[FieldTrip] problem with combing high_pass filter and log transform

[John Begnoche]

Hi Eelke,


Thank you for helping. I am applying the High-Pass filter during my initial pre-processing (6 min resting state EEG data), here is my code for that:

cfg = [];
cfg.dataset = file;
cfg.padding = 0;
cfg.channel = 'all'
cfg.padtype = 'data';
cfg.continuous   = 'yes'
 cfg.hpfilter = 'yes'
 cfg.hpfreq = '1'
cfg.trialdef.triallength = 1
cfg = ft_definetrial(cfg);
data_segmented_preproc= ft_preprocessing(cfg);



here is code for my plotting:

%%% PLOT TEST%%%%

cfg = [];
cfg.channel   = 'eeg 014'
ft_singleplotER(cfg,freqfourier)


Figs are attached.


Thanks again,

Patrick

________________________________
From: fieldtrip <fieldtrip-bounces at science.ru.nl> on behalf of Eelke Spaak <e.spaak at donders.ru.nl>
Sent: Thursday, April 25, 2019 2:27:24 AM
To: FieldTrip discussion list
Subject: Re: [FieldTrip] problem with combing high_pass filter and log transform

Hi Patrick,

Could you provide some more details? First, how are you applying the
high-pass filter? Also, could you give the code you use for plotting
and post the resulting figures?

Best,
Eelke

On Sat, 20 Apr 2019 at 04:53, John Begnoche <jbegnoche at sralab.org> wrote:
>
> Hello,
>
>
> I am plotting outcomes from a frequency analysis of resting state sensor space EEG data, for the analysis I use the code below, and then plot with singleplotER, if I first high pass filter my data at 1Hz during a prepocessing step, my plotting shows no activity until 35Hz then it spikes to a plateau for the rest of he higher frequencies, after a log transform I get a sine wave like shape. With no HP filter the data look like normal power spectrum data, why is the HP filter changing my data in this way?
>
>
>     cfg = [];
>     cfg.output = 'pow' ;
>     cfg.method = 'mtmfft';
>     cfg.pad = 'nextpow2';
>     cfg.taper  = 'hanning';
>     cfg.foilim = [3 50]; %change for appropriate range of frequencies
> %     cfg.tapsmofrq = [2] ;
>     cfg.keeptrials = 'no';
>     %EEG_freq_segmented{i_run} = ft_freqanalysis(cfg, data_segmented_no_artifacts);
>     %EEG_freq_segmented{i_run} = ft_freqanalysis(cfg, data_segmented);
>   % freqfourier{i_run} = ft_freqanalysis(cfg, data_segmented_preproc_ICArm_no_artifacts);
>     freqfourier= ft_freqanalysis(cfg, data_segmented_no_artifacts);
>      %%%%%%log transform%%%%%%%%%%%%%
>     cfg           = [];
>     cfg.parameter = 'powspctrm';
>     cfg.operation = 'log10';
>     freqfourier    = ft_math(cfg, freqfourier);
>
> Thank you,
> Patrick
>
> Confidentiality Notice: This message and any attachments are only for the intended recipient(s) and may contain confidential, privileged and/or protected health information. If you are not the intended recipient of this message, please: 1) be advised that unauthorized review, use, copying, disclosure, or distribution is strictly prohibited and may be unlawful; 2) notify the sender of the delivery by reply e-mail or contact Shirley Ryan AbilityLab's Privacy Officer at 312.238.0766 or privacyofficer at sralab.org; and 3) delete and destroy all copies of the message and its attachments. Thank you.
>
> _______________________________________________
> 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

Confidentiality Notice: This message and any attachments are only for the intended recipient(s) and may contain confidential, privileged and/or protected health information. If you are not the intended recipient of this message, please: 1) be advised that unauthorized review, use, copying, disclosure, or distribution is strictly prohibited and may be unlawful; 2) notify the sender of the delivery by reply e-mail or contact Shirley Ryan AbilityLab's Privacy Officer at 312.238.0766 or privacyofficer at sralab.org<mailto:privacyofficer at sralab.org>; and 3) delete and destroy all copies of the message and its attachments. Thank you.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20190425/6a0ceb97/attachment-0002.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: HPfilterON_beforeLog.jpg
Type: image/jpeg
Size: 12438 bytes
Desc: HPfilterON_beforeLog.jpg
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20190425/6a0ceb97/attachment-0008.jpg>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: HPfilterON_afterLog.jpg
Type: image/jpeg
Size: 13378 bytes
Desc: HPfilterON_afterLog.jpg
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20190425/6a0ceb97/attachment-0009.jpg>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: HPfilterOFF_beforeLog.jpg
Type: image/jpeg
Size: 12280 bytes
Desc: HPfilterOFF_beforeLog.jpg
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20190425/6a0ceb97/attachment-0010.jpg>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: HPfilterOFF_afterLog.jpg
Type: image/jpeg
Size: 14999 bytes
Desc: HPfilterOFF_afterLog.jpg
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20190425/6a0ceb97/attachment-0011.jpg>
-------------- next part --------------
_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
https://doi.org/10.1371/journal.pcbi.1002202