query on channel arrangement
Muthuraman Muthuraman
muthuraman10 at HOTMAIL.COM
Thu Feb 23 11:32:13 CET 2006
hello
Thanks Jan
We have the data for EEG taken with 64-channel(Neuroscan) arrangement
and i need to specify channel arrangement
when i want to calculate the coherence between EEG and EMG
so for example : in real data
FPZ- 45 -in the EEG channel arrangement
AF7-41 -in the EEG channel arrangement
M1-29- EMG channel
M2-30-EMG channel
M3-63-EMG channel
M4-64-EMG channel
but when i calculate the coherence i want them in the 64-channel layout
instead of 151 layout
and to change the channels in the coherence plot as
for example-
FPZ-1 -in the coherence plot
AF7-2 -in the coherence plot
M1-52-in the coherence plot
M2-53-in the coherence plot
M3-54-in the coherence plot
M4-55-in the coherence plot
Like this i wanted to change the channel arrangement in the coherence plot
for all the channels
how can i change it, please can you give me some idea regarding this
with regards
muthu
>From: Jan Mathijs Schoffelen <Jan.Schoffelen at FCDONDERS.RU.NL>
>Reply-To: FieldTrip discussion list <FIELDTRIP at NIC.SURFNET.NL>
>To: FIELDTRIP at NIC.SURFNET.NL
>Subject: Re: [FIELDTRIP] query on loading CNT files
>Date: Tue, 21 Feb 2006 12:37:17 +0100
>
>Dear Muthuraman,
>
>I guess that you should specify the files which the preprocessing-function
>is going to read in. So you should specify a
>
>cfg.headerfile (which causes your crash, since you left it empty)
>
>and a
>
>cfg.datafile
>
>In your case I would try:
>
>cfg.headerfile = headerfile;
>cfg.datafile = headerfile; (since as far as I know, these are one and the
>same).
>
>Good luck,
>
>Jan-Mathijs
>
>PS: Since you already manually defined your trials, you do not need to call
>Definetrial anymore (so the step: [cfg] = definetrial(cfg) can be omitted)
>
>-----Original Message-----
>From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
>Of Muthuraman Muthuraman
>Sent: Tuesday, February 21, 2006 11:27 AM
>To: FIELDTRIP at NIC.SURFNET.NL
>Subject: Re: [FIELDTRIP] query on loading CNT files
>
>hello
>
>I have tried what you have suggested me in the previous mail
>and i have attached the steps i have performed in matlab and the error also
>
>if i skip the preprocessing step
>and go for the calculation of coherence using freqanalysis
>how to specify data in that case for the function
>(freq=freqanalysis(cfg,data));
>please give me suggestion on this
>
>
>
> >>headerfile='pd_mof_tr0_o_0307.cnt';
> >>hdr = read_fcdc_header(headerfile);
>Loading file pd_mof_tr0_o_0307.cnt ...
> >>cfg.trl = [];
>for i=1:floor(hdr.nSamples/hdr.Fs)
> cfg.trl(i,1) = (i-1)*hdr.Fs + 1;
> cfg.trl(i,2) = (i )*hdr.Fs;
> cfg.trl(i,3) = 0;
>end
> >>cfg
>
>cfg =
>
> trl: [172x3 double]
> >>[cfg] = definetrial(cfg);
>retaining exist trial definition
>found 0 events
>created 172 trials
>
> >>data=preprocessing(cfg);
>??? Error using ==> read_fcdc_header
>file '' does not exist
>
>Error in ==> C:\muthu\work\fieldtrip-20060131\preprocessing.m
>On line 236 ==> hdr = read_fcdc_header(cfg.headerfile);
>
>
>
>
>with regards
>muthuraman
>
>
>
> >From: Robert Oostenveld <r.oostenveld at FCDONDERS.RU.NL>
> >Reply-To: FieldTrip discussion list <FIELDTRIP at NIC.SURFNET.NL>
> >To: FIELDTRIP at NIC.SURFNET.NL
> >Subject: Re: [FIELDTRIP] query on loading CNT files
> >Date: Tue, 24 Jan 2006 13:54:16 +0100
> >
> >The relevant warning seems to be
> >
> >>Warning: no events found in pd_mof_tr0_o_0307.cnt
> >
> >That means that the low level code used to read the CNT file does not
>find
>
> >any triggers in your datafile. That either means that the low level
> >reading function (private/read_ns_cnt.m) has a bug, or that your data
>does
>
> >not contain any triggers.
