[FieldTrip] ft_preprocessing high-pass filtering question

[Aaron Schurger]

Thanks, Jörn. If memory is an issue, I suppose I could try doing the
filtering one channel at a time, applying redefinetrial to each
channel (one at a time), and then put the resulting epochs back
together in a field-trip structure. I'll let you know what I come up
with (if I find a good solution). Memory may not end up being an issue
because my recording sessions were only about 5 min long each, and
with 8 Gb of RAM, should be OK.
Cheers,
Aaron

On Fri, Jul 5, 2013 at 2:41 AM, "Jörn M. Horschig"
<jm.horschig at donders.ru.nl> wrote:
> 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.
>
> Best,
> Jörn
> 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
> ________________________________
>
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>
> Dr. Thomas Hartmann
>
> CIMeC - Center for Mind/Brain Sciences
> Università degli Studi di Trento
> via delle Regole, 101
> 38060 Mattarello (TN)
> ITALY
>
> Tel: +39 0461 28 2779
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> Email: thomas.hartmann at th-ht.de
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>
> "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan
> Doyle)
>
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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
>
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-- 
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