[FieldTrip] Eletkta Neuromag data in Fieldtrip

[Gianpaolo Demarchi]

Hi,
just a couple of comments, since nobody chimes in :-)

> Il giorno 16 feb 2016, alle ore 13:51, Seymour, Robert (Research Student) <seymourr at aston.ac.uk> ha scritto:
> 
> Dear all, 
> 
> I am working with Elekta Neuromag data and want to load the raw .fif file into Fieldtrip; i.e. having not undergone Maxfilter cleaning. I have turned off Internal Active Sheilding (IAS) during recording.
> 
> Loading in motion-corrected data is fine and produces reasonable results. However using the same code with un-Maxfiltered data produces some very strange plots - please see some pictures I have uploaded online.. http://imgur.com/a/b0Mrl <http://imgur.com/a/b0Mrl> . It is not an issue with the data themselves because it looks sensible in Graph (the Elekta data visualisation program). 

They look reasonable ... what you see is the effect of the (bp?) filter on your data and the x seconds rectangular window that you’re using for watching at  them. 
The first pic should be grads, and the second mags, if I’m not mistaken, and in the second one you can clearly see 50 Hz mains noise (you’ve 50Hz over there, isn’t :-) ?!) 
If you just want to take a look at the data and scroll trough the time, don’t apply “hardcoded” filters with ft_preprocessing, but fully exploit the power of ft_databrowser, and change filters on the fly there with the button on the right, using a cfg.preproc.xxx syntax. 

For a quick look at e.g. magnetometers, you can use:

cfg = [];
cfg.dataset= rawfile; %in your case
cfg.layout = 'neuromag306mag.lay';
cfg.channel = 'MEGMAG';
ft_databrowser(cfg)

check the help of ft_databrowser to see which option does what, but in this case the important part is cfg.dataset, that ft_databrowser uses to read directly  the file from the disk. The additional stuff is for topoplotting on right click, e.g. to identify eye blinks …
The code above is not applying any filtering, so expect some mess, but then from the data browser click on the grey button on the right and try e.g.:

cfg.preproc.lpfilter        =  'yes' ; % you don't want to see 50 Hz now
cfg.preproc.lpfreq          = 45 ;
cfg.preproc.hpfilter        =  'yes' ; 
cfg.preproc.hpfreq          = 1 ; % try out different value, to suit your needs


then change a bit the values and see how this looks like. Then you can chop the data in epochs as you did (btw, there is no need of both cfg.headerfile and
cfg.datafile, the latter should suffice), but then again don’t apply any “hardcoded” filter values at this stage, if the idea is still to take a general look at the data. You can filter in plotting later … or just put the hardcoded filter values in your final (data in ->  Nature paper out) script.
Hope this helps …
Best,
G.


> 
> My preprocessing code can be loaded here: http://notepad.cc/peebluki61 <http://notepad.cc/peebluki61> . If anyone has any idea what is going on I would be very grateful!
> 
> Many thanks, 
> 
> Robert Seymour (PhD student, Aston Brain Centre)
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip <http://mailman.science.ru.nl/mailman/listinfo/fieldtrip>
Dr. Gianpaolo Demarchi
FB Psychologie - Universität Salzburg
Hellbrunnerstr, 34  5020 Salzburg (A)
Tel: +43 (0) 662 / 8044 - 5135
gianpaolo.demarchi at sbg.ac.at



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160216/ef0083eb/attachment-0002.html>