[FieldTrip] Interpolation and ft_channelrepair
Grazia Di Pisa
g.dipisa at gmail.com
Wed Oct 21 12:27:40 CEST 2015
Hi Jörn,
Thanks for the advice - I've just tried to add cfg.sens = sens but still the same error.
Any other suggestions?
thanks,
~ grazia
> On 21Oct, 2015, at 12:00, fieldtrip-request at science.ru.nl wrote:
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> Today's Topics:
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> 1. Call for new post docs in the Obleser lab | Auditory
> Cognition (Jonas Obleser)
> 2. Spectrum normalization (Wunderle, Thomas)
> 3. Interpolation and ft_channelrepair (Grazia Di Pisa)
> 4. Re: Interpolation and ft_channelrepair
> (=?UTF-8?Q?J=C3=B6rn_M._Horschig?=)
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> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 20 Oct 2015 06:07:51 -0500
> From: Jonas Obleser <jonas at obleser.de>
> To: fieldtrip at science.ru.nl, AUDITORY at LISTS.MCGILL.CA
> Subject: [FieldTrip] Call for new post docs in the Obleser lab |
> Auditory Cognition
> Message-ID: <71625964-4C4D-41CA-BEDB-171CEFBC87F8 at obleser.de>
> Content-Type: text/plain; charset=utf-8
>
> The research group ?Auditory Cognition? (headed by Jonas Obleser; auditorycognition.com), now at the University of L?beck, is seeking to hire two Postdoctoral researchers, initially for 3 years, with the option of extension.
>
> These positions fall into the larger framework of an ERC Consolidator grant ?The listening challenge: How ageing brains adapt? (AUDADAPT) recently awarded to Jonas Obleser, and will allow the joint development of cognitive-neuroscience and psychological research projects targeting adaptive control in the auditory modality of middle-aged adults.
>
> Please download the full job advert here: https://www.dropbox.com/s/sqc9c94ewl6bjjh/Ausschreibung_1031_15_Wiss%20MitarbeiterIn_Psychologie_EN.pdf?dl=1
>
> Note the application deadline of November 12 (postal receipt).
>
> http://auditorycognition.com
> http://uni-luebeck.de
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 20 Oct 2015 14:58:25 +0000
> From: "Wunderle, Thomas" <thomas.wunderle at esi-frankfurt.de>
> To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] Spectrum normalization
> Message-ID:
> <27E5CAD9145EEC41BB9B34C01716A198880C3CD4 at UM-excdag-a02.um.gwdg.de>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi all,
>
> I have a question about how FieldTrip normalizes the output of a spectral analyses using ft_freqanalysis.
> This is important for me, because I need the absolute value of the spectrum for a publication.
>
> I was scanning through the code trying to find the normalization steps.
> In particular, I don't understand the following steps:
>
>
> 1.) The tapers (e.g. hanning) are normalized prior to the multiplication with the data by the following code:
> tap = tap./norm(tap, 'fro'); (line 195 in the function fr_specest_mtmfft)
> What is the rationale of dividing through this special norm of the taper itself?
>
>
> 2.) After calculating the fft, the specrum is scaled (i.e. in the function fr_specest_mtmfft) by:
>
> dum = dum .* sqrt(2 ./ endnsample); (line 251)
>
> Later on, to get to the power spectrum, the abs of the spectrum is taken and squared
>
> powdum = abs(spectrum(acttap,:,foiind(ifoi),acttboi)) .^2; (line 629 in ft_frequanalysis)
>
>
>
> This puzzles me, because scanning through the literature, the power spectrum should be given by
>
> (2*abs(X)^2) ./ (nfft^2) -> unit: V^2 (X=signal, nfft = number of data points)
>
> and the PSD by
>
> (2*abs(X)^2) ./ (nfft*Fs) -> unit: V^2/Hz (X=signal, nfft = number of data points, Fs=sampling rate)
>
>
>
> Alternatively, one can get the amplitude spectrum from the power spectrum by taking the square root of the PSD:
>
> sqrt(PSD) -> unit: V/sqrt(Hz)
>
> which is still different from
>
> (2*abs(X)) ./ (nfft*Fres) -> unit: V/Hz ? (Fres = frequency resolution = Fs/nfft)
>
>
>
> The result of these equations are different from what comes out of the FieldTrip code.
>
> So what is the unit of the spectrum in FieldTrip?
>
> What is the rationale of scaling the complex spectrum by sqrt(2/nfft) ?
>
> Furthermore, is the unit for the different spectral estimation methods the same? That is, using mtmfft, mtmconvol, wavelet,...?
>
> It would help me a lot if someone could clarify these points.
>
> Thanks in advance,
> Thomas
>
>
> -----
> Dr. Thomas Wunderle
> Ernst Str?ngmann Institute (ESI) for Neuroscience<http://www.ncbi.nlm.nih.gov/feed/rss.cgi?ChanKey=PubMedNews>
> in Cooperation with Max Planck Society <http://www.ncbi.nlm.nih.gov/feed/rss.cgi?ChanKey=PubMedNews>
> Deutschordenstrasse 46
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> Tel: +49 69 96769 516
> Fax: +49 69 96769 555
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> ------------------------------
>
> Message: 3
> Date: Wed, 21 Oct 2015 10:30:07 +0200
> From: Grazia Di Pisa <g.dipisa at gmail.com>
> To: fieldtrip at science.ru.nl
> Subject: [FieldTrip] Interpolation and ft_channelrepair
> Message-ID: <A46541FB-BC67-44E7-A9CD-541FB39B7C54 at gmail.com>
> Content-Type: text/plain; charset=utf-8
>
> Dear all,
>
> I?m trying to do interpolation to repair some bad channels, but I?m getting the error below.
