[FieldTrip] Referencing (Hwee Ling Lee)

Pierre M├ęgevand pierre.megevand at gmail.com
Tue Feb 25 17:14:42 CET 2014


Dear Hweeling,

ft_apply_montage is the function that you are looking for.
http://fieldtrip.fcdonders.nl/reference/ft_apply_montage

The documentation for that function shows exactly what you want to do.

Pierre

--
Pierre M├ęgevand, MD, PhD
Post-doctoral research fellow
Laboratory for Multimodal Human Brain Mapping
Feinstein Institute for Medical Research
Manhasset, NY, USA


On Tue, Feb 25, 2014 at 6:00 AM, <fieldtrip-request at science.ru.nl> wrote:

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> Today's Topics:
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>    1. Referencing (Hwee Ling Lee)
>    2. Band Limited Power Analysis in Fieldtrip? (Ian M. Andolina)
>
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> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 25 Feb 2014 10:32:39 +0100
> From: Hwee Ling Lee <hweeling.lee at gmail.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] Referencing
> Message-ID:
>         <CABG7z0RBBMJCuXCsAN=
> BkryfFvXKuLR2SNpdTxsjWN_rQcAKEA at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear all,
>
> I have 4 electrodes, and I would like to reference my data by subtracting
> from the neighbouring electrode. In other words, E2-E1, E3-E2, E4-E3.
>
> I was wondering if there is an easier way in fieldtrip to perform this
> calculation, and then to change the data structure with these new channel
> labels.
>
> Thanks.
>
> Cheers,
> Hweeling
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> Message: 2
> Date: Tue, 25 Feb 2014 10:25:02 +0000
> From: "Ian M. Andolina" <i.andolina at ucl.ac.uk>
> To: <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] Band Limited Power Analysis in Fieldtrip?
> Message-ID: <530C6F7E.2000702 at ucl.ac.uk>
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>
> Hi, I wanted to use Fieldtrip to recreate the methodology used in a
> paper by Leopold et al., 2003
> <http://dx.doi.org/10.1093/cercor/13.4.422> ? the relevant methods
> section is the following:
>
> /?The LFP signals were resampled to 1 kHz, and then band-pass filtered
> into seven frequency ranges using a second order, bi-directional,
> zero-phase Chebyshev type-1 filter. The frequency ranges, as well as
> their rough mapping onto classically defined electroencephalographic
> conventions, were the following: ? (1?4 Hz), ? (5?8 Hz), ? (9?14 Hz), ?
> (15?30 Hz), ?L (30?50 Hz), ?H (50?100 Hz), and ?VH (100?150 Hz). The
> resulting band-limited signals were full-wave rectified by taking their
> absolute value. They were then resampled to 20 Hz after low-pass
> filtering with an eighth order Chebyshev type-1 filter (cutoff = 8 Hz).?/
>
> My LFP data is sampled at 1kHz, and I manually pad with data either side
> of the event triggered region of interest. Fieldtrip doesn?t have a
> |chebyshev type-1| filter, but would a second order two-pass (aka zero
> phase?) butterworth be good enough considering the frequency bands used?
> I?m using the following cfg passed to |ft_preprocessing| for the initial
> bandpass filtering and rectification:
>
> |freq ={[1  4], [5  8], [9  14], [15  30], [30  50], [50  100], [100
>  150]};
> for  j  =1:length(freq)
>   cfg                        =[];
>   cfg.padding                =0;
>   cfg.bpfilter            ='yes';
>   cfg.bpfilttype            ='but';
>   cfg.bpfreq                = freq{j};
>   cfg.bpfiltdir            ='twopass';
>   cfg.bpfiltord            =2;
>   cfg.bpinstabilityfix    ='reduce';
>   cfg.rectify                ='yes';
>   bp{j}  = ft_preprocessing(cfg,ft);
> end
> |
>
> As far as I can see in |ft_preprocessing| rectification occurs after
> filtering, so this is as specified by Leopold /et al.,/
>
> Then for downsampling/resampling:
>
> |cfg                        =[];
> cfg.padding                =0;
> cfg.lpfilter            ='yes';
> cfg.lpfreq                =8;
> cfg.lpfilttype            ='but';
> cfg.lpfiltdir            ='twopass';
> cfg.lpfiltord            =8;
> cfg.lpinstabilityfix    ='reduce';
> bp{j}  = ft_preprocessing(cfg,bp{j});
> cfg                        =[];
> cfg.resample            ='yes';
> cfg.resamplefs            =20;
> cfg.detrend                ='no';
> bp{j}  = ft_resampledata(cfg,bp{j});
> |
>
> Does this seem a correct translation of this method in Fieldtrip? Are
> there any caveats other than the filter differences?
>
> Thanks, Ian
>
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