[FieldTrip] troubles while reading 4D MEG files in getting the MEG channels
jan-mathijs schoffelen
jan.schoffelen at donders.ru.nl
Mon Mar 4 07:16:04 CET 2013
Hi Sophie,
That's strange. I assume that the same problem occurs when you try it with the xxx.COH dataset? Could you create yourself an account on our bugzilla.fcdonders.nl website, and file a bug about this? If you then upload one of the xxx.COH datasets (along with the config-file), as well as the MEG_LABEL variable we can have a look at it.
Best wishes,
Jan-Mathijs
On Feb 27, 2013, at 1:51 PM, sophie chen wrote:
> Dear all,
>
> I am trying to read MEG 4D files with Fieldtrip version 20130226 using ft_preprocessing file with a preselection of MEG channels ( 'MEG' or a cell array of channel names, here is MEG_LABEL) but the output
> data contains only 152 channels while I have 248 channels... I tried the same code with Fieldtrip version 20121015, and I get everything properly (i.e. 248 channels)
> Following the script I am running and the corresponding results in matlab.
>
>
> cfg = [];
> cfg.dataset = 'c,rfDC';
> cfg.trialdef.eventtype = 'TRIGGER';
> cfg.trialdef.eventvalue = 2;
> cfg.trialdef.prestim = 1;
> cfg.trialdef.poststim = 2;
> [cfg] = ft_definetrial(cfg);
>
> % cfg.channel = 'MEG';
> cfg.channel = MEG_LABEL;
> cfg.continous = 'yes';
> data_2 = ft_preprocessing (cfg)
>
> I get this >>
>
> Warning: no trialfun was specified, using ft_trialfun_general
> > In ft_definetrial at 123
> evaluating trialfunction 'ft_trialfun_general'
> applying digital weights in the gradiometer balancing matrix
> Warning: all channels must have unique labels, creating unique labels
> > In ft_read_header at 1681
> In ft_trialfun_general at 71
> In ft_definetrial at 162
> undoing the Supine balancing
> reading the events from 'c,rfDC'
> applying digital weights in the gradiometer balancing matrix
> Warning: all channels must have unique labels, creating unique labels
> > In ft_read_header at 1681
> In ft_read_event at 174
> In ft_trialfun_general at 80
> In ft_definetrial at 162
> found 677 events
> created 249 trials
> the call to "ft_definetrial" took 5 seconds
> applying digital weights in the gradiometer balancing matrix
> Warning: all channels must have unique labels, creating unique labels
> > In ft_read_header at 1681
> In ft_preprocessing at 394
> processing channel { 'A2' 'A104' 'A241' 'A138' 'A71' 'A125' 'A20' 'A65' 'A9' 'A114' 'A175' 'A228' 'A35' 'A191' 'A37' 'A170' 'A207' 'A224' 'A82' 'A238' 'A28' 'A239' 'A13' 'A165' 'A204' 'A25' 'A70' 'A11' 'A47' 'A64' 'A177' 'A127' 'A247' 'A194' 'A5' 'A242' 'A168' 'A31' 'A245' 'A219' 'A105' 'A222' 'A76' 'A188' 'A215' 'A235' 'A181' 'A38' 'A230' 'A91' 'A212' 'A24' 'A96' 'A57' 'A86' 'A116' 'A141' 'A120' 'A80' 'A210' 'A113' 'A27' 'A135' 'A167' 'A206' 'A100' 'A43' 'A200' 'A102' 'A132' 'A122' 'A62' 'A21' 'A229' 'A55' 'A32' 'A85' 'A58' 'A60' 'A88' 'A79' 'A203' 'A145' 'A139' 'A156' 'A68' 'A159' 'A236' 'A161' 'A6' 'A126' 'A94' 'A15' 'A193' 'A150' 'A36' 'A225' 'A195' 'A172' 'A108' 'A81' 'A171' 'A218' 'A173' 'A201' 'A74' 'A29' 'A164' 'A232' 'A69' 'A157' 'A97' 'A124' 'A40' 'A178' 'A179' 'A33' 'A147' 'A148' 'A89' 'A119' 'A52' 'A190' 'A73' 'A136' 'A184' 'A51' 'A77' 'A129' 'A197' 'A182' 'A46' 'A92' 'A41' 'A90' 'A23' 'A154' 'A18' 'A248' 'A149' 'A118' 'A152' 'A140' 'A110' 'A185' 'A162' 'A106' 'A187' 'A221' 'A133' 'A158' 'A216' }
> reading and preprocessing
> reading and preprocessing trial 249 from 249
>
> the call to "ft_preprocessing" took 20 seconds
