[FieldTrip] Fwd: Getting data from a database instead of files

[Thomas Lusignan]

Hi  Jan-Mathijs,

Thank you so much for your swift and thorough answer!

Sadly, removing the .trl, .channels and .dimord fields did not solve my
problem. It did halve the number of warnings I get (from 8 to 4). A few
quick tests showed me this came down to removing the .trl field and not the
other ones.
I also get a warning about inconsistent sampleinfo, which I forgot to
mention in my original email.

Could it be a problem with my FT path? I had path-related errors with SPM
earlier, and I ended up solving them by adding ft_defaults in my startup.m
file.

Another thing I found out is that the error I get (Array dimensions must
match for binary array op.) doesn't always happen at the same time. The
processing counter goes up to trial 3, and then frequency somewhere between
1 and 24.  I'm not sure what this means, though.

Do you have any suggestions?

Thank you!

Thomas


Le lun. 3 juin 2019 à 11:35, Schoffelen, J.M. (Jan Mathijs) <
jan.schoffelen at donders.ru.nl> a écrit :

> Hi Thomas,
>
> Thanks for your informative e-mail :).
>
> Here's what I did:
>
>
>
>
> *1- Get the data for a subset of my choosing (I tried everything with a
> small 4-channel, 55-trials subset) *
> *2- Put that data into a structure built as follows, adding fields that
> FieldTrip required:*
>
>     fsample: 1017           (I know this is weird but we're stuck with it)
>    channels: [1 17 25 29]   Added to keep track of in-house bookkeeping
>       label: {'Ch:1 idElectrodeSite:181'  'Ch:17 idElectrodeSite:183'
> 'Ch:25 idElectrodeSite:184'
>               'Ch:29 idElectrodeSite:185'}  Not the right structure, but
> I don't have header files to get them from
>       trial: {55×1 cell}    One cell per trial, with each being [chan x
> time]
>        time: {55×1 cell}    One cell per trial, each going from -750ms to
> 750ms (around target onset) This includes a 250ms pad on each side.
>         trl: [55×3 double]  Built from scratch as if the trials were
> continuous. (Inspired by the FT function that does this)
>      dimord: 'chan_time'    Added by hand, can't get Fieldtrip to
> recognize it
>  sampleinfo: [55×2 double]  The first two columns of trl
>
>
> You may need to get rid of the following fields: ’trl’ ‘dimord’ and
> ‘channels’. Once this is done, I think you are ready to go, without
> warnings and errors.
>
>
>
>
> *3- Try to use ft_freqanalysis using the following cfg (also attached) *
> cfg = [];
> cfg.method= 'tfr';
> cfg.pad = 'nextpow2';
> cfg.width = 7;
> cfg.gwidth = 3;
> cfg.foi = [15:1:60];
> cfg.toi = 'all';
>
> I first get the message:
> the input is raw data with 4 channels and 55 trial
> This would be encouraging, but then, I get the following warnings:
>
> Warning: could not determine dimord of "trial" in: (structure shown above)
> Warning: could not determine dimord of "trl" in:   (structure shown above)
> ...but four pairs of them.
>
> Looking through the debugger, I found out they're given when ft_freqanalysis,
> calls ft_checkdata and ft_selectdata.
> *Are these warnings something I should be worried about, or can everything
> work well the way it is?*
> Also, how is it that FT 'could not determine dimord' when I give it one in
> the data structure, and it seems to understand the way it works given the
> message it sends at the beginning?
>
> After the warnings, I get this:
>
> the call to "ft_selectdata" took 16 seconds
> processing trials
> trial 2, frequency 32 (46.18 Hz)
> Array dimensions must match for binary array op.
>
> Error in ft_freqanalysis (line 679)
>             trlcnt(1, ifoi, :) = trlcnt(1, ifoi, :) +
> shiftdim(double(acttboi(:)'),-1);
>
> ...which I simply don't know how to solve.
>
>
> *So in summary:*
>
> 1- Is it possible to make FT work without using original files to get the
> data?
>
>
>
> Yes!
>
> 2- If it is, what have I done wrong, and how could I make it work?
>
>
> See above.
>
>
> 3- Are the warnings worrisome or is it just a natural consequence of
> trying to jerry-rig data in FT?
>
>
> Not worrisome, they should go away if you do exactly as I told :).
>
> 4- Any idea on how to solve the error message I get is appreciated, but a
> secondary objective.
>
>
> Probably it goes away.
>
> Keep up the good work and with best wishes,
> Jan-Mathijs
>
>
>
> I attached the function I made to build the data structure in case it
> could help.
>
>
> Thank you very much for reading this long-winded message!
>
> Regards
>
> Thomas Lusignan, B. Sc.
> Paul Cisek's Lab
> Université de Montréal
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