[Mne_analysis] concatenation raws and events

Mainak Jas mainakjas at gmail.com
Fri Sep 12 08:45:57 EDT 2014
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Hi Jonathan,

On Fri, Sep 12, 2014 at 3:36 PM, J.A. Entakli <jae40 at cam.ac.uk> wrote:

> Hi,
>
> 1) Mainak : I've already try your idea, the concatenation works but the
> samples are not added, so I can't use events concatenated in the big raw
> file.
>

What I was suggesting was the following: concatenate the raws as you do
right now

raw_conc= concatenate_raws([raw1,raw2], events_list=events_list)

but when computing the epochs, you need to use

epochs = mne.Epochs(raw,  np.concatenate((events1, events2)), event_id,
tmin, tmax, picks=picks, baseline= baseline, reject=reject)

because events is usually a numpy array when computing epochs. How were
these events computed? Maybe you need to do:

events2[0, :] += raw1.last_samp

or something of that sort before you do np.concatenate((events1, events2))?

Mainak


> 2) dgw : Actually I like all the 3 options. I tried the option 2. It
> seems very long to do but it seems the most coherent for me. And above
> all it works perfectly :)
>
> Thank you very much,
> Cheers,
>
> John
> On 11/09/2014 18:35, Mainak Jas wrote:
> > Hi Jonathan,
> >
> > I spotted a bug in your script here:
> >
> > On Thu, Sep 11, 2014 at 5:44 PM, J.A. Entakli <jae40 at cam.ac.uk> wrote:
> >
> >> Hello Everybody,
> >> During my experiment I recorded 2 blocs per subject. I am just
> >> started
> >> with mne_python.
> >>
> >> I have two questions in one ::
> >> 1) I would like to know how can I concatenate the blocs and above
> >> all
> >> the events (corresponding to each bloc) to have just one bloc.
> >> In brief, for each subject I have one bloc with its events and
> >> another
> >> bloc with its events also.
> >>
> >> raw_fname1= '...'
> >> raw_fname2= '...'
> >> event_fname1= '...'
> >> event_fname2= '...'
> >>
> >> raw1 = io.Raw(raw_fname1)
> >> raw2 = io.Raw(raw_fname2)
> >>
> >> events1 = mne.read_events(event_fname1)
> >> events2 = mne.read_events(event_fname2)
> >> events_list = [events1,events2]
> >
> > events is a numpy array, not a list. So, you need to use
> > np.concatenate() to stitch the events together. Something like:
> >
> > import numpy as np
> > events = np.concatenate((events1, events2))
> >
> > Does this solve your problem?
> >
> > Mainak
> >
> >> raw_conc= concatenate_raws([raw1,raw2], events_list=events_list)
> >>
> >> Until here I think these several code lines work correctly...
> >>
> >> 2) But when I try to extract the epochs from raw_conc I have some
> >> error
> >> messages (concerning I think the events_list)
> >>
> >> picks =
> >> mne.pick_types(raw1.info
> >> [1],meg='mag',eeg=False,ecg=False,eog=False,stim=False,
> >> exclude='bads')
> >> epochs = mne.Epochs(raw, events_list, event_id, tmin, tmax,
> >> picks=picks,
> >> baseline= baseline, reject=reject)
> >>
> >> The aim of both questions is to use the tfr_morlet function which
> >> asks
> >> in input the epochs.
> >>
> >> power, itc = tfr_morlet(epochs, freqs=freqs, n_cycles=n_cycles,
> >> use_fft=False, return_itc=True, decim=3,n_jobs=1)
> >>
> >> Someone has an idea about this?
> >>
> >> Bests,
> >>
> >> Jonathan
> >> --
> >> Dr Jonathan Entakli - Research Associate Post doctoral position
> >>
> >> Department of Psychology
> >> University of Cambridge, Downing St
> >> Cambridge CB2 3EB
> >>
> >> Sir William Hardy Building
> >> Office : 314
> >> Mobile : 07778 692 458
> >>
> >> http://www.viscog.psychol.cam.ac.uk/ [2]
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> >>
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> >
> >
> > Links:
> > ------
> > [1] http://raw1.info
> > [2] http://www.viscog.psychol.cam.ac.uk/
> > [3] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> > [4] http://www.partners.org/complianceline
> >
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> > it is
> > addressed. If you believe this e-mail was sent to you in error and the
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>
> --
> Dr Jonathan Entakli - Research Associate
>
> Department of Psychology
> University of Cambridge, Downing St
> Cambridge CB2 3EB
>
> Sir William Hardy Building
> Office : 314
> Mobile : 07778 692 458
>
> http://www.viscog.psychol.cam.ac.uk/
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
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