[FieldTrip] Question on Cluster-based permutation tests on time-frequency data

Wed Apr 2 17:25:29 CEST 2014

Dear Nithin,

I use Fieldtrip's permutation testing routines quite often on non-fieldtrip
analyzed data. It is quite straightforward as long as you have your
channel/neighbour layout the way Fieldtrip needs it. Try playing around
with the ft_read_sens(*[EEG file with readable channel locations]*), or
simply choose a layout file from the folder /template/layout/ inside your
fieldtrip folder; from this you need to use ft_prepare_neighbours; or more
simple, choose a predefined neighbour structure from /template/neighbours.
This covers quite a lot of systems; of course yours may not be in there;
then I think ft_read_sens is your only option. I use EEGLAB for example,
and I could import a .set file with a field EEG.chanlocs using ft_read_sens.

Then, I do the following for time-frequency data (but in principle this
should be very similar for time-domain ERP data):

- I first configure the cfg as described in the cluster permutation testing
tutorial
- Then I manually put my own analyzed data into a "freqs" structure; name
is of course arbitrary, but should have the same fields as the output from
ft_freqanalysis:

freq1.freq = [the values of the different frequencies];
freq1.time = [the different time points];
freq1.dimord = 'subj_chan_freq_time';
freq1.grad = [the result from ft_read_sense];
freq1.label = [the labels from the result of ft_read_sense];
freq1.powspctrm = [the result of your own custom/EEGLAB/whatever
non-fieldtrip analysis, provided this has the dimensions of freqs.dimord];

Then I do this for example for two different conditions, make my design
matrix in cfg.design, and put it into ft_freqstatistics(cfg,freq1,freq2)

Hope this helps.
- Joram

On Wed, Apr 2, 2014 at 4:39 PM, Lam, Nietzsche <n.lam at fcdonders.ru.nl>wrote:

> Dear Nithin,
>
> FieldTrip was primarily set up for MEG data but we definitely have several
> tutorials discussing similar procedures for EEG data.  Perhaps these
> tutorials can help you out.
>
> http://fieldtrip.fcdonders.nl/tutorial/eeg_preprocessing_erp
>
> http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_timelock
> http://fieldtrip.fcdonders.nl/tutorial/eventrelatedstatistics
> Although these later two links are performed on MEG data, I think they are
> useful to you because functions used to calculate ERFs are also used for
> ERPs. For example, in FieldTrip you can use ft_timelockanalysis and
> ft_timelockstatistics for both EEG and MEG data.
>
> Regarding the use of non-FieldTrip data for cluster-permutations.
> Theoretically, I think it is possible, but probably more experienced users
> can answer this. Nevertheless, you could look into this FAQ about how to
> import your data so that it ca be used by FieldTrip here:
>
> http://fieldtrip.fcdonders.nl/faq/how_can_i_import_my_own_dataformat?s[]=import&s[]=data
>
> best,
> Nietzsche
>
>
>
> ----- Original Message -----
> > From: "Nithin Krishna" <nkrishna at mprc.umaryland.edu>
> > To: "FieldTrip discussion list" <fieldtrip at science.ru.nl>
> > Sent: Wednesday, 2 April, 2014 4:23:01 PM
> > Subject: [FieldTrip] Question on Cluster-based permutation tests on
> time-frequency data
> > Dear All,
> > I read the tutorial section on Cluster-based permutation tests on
> > time-frequency data as well as the Maris and Oostenveld, Journal of
> > Neuroscience Methods, 2007 report. I am interested in setting up a ERP
> > experiment on EEG data in this regard I like the procedure and
> > processing section of the tutorial, however I would like to know if
> > there is any section for EEG, I understand that megplanar is specific
> > for MEG.
> > Also is it possible to use 3D matrix (TFR) (time, Freq channels ) non
> > feild trip output to run the cluster based permutation tests.
> > Looking forward
> > Nithin
> >
> >
> > >>> "Jörn M. Horschig"<jm.horschig at donders.ru.nl> 4/2/2014 6:39 AM >>>
> >
> > Hi Marco,
> >
> > could you be more specific, in the style of e.g.
> >
> http://fieldtrip.fcdonders.nl/faq/how_to_ask_good_questions_to_the_community#how_to_ask_a_questio
> > ?
> >
> > Best,
> > Jörn
> >
> > On 4/2/2014 12:31 PM, Marco Rotonda wrote:
> > > Hi all,
> > > I would like to compute a simple alpha-theta ratio and do some
> > > statistics on it.
> > > I had my data from freqanalysis.
> > > Then I averaged with selectdata_new to have the mean for a band.
> > > Then the simple ratio for each channel.
> > > If now I call freqstatistics I have an error.
> > > Any suggestion?
> > >
> > > Thanks
> > >
> > > Marco
> > >
> > >
> > > _______________________________________________
> > > fieldtrip mailing list
> > > fieldtrip at donders.ru.nl
> > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >
> >
> > --
> > 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
> >
> > Contact:
> > E-Mail: jm.horschig at donders.ru.nl
> > Tel: +31-(0)24-36-68493
> > Web: http://www.ru.nl/donders
> >
> > Visiting address:
> > Trigon, room 2.30
> > Kapittelweg 29
> > NL-6525 EN Nijmegen
> > The Netherlands
> >
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> --
> Nietzsche H.L. Lam, MSc
> PhD Candidate
>
> Max Planck Institute for Psycholinguistics
> Wundtlaan 1, 6525 XD Nijmegen, The Netherlands
>
> Donders Institute for Brain, Cognition and Behaviour,
> Centre for Cognitive Neuroimaging,
> Kapittelweg 29, 6525EN Nijmegen, The Netherlands
>
> n.lam at fcdonders.ru.nl
> +31-24-3668219
>
>
> neurobiologyoflanguage.com
>
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-- 
Joram van Driel, MSc.
PhD student @ University of Amsterdam
Brain & Cognition @ Department of Psychology
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