[FieldTrip] Interpolation and ft_channelrepair
Vitória Piai
v.piai.research at gmail.com
Wed Oct 21 19:44:28 CEST 2015
Hi Grazia,
I'm using the following code and it works:
cfgn = [];
cfgn.method = 'template';
cfgn.layout = 'biosemi64.lay';
cfg = [];
cfg.neighbours = ft_prepare_neighbours(cfgn, data);
cfg.elec = ft_read_sens('standard_1005.elc');
cfg.missingchannel = [];
cfg.badchannel = chanrepair; % these are my channels
cfg.trials = [1 3 5]; % for particular trials, otherwise use 'all'
data = ft_channelrepair(cfg,data);
Hope this helps
Vitoria
On 10/21/2015 3:27 AM, Grazia Di Pisa wrote:
> 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
>> <mailto:fieldtrip-request at science.ru.nl> wrote:
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>> Today's Topics:
>>
>> 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?=)
>>
>>
>> ----------------------------------------------------------------------
>>
>> 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 |
>> AuditoryCognition
>> 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
>> 60528 Frankfurt am Main, Germany
>> www.esi-frankfurt.de<http://www.esi-frankfurt.de/>
>> thomas.wunderle at esi-frankfurt.de<mailto:thomas.wunderle at esi-frankfurt.de>
>> Tel: +49 69 96769 516
>> Fax: +49 69 96769 555
>>
>> Sitz der Gesellschaft: Frankfurt am Main
>> Registergericht: Amtsgericht Frankfurt - HRB 84266
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>>
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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 = [];
>> 17cfg_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 = [];
>>> 17cfg_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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>>
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>> End of fieldtrip Digest, Vol 59, Issue 17
>> *****************************************
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