[FieldTrip] about detrend

Jörn M. Horschig jorn at artinis.com
Mon Dec 8 10:18:09 CET 2014


Hey guys,

 

FieldTrip is subtracting the DC component prior to filtering to reduce
artifacts arising from DC components (and then adding it back). FieldTrip is
doing this always, i.e. also if you do not want a demeaned signal.

 

As FieldTrip is open source, you can easily check all this by browsing
through the functions yourself.Then you’ll also see the order in which
preprocessing options are applied. They do NOT depend on the how you set
them in your script, but follow a hard-coded logic. First the
detrending/demeaning (called polyremoval in FieldTrip) is applied, and then
the filters are applied.

 

For checking these things yourself, checkout the fieldtrip/private/preproc.m
function and the fieldtrip/preproc/ft_preproc_*filter. functions.

 

Best,

Jörn

 

 

--

 

Jörn M. Horschig, Software Engineer

 <http://www.artinis.com/> Artinis Medical Systems  |  +31 481 350 980 

 

From: fieldtrip-bounces at science.ru.nl
[mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Alexander Nakhnikian
Sent: Sunday, December 7, 2014 5:50 PM
To: FieldTrip discussion list
Subject: Re: [FieldTrip] about detrend

 

I would.  Baseline correction removes background components from the ERP but
it does remove linear offset that is part of the post-stimulus time series.
In addition to getting ride of DC, detrending also removes certain
non-stationarities and reduces the severity of edge effects.  I use it as a
matter of course unless there is a compelling reason to omit it from the
analysis pipeline.  



 

On 12/7/14, 5:53 AM, Yun Wen wrote:

Hi, Alexander. Thank you for your help. Do you suggest that I do baseline
correction plus detrend, e,g,  cfg.blc = 'yes' & cfg.detrend = 'yes' on
epoched data? 

Best,

Yun

 

 

From: fieldtrip-bounces at science.ru.nl
<mailto:fieldtrip-bounces at science.ru.nl>
[mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Alexander Nakhnikian
Sent: Saturday, December 06, 2014 1:14 AM
To: FieldTrip discussion list
Subject: Re: [FieldTrip] about detrend

 

It looks as though the take home message is that in theory high pass filters
remove DC but you can't be sure how they will interact with empirical data
since there is no perfect filter in the real world.  If other people report
substantial artifacts after filtering data without removing the DC component
I suggest getting rid of it.  To answer your original question, assuming
you're detrending each epoch individually it should remove the DC component
or at least reduce it substantially.   

I hope that helps.



On 12/5/14, 6:20 PM, Yun Wen wrote:

Hi, Alexander & Rodrigo. Thank you very much for your help. I collected my
data with DC recordings (BioSemi system). I have seen some discussion on the
DC offset:

http://sccn.ucsd.edu/pipermail/eeglablist/2014/008068.html

http://sccn.ucsd.edu/pipermail/eeglablist/2008/002229.html

http://sccn.ucsd.edu/pipermail/eeglablist/2010/003315.html

http://erpinfo.org/erplab/erplab-documentation/manual/Filtering.html

 

It seems to me that I’d better remove DC offset of continuous data before
high-pass filter. Am I right?

Best,

Yun

 

From: fieldtrip-bounces at science.ru.nl
<mailto:fieldtrip-bounces at science.ru.nl>
[mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Alexander Nakhnikian
Sent: Friday, December 05, 2014 10:19 PM
To: FieldTrip discussion list
Subject: Re: [FieldTrip] about detrend

 

Hello Again,

I think there's an error in my response. I think removing the linear trend
should also set the mean to zero already since the best fit line
incorporates vertical offset.  Sorry about that.  

A





 

On 12/5/14, 4:20 PM, Yun Wen wrote:

Hi all, I want to remove DC offset before applying the high-pass filter. I
was wondering if I can achieve that by putting cfg.detrend = 'yes' before
cfg.hpfilter = 'yes', something like:

 

cfg = []; 

cfg.dataset = filename_raweeg;

cfg.detrend = 'yes'; 

cfg.hpfilter = 'yes';

cfg.hpfiltord = 2; % Order of the filter = 2.

cfg.hpfreq = 0.1; % High-pass cutoff at 0.1 Hz;

[data] = ft_preprocessing (cfg);

 

Thank you in advance.

 

Best,

Yun

 

 
 
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This message has been checked for viruses but the contents of an attachment
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University of Nottingham may be monitored as permitted by UK legislation.

 

 
 
This message and any attachment are intended solely for the addressee and
may contain confidential information. If you have received this message in
error, please send it back to me, and immediately delete it.   Please do not
use, copy or disclose the information contained in this message or in any
attachment.  Any views or opinions expressed by the author of this email do
not necessarily reflect the views of the University of Nottingham.
 
This message has been checked for viruses but the contents of an attachment
may still contain software viruses which could damage your computer system,
you are advised to perform your own checks. Email communications with the
University of Nottingham may be monitored as permitted by UK legislation.

 

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