> I've read the ft_fetch_sens help but I don?t understand how I should specify the electrodes.
>
> Is there a file I should upload or am I missing something in my code?
> Any help or hint is very much appreciated!
>
> thanks in advance,
> ~ grazia
>
>
> //
> Error using ft_fetch_sens (line 183)
> no electrodes or gradiometers specified.
>
> Error in ft_channelrepair (line 115)
> sens = ft_fetch_sens(cfg, data);
>
> Error in new_analyse_GDP (line 42)
> ft_channelrepair(cfg, data)
> //
>
> This is my code:
>
> 15 cfg = [];
> 16 cfg_neighb = [];
> 17 cfg_neighb.method = 'triangulation';
> 18 cfg.senstype = 'EEG';
> 19 cfg_neighb.layout = 'biosemi64.lay';
> 20 neighbours = ft_prepare_neighbours(cfg_neighb);
> 21
> 22 cfg.neighbours = neighbours;
> 23 cfg.channel = {'Fp1', 'Fp2', 'AF7', 'AF3','AF8','F7','F5','FT9',};
> 24 cfg.feedback = 'yes';
> 25 cfg.layout = 'biosemi64.lay';
> 26 lay = ft_prepare_layout(cfg);
> 27
> 28 sens = data;
> 29 sens.type = 'eeg';
> 30 sens.label = lay.label;
> 31 sens.chanpos = lay.pos;
> 32 sens.chanpos(:,3) = 0;
> 33
> 34 ft_neighbourplot(cfg, data)
> 35
> 36 cfg = [];
> 37 cfg.method = 'nearest';
> 38 cfg.badchannel = {'Fp1', 'Fp2', 'AF7', 'AF3','AF8','F7','F5','FT9'};
> 39 cfg.neighbours = neighbours;
> 40 cfg.trials = 'all';
> 41
> 42 ft_channelrepair(cfg, data)
>
>
>
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 21 Oct 2015 10:42:03 +0200
> From: "=?UTF-8?Q?J=C3=B6rn_M._Horschig?=" <jorn at artinis.com>
> To: "'FieldTrip discussion list'" <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] Interpolation and ft_channelrepair
> Message-ID: <002b01d10bdc$5d377040$17a650c0$@artinis.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear Grazia,
>
> try adding cfg.sens = sens; before line 42. That will set the sensor definition so that ft_channelrepair knows the location of your channels, which is otherwise not obvious.
>
> Best,
> J?rn
>
> --
>
> J?rn M. Horschig, PhD, Software Engineer
> Artinis Medical Systems | +31 481 350 980
>
>> -----Original Message-----
>> From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-
>> bounces at science.ru.nl] On Behalf Of Grazia Di Pisa
>> Sent: Wednesday, October 21, 2015 10:30 AM
>> To: fieldtrip at science.ru.nl
>> Subject: [FieldTrip] Interpolation and ft_channelrepair
>>
>> Dear all,
>>
>> I?m trying to do interpolation to repair some bad channels, but I?m getting
>> the error below.
>> I've read the ft_fetch_sens help but I don?t understand how I should specify
>> the electrodes.
>>
>> Is there a file I should upload or am I missing something in my code?
>> Any help or hint is very much appreciated!
>>
>> thanks in advance,
>> ~ grazia
>>
>>
>> //
>> Error using ft_fetch_sens (line 183)
>> no electrodes or gradiometers specified.
>>
>> Error in ft_channelrepair (line 115)
>> sens = ft_fetch_sens(cfg, data);
>>
>> Error in new_analyse_GDP (line 42)
>> ft_channelrepair(cfg, data)
>> //
>>
>> This is my code:
>>
>> 15 cfg = [];
>> 16 cfg_neighb = [];
>> 17 cfg_neighb.method = 'triangulation';
>> 18 cfg.senstype = 'EEG';
>> 19 cfg_neighb.layout = 'biosemi64.lay';
>> 20 neighbours = ft_prepare_neighbours(cfg_neighb);
>> 21
>> 22 cfg.neighbours = neighbours;
>> 23 cfg.channel = {'Fp1', 'Fp2', 'AF7', 'AF3','AF8','F7','F5','FT9',};
>> 24 cfg.feedback = 'yes';
>> 25 cfg.layout = 'biosemi64.lay';
>> 26 lay = ft_prepare_layout(cfg);
>> 27
>> 28 sens = data;
>> 29 sens.type = 'eeg';
>> 30 sens.label = lay.label;
>> 31 sens.chanpos = lay.pos;
>> 32 sens.chanpos(:,3) = 0;
>> 33
>> 34 ft_neighbourplot(cfg, data)
>> 35
>> 36 cfg = [];
>> 37 cfg.method = 'nearest';
>> 38 cfg.badchannel = {'Fp1', 'Fp2', 'AF7', 'AF3','AF8','F7','F5','FT9'};
>> 39 cfg.neighbours = neighbours;
>> 40 cfg.trials = 'all';
>> 41
>> 42 ft_channelrepair(cfg, data)
>>
>>
>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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