[FieldTrip] Trigger values in data matrix

[Robert Oostenveld]

Dear Hamza,

For the GDF format, the low-level reading function underneath ft_read_data uses the Biosig toolbox (which contains the sopen and sread function) as you already had figured out. The problem with biosig is that it does not have a consistent way of representing the events in a dataset for all data formats that it represents, so the general wrapper around it in fieldtrip cannot get the events. So in short: fieldtrip explicitely recognizes header+data+event, whereas biosig only has header+data as a consistent representaiton of the file content.

In your gdf file there is probably a trigger or status channel, which can be used for flank detection. In ft_read_event around line 354 you see the relevant code, where the fieldtrip/fileio/private/read_trigger function is used to read the channel and detect the triggers. I can imagine that the calibration of the trigger/status channel is incorerct, resulting in values that are not integers (as you would expect on a trigger channel). 

We recently internally discussed the gdf writer linked to the biosemi2ft realtime application. It would be good to have more example data from another system. We don't have a biosemi system ourselves, but a collaborating group in Nijmegen (Peter Desain's lab) has one. They have not yet reported a problem like yours, but it would be good to check. Therefore I suggest that you report it as a bug on bugzilla.fcdonders.nl and upload a problematic example file (see http://fieldtrip.fcdonders.nl/faq/how_should_i_send_example_data_to_the_developers).

best
Robert 
 



On 5 Jan 2012, at 15:14, Hamza Fawzi Altakroury (Student) wrote:

> Dear Boris
> 
> I sent that email when I was trying to read from .gdf file (by sread) while it is acquiring the data through biosemi2ft. But it did not work.
> 
> My question was if I do the following:
> 
> >> H = sopen('test.gdf');
> >> data = sread(H,2048);     % I did not here 2048 sample I did not know why.
> >> data = data';                  
> >> trig = data(1,:);               % The status channel
> >> plot(trig)
> 
> I am not going to get the trigger values that I desired.
> 
> Best.
> 
> On Thu, Jan 5, 2012 at 1:19 PM, Boris Reuderink <b.reuderink at donders.ru.nl> wrote:
> Dear Hamza,
> 
> Could you elaborate on what you mean here? Could you perhaps provide some context, and a minimal working example?
> 
> Best,
> 
> Boris
> 
> On Sunday, December 25, 2011, Hamza Fawzi Altakroury (Student) wrote:
> Hello,
> 
> I can't get the real trigger values if use sopen function (or ft_read_data), even after adding the min value -1.7281e+009 to get a positive values.
> 
> Note: I plotted the triggers and their proportion is right but I can't get their exact values, what should I do.
> 
> Best,
> 
> -- 
> Hamza Fawzi Altakroury
> Graduate student - MA
> Faculty of Engineering and Natural Sciences
> Sabancı University
> 
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> 
> 
> 
> -- 
> Hamza Fawzi Altakroury
> Graduate student - MA
> Faculty of Engineering and Natural Sciences
> Sabancı University
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> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip