[FieldTrip] ft_preprocessing error message during reading some files
Beom Jun Min
mbj0310 at gmail.com
Fri May 31 11:11:33 CEST 2013
Dear respondent,
Thank you for your advices.
I will try these methods.
Best regards
2013/5/30 Chungki Lee <dr.chungki.lee at gmail.com>
> 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
>>> _______________________________________________
>>> fieldtrip mailing list
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>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>>
>>>
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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
> ----------------------------------------------------------------
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
--
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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