[FieldTrip] Problems with ft_appendata - merging datasets

[styll at med.ovgu.de]

Hi Jörn,

thank you for useful information. I will try to set up the workaround that
you mentioned in your mail. In the case of problems I contact you by mail

:0)

Best regards

Sascha



> Dear Sascha,
>
> What you do is perfectly fine, but what you want is not possible in
> FieldTrip (yet?). FieldTrip is designed such that triggers (and all
> other events) are stored with respect to sample number from the
> beginning of the recording, i.e. datafile on disk. However, when you
> merge datasets, FieldTrip cannot infer to what dataset a specific sample
> number belongs - in your case it could be coming from 4 different
> datasets - and thus dismisses this information completely.
>
> So, what you would need to as a workaround is to save the events with
> respect to your trials of interest (and dataset), and after merging,
> create a fake sampleinfo and event structure. Then, you would need to
> create events with samples respective to the fake sampleinfo. This is a
> somewhat tedious work, and only a hack to get what you want, but it's
> the only way so far :) But be aware that this work might result in a lot
> of nasty errors if you are not careful enough.
>
> If you do not know what I mean, feel free to send me a mail and I can
> try my best to explain what I mean with a short example script.
>
> Best,
> Jörn
>
> On 7/9/2012 3:56 PM, styll at med.ovgu.de wrote:
>> Hello,
>>
>> I probably have a problem with the use of ft_appendata. I want to merge
>> 4
>> MEG datasets (i.e. 4 runs, all the same number of channels, sampling
>> rate,
>> etc.) of the same subject after I defined my trials of interest and
>> preprocessed the 4 datasets individually. If I use ft_databrowser for a
>> look into every single dataset, all trials (10 in each run/dataset)
>> seems
>> to be OK with the correct sequence: defined prestim time range, trigger
>> and poststim time range. If I check the merged dataset I can go through
>> all of the 40 trials, but there is no sequence like: prestim time range,
>> trigger and poststim-time.  Here is my pipeline for the first steps:
>>
>> %%%% run1
>> cfg.dataset='
\train01_64\run1\c,rfDC';
>> cfg.trialdef.prestim=1;      %%% in sec
>> cfg.trialdef.poststim=5;     %%% in sec
>> cfg.trialfun = 'traildef_train01_all_pics_run1';
>> data_run1 = ft_definetrial(cfg)
>>
>> cfg.channel    = {'MEG'};
>> cfg.dftfilter='yes';
>> prepro_run_1 = ft_preprocessing(cfg)
>>
>> %%%% run2
>> cfg.dataset='
\train01_64\run2\c,rfDC';
>> cfg.trialdef.prestim=1;      %%% in sec
>> cfg.trialdef.poststim=5;     %%% in sec
>> cfg.trialfun = 'traildef_train01_all_pics_run2';
>> data_run1 = ft_definetrial(cfg)
>>
>> cfg.channel    = {'MEG'};
>> cfg.dftfilter='yes';
>> prepro_run_2 = ft_preprocessing(cfg)
>>
>> the same for run3 and run4
>>
>> %%%% merging the data
>>
>> cfg=[];
>> merged_data = ft_appenddata(cfg, prepro_run_1, prepro_run_2,
>> prepro_run_3,
>> prepro_run_4)
>>
>> Do I miss something or is there in error in my pipeline or in my
>> strategy

>>
>> Best regards
>>
>> Sascha
>>
>>
>> _______________________________________________
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>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
> --
> Jörn M. Horschig
> PhD Student
> Donders Institute for Brain, Cognition and Behaviour
> Centre for Cognitive Neuroimaging
> Radboud University Nijmegen
> Neuronal Oscillations Group
>
> P.O. Box 9101
> NL-6500 HB Nijmegen
> The Netherlands
>
> Contact:
> E-Mail: jm.horschig at donders.ru.nl
> Tel:    +31-(0)24-36-68493
> Web: http://www.ru.nl/donders
>
> Visiting address:
> Trigon, room 2.30
> Kapittelweg 29
> NL-6525 EN Nijmegen
> The Netherlands
>
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