[FieldTrip] ft_preprocessing high-pass filtering question

"Jörn M. Horschig" jm.horschig at donders.ru.nl
Fri Jul 5 08:41:50 CEST 2013

Hi Aaron,

in that case you need to define only one trial, going from 0 to the end 
of the recording and call ft_preprocessing. Not sure if this will work, 
but  something like

/  cfg = [];//
//   ...//
//  hdr = ft_read_header(cfg.dataset);//
//  cfg.trl = [0 hdr.nSamples 0];//
//  data = ft_preprocessing(cfg);/

Subsequently you might want to try using ft_redefinetrial to get the 
epochs you are interested in.

Note however that you need to have sufficient memory for reading all 
your data in. I am not sure how much memory you have, how long your 
recording is, how high your sampling rate and how many channels you 
have. If Matlab crashes when reading in everything, you would need to 
use trialpadding, or need to think of something clever yourself :)

Would be great if you could let us know how you solve this in the end so 
that we can refer to that if someone else in future has a similar question.

On 7/5/2013 3:51 AM, Aaron Schurger wrote:
> Thanks, Thomas. What if I wanted to apply the filtering to the entire
> time series first, and then extract the trial epochs after filtering?
> Is there a way to do that?
> Thanks,
> Aaron
> On Thu, Jul 4, 2013 at 4:31 PM, Thomas Hartmann
> <thomas.hartmann at th-ht.de> wrote:
>> hi aaron,
>> filtering is generally applied after the data have been epoched. to avoid
>> the filter artifacts you are speaking about, we normally define epochs that
>> are sufficiently larger so that these artifacts would be in data we are not
>> interested in. about 1s at both ends of the epoch should be enough in most
>> cases. but you better check... later you can use ft_redefinetrial to discard
>> that extra data.
>> hope this helps.
>> best,
>> thomas
>> Aaron Schurger <aaron.schurger at gmail.com> schrieb:
>>> Hi,
>>> When you read in a data file using ft_preprocessing, with high-pass
>>> filtering, is the high-pass filter applied before the data are epoched
>>> (i.e. on the entire time series for the whole data file), or is the
>>> high-pass filter applied separately to each epoch? For very low
>>> frequencies (with period longer than one data epoch) this will make a
>>> difference.
>>> Thanks!
>>> Aaron
>>> --
>>> Aaron Schurger, PhD
>>> Post-doctoral researcher
>>> INSERM U992 / NeuroSpin
>>> CEA - Saclay, France
>>> +33-1-69-08-66-47
>>> aaron.schurger at gmail.com
>>> http://www.unicog.org
>>> ________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>> Dr. Thomas Hartmann
>> CIMeC - Center for Mind/Brain Sciences
>> Università degli Studi di Trento
>> via delle Regole, 101
>> 38060 Mattarello (TN)
>> Tel: +39 0461 28 2779
>> Fax: +39 0461 28 3066
>> Email: thomas.hartmann at th-ht.de
>> Homepage: http://sites.google.com/site/obobcimec/
>> "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan
>> Doyle)
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
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Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
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Visiting address:
Trigon, room 2.30
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