opt.h1, xval, yval, 'linestyle', '-', 'color', 'b',
> 'displayname', 'data');
>
>
>
> Error in ft_artifact_zvalue (line 512)
>
> redraw_cb(h);
>
>
>
> I’ve noticed that the xval and yval are different numbers,
> which of course doesn’t allow plotting. It seems like the xval changes
> according to the epoch length, however the yval remains the same and
> equals the amount of samples in my continuous data.
>
>
>
> 3) When choosing no for the interactive plot, I also get an error:
>
> Error using zeros
>
> Size inputs must be integers.
>
>
>
> Error in ft_artifact_zvalue (line 568)
>
> dum = zeros(1,max(opt.trl(:,2)));
>
>
>
> I’ve been looking into the functions and where it goes wrong, but I
> can’t seem to pinpoint what exactly is causing these issues. Anyone
> here that can help or provide me some tips?
>
>
>
> Thanks in advance!
>
>
>
> Kind regards,
>
>
>
> Gaëlle Leys
>
>
>
> Research Associate
> Brain & Cognition
> Tiensestraat 102 box 3714
> 3000 Leuven
>
> Room PSI 02.33
> tel. +32 16 37 61 98
>
>
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://doi.org/10.1371/journal.pcbi.1002202
>
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Message: 3
Date: Fri, 19 Jun 2020 18:58:36 +0200
From: "SILVA PEREIRA, SILVANA" <silvana.silva at upf.edu>
To: fieldtrip at science.ru.nl
Subject: [FieldTrip] MNI coordinates for the EEG easycap-M1 layout
Message-ID:
<CA+_MWm1NufDWa-fjR71OzQ5ab88ioyUT8OJ-QFYX9ABr7gNQrA at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Dear community,
I've been struggling to find the 3D positions (montages) for the
Acticap-64ch-standard2 on the web, which is a modified version of the easycap-M1, but I have not succeeded. In the Fieldtrip page http://www.fieldtriptoolbox.org/template/electrode/ you have the following:
You can find the template 3-D electrode sets included in FieldTrip here <https://github.com/fieldtrip/fieldtrip/tree/master/template/electrode>.
But in that link you only find a txt file with theta-phi coordinates (easycap-M1.txt). Is there any place where I could find these positions in MNI space?
Thank you and best regards,
Silvana
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