>
> data_2 =
>
> hdr: [1x1 struct]
> label: {152x1 cell}
> time: {1x249 cell}
> trial: {1x249 cell}
> fsample: 2.0345e+03
> sampleinfo: [249x2 double]
> trialinfo: [249x1 double]
> grad: [1x1 struct]
> cfg: [1x1 struct]
>
>
> This is what I get with Fieldtrip 20121015:
>
> Warning: no trialfun was specified, using ft_trialfun_general
> > In ft_definetrial at 123
> evaluating trialfunction 'ft_trialfun_general'
> applying digital weights in the gradiometer balancing matrix
> undoing the Supine balancing
> reading the events from 'c,rfDC'
> applying digital weights in the gradiometer balancing matrix
> undoing the Supine balancing
> found 677 events
> created 249 trials
> the call to "ft_definetrial" took 7 seconds
> applying digital weights in the gradiometer balancing matrix
> undoing the Supine balancing
> processing channel { 'A22' 'A2' 'A104' 'A241' 'A138' 'A214' 'A71' 'A26' 'A93' 'A39' 'A125' 'A20' 'A65' 'A9' 'A8' 'A95' 'A114' 'A175' 'A16' 'A228' 'A35' 'A191' 'A37' 'A170' 'A207' 'A112' 'A224' 'A82' 'A238' 'A202' 'A220' 'A28' 'A239' 'A13' 'A165' 'A204' 'A233' 'A98' 'A25' 'A70' 'A72' 'A11' 'A47' 'A160' 'A64' 'A3' 'A177' 'A63' 'A155' 'A10' 'A127' 'A67' 'A115' 'A247' 'A174' 'A194' 'A5' 'A242' 'A176' 'A78' 'A168' 'A31' 'A223' 'A245' 'A219' 'A12' 'A186' 'A105' 'A222' 'A76' 'A50' 'A188' 'A231' 'A45' 'A180' 'A99' 'A234' 'A215' 'A235' 'A181' 'A38' 'A230' 'A91' 'A212' 'A24' 'A66' 'A42' 'A96' 'A57' 'A86' 'A56' 'A116' 'A151' 'A141' 'A120' 'A189' 'A80' 'A210' 'A143' 'A113' 'A27' 'A137' 'A135' 'A167' 'A75' 'A240' 'A206' 'A107' 'A130' 'A100' 'A43' 'A200' 'A102' 'A132' 'A183' 'A199' 'A122' 'A19' 'A62' 'A21' 'A229' 'A84' 'A213' 'A55' 'A32' 'A85' 'A146' 'A58' 'A60' 'A88' 'A79' 'A169' 'A54' 'A203' 'A145' 'A103' 'A163' 'A139' 'A49' 'A166' 'A156' 'A128' 'A68' 'A159' 'A236' 'A161' 'A121' 'A4' 'A61' 'A6' 'A126' 'A14' 'A94' 'A15' 'A193' 'A150' 'A227' 'A59' 'A36' 'A225' 'A195' 'A30' 'A109' 'A172' 'A108' 'A81' 'A171' 'A218' 'A173' 'A201' 'A74' 'A29' 'A164' 'A205' 'A232' 'A69' 'A157' 'A97' 'A217' 'A101' 'A124' 'A40' 'A123' 'A153' 'A178' 'A1' 'A179' 'A33' 'A147' 'A117' 'A148' 'A87' 'A89' 'A243' 'A119' 'A52' 'A142' 'A211' 'A190' 'A53' 'A192' 'A73' 'A226' 'A136' 'A184' 'A51' 'A237' 'A77' 'A129' 'A131' 'A198' 'A197' 'A182' 'A46' 'A92' 'A41' 'A90' 'A7' 'A23' 'A83' 'A154' 'A34' 'A17' 'A18' 'A248' 'A149' 'A118' 'A208' 'A152' 'A140' 'A144' 'A209' 'A110' 'A111' 'A244' 'A185' 'A246' 'A162' 'A106' 'A187' 'A48' 'A221' 'A196' 'A133' 'A158' 'A44' 'A134' 'A216' }
> reading and preprocessing
> reading and preprocessing trial 249 from 249
>
> the call to "ft_preprocessing" took 24 seconds
>
> data_2 =
>
> hdr: [1x1 struct]
> label: {248x1 cell}
> time: {1x249 cell}
> trial: {1x249 cell}
> fsample: 2.0345e+03
> sampleinfo: [249x2 double]
> trialinfo: [249x1 double]
> grad: [1x1 struct]
> cfg: [1x1 struct]
>
>
> I hope this helps to find out where the problem is coming from...
> Thanks in advance for your help
>
> Cheers,
>
> Sophie Chen
>
>
>
>
>
> _______________________________________________
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> fieldtrip at donders.ru.nl
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Jan-Mathijs Schoffelen, MD PhD
Donders Institute for Brain, Cognition and Behaviour,
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands
Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands
J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793
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