query on loading CNT files

Tue Feb 21 12:37:17 CET 2006

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/
>>>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>