query on coherence and layout

Muthuraman Muthuraman muthuraman10 at HOTMAIL.COM
Mon Apr 3 11:00:22 CEST 2006


hello

I have used freqdescriptives to calculate the coherence between EEG and EMG
the problem is i get a very less coherence value from 0.01 to 0.1
is there the range specified in the programs
and what is the method you use to calculate the coherence can you give a
brief explanation

i have also a problem with the layout
i would like to create my own layout if it is  possible
how it can be done
because in the the previous mail you have mentioned about the elec1010
layout file
but it does not match my requirements
do i need the CTF software for this in all the layout files it is mentioned
to be CTF 151 and so on.

thanking you
with regards
muthu


>From: Muthuraman Muthuraman <muthuraman10 at HOTMAIL.COM>
>Reply-To: FieldTrip discussion list <FIELDTRIP at NIC.SURFNET.NL>
>To: FIELDTRIP at NIC.SURFNET.NL
>Subject: Re: [FIELDTRIP] query on channel arrangement
>Date: Thu, 23 Feb 2006 10:32:13 +0000
>
>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/
>> >>>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> >>



More information about the fieldtrip mailing list