[FieldTrip] ft_preprocessing error message during reading some files
Chungki Lee
dr.chungki.lee at gmail.com
Thu May 30 11:56:02 CEST 2013
Hi Min
you'd better use ft_definetrial routine before ft_preprocessing.
example)
cfg = [];
cfg.dataset = filename; % string
cfg.trialdef.eventtype = your define text; % string
cfg.trialdef.eventvalue = your label value; % integer
cfg.trialdef.prestim = before onset time (sec); % positive integer,
not negative integer
cfg.trialdef.poststim = after onset time (sec); % positve integer
cfg = ft_definetrial(cfg);
data = ft_preprocessing(cfg);
have fun ^^
2013/5/30 Beom Jun Min <mbj0310 at gmail.com>
> Dear Julian Keil,
>
> Thank you for your reply.
> I agree with that your problem was similar with mine.
> My data was acquired by Neuroscan also.
> There might a problem associated with .CNT file in the newer version.
>
> Could you tell me the number of the older version you used?
>
> Best Regards
>
>
>
> 2013/5/29 Julian Keil <julian.keil at gmail.com>
>
>> Dear BJ Min,
>>
>> what type of data are you trying to read in?
>> I had similar problems when reading in .CNT data.
>> Also, with some systems you have to specify the bit rate (e.g. Neuroscan).
>> For me, reading in data with an older version of FieldTrip solved the
>> problem, but this was in 2011, so I cannot say if the problem with .CNT
>> files has been solved.
>>
>> Good Luck
>>
>> Julian
>>
>> ********************
>> *Dr. Julian Keil*
>> *
>> *
>> AG Multisensorische Integration
>> Psychiatrische Universitätsklinik
>> der Charité im St. Hedwig-Krankenhaus
>> Große Hamburger Straße 5-11, Raum E 307
>> 10115 Berlin
>>
>> Telefon: +49-30-2311-1879
>> Fax: +49-30-2311-2209
>>
>> http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration
>>
>> Am 29.05.2013 um 11:47 schrieb Beom Jun Min:
>>
>> Dear all,
>>
>> Hello, my name is BJ Min from Korea.
>>
>> I'm dealing with EEG data of many subjects.
>>
>> When I run ft_preprocessing, the error message below shows with only some
>> files of my data. (not all files)
>>
>> Warning: rounding "endsample" to the nearest integer
>> > In ft_read_data at 100
>> In ft_preprocessing at 577
>> ??? Error using ==> ft_read_data at 149
>> cannot read data after the end of the file
>>
>> Error in ==> ft_preprocessing at 577
>> dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample',
>> begsample, 'endsample', endsample, 'chanindx', rawindx,
>> 'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat',
>> cfg.dataformat)
>>
>> I think that there might be a kind of problem in data acquisition, and I
>> modified below scripts in the ft_read_data function with comment %.
>>
>> % % test whether the requested data segment is not outside the file
>> % if any(begsample<1)
>> % error('FILEIO:InvalidBegSample', 'cannot read data before the begin
>> of the file');
>> % elseif any(endsample>(hdr.nSamples*hdr.nTrials))
>> % error('FILEIO:InvalidEndSample', 'cannot read data after the end of
>> the file');
>> % end
>>
>> After that, the ft_preprocessing worked well.
>>
>> However, the files with the first problem showed additional warning
>> message while running ft_definetrial. (not error message)
>>
>> Warning: Integer operands are required for colon operator when used as
>> index
>> > In fileio\private\loadcnt at 464
>> In ft_read_header at 1450
>> In ft_preprocessing at 398
>>
>> Warning: rounding "endsample" to the nearest integer
>> > In ft_read_data at 100
>> In ft_preprocessing at 577
>>
>> Also, during ft_redefinetrial, following warning message occurs.(not
>> error message)
>>
>> Warning: removing inconsistent sampleinfo
>> > In ft_datatype_raw at 97
>> In ft_checkdata at 213
>> In ft_redefinetrial at 104
>>
>> Warning: the trial definition in the configuration is inconsistent with
>> the actual data
>> > In utilities\private\warning_once at 116
>> In utilities\private\fixsampleinfo at 74
>> In ft_datatype_raw at 154
>> In ft_checkdata at 213
>> In ft_redefinetrial at 206
>>
>> Warning: reconstructing sampleinfo by assuming that the trials are
>> consecutive segments of a continuous recording
>> > In utilities\private\warning_once at 116
>> In utilities\private\fixsampleinfo at 79
>> In ft_datatype_raw at 154
>> In ft_checkdata at 213
>> In ft_redefinetrial at 206
>>
>> I wonder if these messages during ft_redefinetrial mean wrong defining
>> trials.
>> Should I continue these process like this, modifying the ft_preprocessing
>> function?
>> Or, is it better to exclude some erroneous files?
>>
>> Best regards
>>
>> --
>> BeomJun Min, M.D.
>>
>> Department of Medical System Engineering (DMSE)
>> Gwangju Institute of Science and Technology (GIST)
>> 261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
>> 500-712, Republic of Korea (South)
>> Phone: +82-62-715-3266 / Fax: +82-62-715-3244
>> E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
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>>
>>
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>
>
>
> --
> BeomJun Min, M.D.
>
> Department of Medical System Engineering (DMSE)
> Gwangju Institute of Science and Technology (GIST)
> 261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
> 500-712, Republic of Korea (South)
> Phone: +82-62-715-3266 / Fax: +82-62-715-3244
> E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
--
----------------------------------------------------------------
Chungki Lee, Ph.D.
Post-doc
Biomedical Research Institute
Korea Institute of Science and Technology
E-mail: chungki at kist.re.kr
Tel:+82-2-958-5636, C.P: +82-10-5223-7309
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