> >
> >If it does not contain triggers (i.e. if there are no trials in the
>data),
>
> >you should make your own cfg.trl field prior to calling PREPROCESSING
>and
> >skip preprocessing. The documentation of DEFINETRIAL explains what
>cfg.trl
>
> >means. I suggest that you try something like
> >
> >hdr = read_fcdc_header(headerfile);
> >cfg.trl = [];
> >for i=1:floor(hdr.nSamples/hdr.Fs)
> > cfg.trl(i,1) = (i-1)*hdr.Fs + 1; % begin sample of each trial
> > cfg.trl(i,2) = (i )*hdr.Fs; % end sample
> > cfg.trl(i,3) = 0; % offset, i.e. relative location of
> >the time axis
> >end
> >data = preprocessing(cfg);
> >
> >This segments your continuous data in trials of one second length.
> >
> >best,
> >Robert
> >
> >
> >
> >On 24-jan-2006, at 11:46, Muthuraman Muthuraman wrote:
> >
> >>hello
> >>
> >>I am beginner with field trip
> >>as in the previous mail i have asked about the query on loading CNT
>files
> >>and according to the reply i need to call the function DEFINETRAIL
> >>in the function DEFINETRAIL i have to use the READ_FCDC_EVENT to find
>the
>
> >>events in the data
> >>which gave warnings
> >>
> >>i have attached in the mail what were exactly the steps carried out for
> >>the EEG analysis
> >>
> >>'pd_mof_tr0_o_0307.cnt' is the file which contains the data
> >>
> >>
> >> >>headerfile='pd_mof_tr0_o_0307.cnt';
> >>>>[hdr] = read_fcdc_header(headerfile);
> >>Loading file pd_mof_tr0_o_0307.cnt ...
> >>>>hdr
> >>
> >>hdr =
> >>
> >> Fs: 1000
> >> nChans: 64
> >> nSamples: 172040
> >> nSamplesPre: 0
> >> nTrials: 1
> >> label: {1x64 cell}
> >>
> >>>>datafile='pd_mof_tr0_o_0307.cnt';begsample=1;endsample=172;chanindx=
> >>>>64;continuous=1;
> >>>>[dat] = read_fcdc_data(datafile, hdr, begsample, endsample, chanindx,
> >>>>continuous);
> >>Loading file pd_mof_tr0_o_0307.cnt ...
> >>done
> >>>>filename='pd_mof_tr0_o_0307.cnt';
> >>>>[event] = read_fcdc_event(filename)
> >>Warning: handling of event structure has not been fully tested for
> >>Neuroscan *.cnt files
> >>>In C:\muthu\work\fieldtrip-20060118\read_fcdc_event.m at line 414
> >>Loading file pd_mof_tr0_o_0307.cnt ...
> >>done
> >>Warning: no events found in pd_mof_tr0_o_0307.cnt
> >>>In C:\muthu\work\fieldtrip-20060118\read_fcdc_event.m at line 620
> >>
> >>event =
> >>
> >> []
> >>
> >>
> >>Thanking you
> >>with regards
> >>muthuraman
> >>
> >>>From: Robert Oostenveld <r.oostenveld at FCDONDERS.RU.NL>
> >>>Reply-To: FieldTrip discussion list <FIELDTRIP at NIC.SURFNET.NL>
> >>>To: FIELDTRIP at NIC.SURFNET.NL
> >>>Subject: Re: [FIELDTRIP] query on loading CNT files
> >>>Date: Wed, 18 Jan 2006 21:20:37 +0100
> >>>
> >>>Dear Muthuraman
> >>>
> >>>All analyses start by calling the PREPROCESSING function, which reads
> >>>the data segments of interest into memory. Prior to that, you should
> >>>call DEFINETRIAL to determine the data segments of interest (usually
> >>>based on the triggers present in the datafile). Please see the help
>of
> >>>those two functions (type "help function_name" on the matlab command
> >>>line) or look at http:// www2.ru.nl/fcdonders/fieldtrip/ reference.html
> >>>
> >>>best regards
> >>>Robert
> >>>
> >>>
> >>>On 18-jan-2006, at 11:44, Muthuraman Muthuraman wrote:
> >>>
> >>>>hello
> >>>>
> >>>>I would like to use fieldtrip to analyse EEG recordings
> >>>>how to load CNT files which contains the data
> >>>>how can i load the data and do the analysis
> >>>>
> >>>>
> >>>>with regards
> >>>>muthuraman
> >>>>
> >>>
> >>>
> >>>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> >>>Robert Oostenveld, PhD
> >>>F.C. Donders Centre for Cognitive Neuroimaging
> >>>Radboud University Nijmegen
> >>>phone: +31-24-3619695
> >>>http://www.ru.nl/fcdonders/
> >>>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> >>
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