[FieldTrip] Sample discrepancy, and 50Hz line noise filtering

[Per Knutsen]

Dear Florian,
You are not clear about your actual sample rate:

> I do not know either how much trust I have to put in that warning and
correction of the sampling rate in the first place.

Clearly, you should know your own sampling rate from the Neurolynx
acquisition software.

It would seem this is the primary thing you need to resolve.


Regards,
Per




*Per M Knutsen*
University of Oslo
Dept. of Molecular Medicine, Physiology Sect.
PB 1103 Blindern, NO-0317 Oslo
+47.45103762

On Sat, Oct 15, 2016 at 9:25 AM, Florian Gerard-Mercier <
florian at brain.riken.jp> wrote:

> Dear all,
>
> I am wondering, was my question unclear, or maybe no one is using
> Neuralynx data?
> I can think of ways to avoid these two problems, but I would prefer to
> find a proper solution if possible.
>
> Thanks in advance,
>
> Florian Gerard-Mercier
>
>
>
> On 14 Oct, 2016, at 3:08 PM, Florian Gerard-Mercier <
> florian at brain.riken.jp> wrote:
>
> Dear community,
>
>
> My name is Florian Gerard-Mercier and I work in Keiji Tanaka’s laboratory
> in Riken BSI, Japan.
>
>
> I am new to Fieldtrip.
> My goal is to do a simple analysis of ECoG data in response to electrical
> stimulation (all in monkey cortex). To this effect I followed the TMS-EEG
> tutorial (since the issues are almost identical).
> The recording system is Neuralynx.
>
> I have encountered 2 problems which I don’t believe are related.
> I have basically followed the tutorials to the letter so except if I
> mention otherwise, the cfg, etc. are standard.
>
> *1) Fsample discrepancy between data and header.*
> When I load Neuralynx data, I get warnings that the sample rate is
> actually half that in the header, and is thus being corrected (note, 16129
> instead of 32258Hz).
> This is no problem, until I get the final results where I noticed that my
> 50Hz noise is now represented as lasting 40ms for each cycle (= twice
> longer than it actually is).
> Navigating in the workspace, I noticed that even though cfg.Fs is 16129 as
> expected, somehow the data outputted by ft_preprocessing has a field
> fsample equal to half that number (8064.5).
> This later gives many conflicts such as: if I force data.fsample to be
> 16129, I have the correct time axis in the end, but now my trial duration
> is only half that which I want…
> Any idea on how to solve this issue? I haven’t found any previous ticket
> on this Fsample discrepancy issue.
> I do not know either how much trust I have to put in that warning and
> correction of the sampling rate in the first place.
>
> *2) 50Hz line noise filtering*
> The previous point makes it so that if I filter 50Hz, of course nothing
> happens. But even if I filter 25Hz (or 50Hz with the Fsample corrected back
> to 16129), the attenuation is far too small (whether I use padding or not).
> I did look up the similar problems that had been submitted to this list in
> the past, but didn’t find any satisfactory fix.
> To give an idea:
> cfg = [];
> cfg.Fsample   = 1000;  % I downsampled the data in the meantime as said in
> the tuto
> cfg.bsfilter  = 'yes';
> cfg.bsfiltord = 2;           % somehow I have an error that the filtering
> doesn’t work every time I try to run it with an order >2
> cfg.bsfreq    = [49.9 50.1];
> filtDat           = ft_preprocessing(cfg, data_lite);
>
> cfgbrowse = []; cfgbrowse.viewmode = 'butterfly';
> ft_databrowser(cfgbrowse, dat_lite /// filtDat); % screenshots of both
> below
>
> changes this
> <data_lite.jpeg>
>
> into that
>
> <filtDat.jpeg>
>
> {Note also the issue with Fsample: here I have a time axis that
> corresponds to my 50Hz noise, but the duration of the trial is reduced from
> [-0.05, 0.45] by a factor of 2.}
>
> This is in stark contrast to what happens if I use the bandstop filter
> directly on the raw data:
> dat = ft_read_data(dataset_dir);
> dat_filt = ft_preproc_bandstopfilter(dat, 16129, [49.9 50.1], 2);
> changes this
> <RawData.jpeg>
>
> into that
>
> <RawData_after_filter.jpeg>
>
> Which should be perfect for my simple purposes.  (Here I just did a simple
> Matlab plot, so the x axis numbering is not actual time)
>
> Of course, I tried to feed that filtered data into the preprocessing
> pipeline by doing
> cfg = ft_rejectartifact(cfg_artifact);    %cfg_artifact is defined as in
> the tutorial, it is to reject the electrical stimulation artifacts. The
> problem should not stem from here.
> data_artifact_rejected = ft_preprocessing(cfg, dat_filt);
> But I get the error that dat_filt is not raw or comp data.
>
> I have read that it is recommended to do the line noise filtering after
> the trial segmentation and stimulation artefact removal, but 1) it doesn’t
> seem to work well, 2) I don’t really understand why, given that my
> artefacts are nowhere near the 50Hz frequency.
>
> So for this point:
> - how to make the (recommended) 50Hz post processing work?
> - or more simply, how could I feed prefiltered data to ft_preprocessing?
>
>
>
>
> Thank you very much for your consideration and I look forward to your help.
>
> All the best,
>
>
> Florian
>
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