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

[Schoffelen, J.M. (Jan Mathijs)]

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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