[Mne_analysis] Redefine Onset

Dan McCloy dan.mccloy at gmail.com
Mon Nov 4 18:36:28 EST 2019
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        External Email - Use Caution        

Do you mean that you created epochs, but now you want the epochs to include
different samples (i.e., start earlier and/or end later)?  If so, you have
to go back to the Raw data and re-do epoching with different tmin/tmax
values.

Or do you mean that the *data* in the epochs is what you want, but you just
want to change the *time labels* associated with each sample?  If so,
`epochs.shift_time()` should do what you want; please say more about why it
does not get you what you need.  Note that behavior of `shift_time` is
currently being changed in the development version of MNE-Python;
previously time shifts were forced to be integer multiples of the sampling
period, but soon (as soon as
https://github.com/mne-tools/mne-python/pull/6996 gets merged) it will be
possible on the development version to shift by any arbitrary amount of
time.


On Mon, Nov 4, 2019 at 12:37 PM Geller, Jason <jason-geller at uiowa.edu>
wrote:

>         External Email - Use Caution
>
> Hello,
>
> I have an issue where I need to realign the zero point of epochs (there is
> 500 ms of silence at the start of an audio event). Is there an MNE function
> that will allow me to do this? I thought shift_time might get me what I
> need, but it does not.
>
>
>
> > On Nov 4, 2019, at 11:00 AM, mne_analysis-request at nmr.mgh.harvard.edu
> wrote:
> >
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> > Today's Topics:
> >
> >   1. Re: How to edit time attribute in a raw object (Eric Larson)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Mon, 4 Nov 2019 09:21:41 -0500
> > From: Eric Larson <larson.eric.d at gmail.com>
> > Subject: Re: [Mne_analysis] How to edit time attribute in a raw object
> > To: Discussion and support forum for the users of MNE Software
> >       <mne_analysis at nmr.mgh.harvard.edu>
> > Message-ID:
> >       <
> CAGu2niUwUAU4ZUGeLYEqKCih1VN1fXBisVecpe0ii4ynrmPb8g at mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> >        External Email - Use Caution
> >
> > If the time of recording start is properly encoded in the file and read
> by
> > MNE (which is hopefully the case), then you should be able to use it. You
> > can manually convert from relative (starting from zero) to absolute time
> by
> > looking at `raw.info['meas_date']` and `raw.first_samp`. But the eaiser
> > thing to do would be to construct an Annotations
> > <https://mne.tools/stable/generated/mne.Annotations.html> class with
> your
> > behavioral/pupil events (in whatever starting time frame you prefer),
> then
> > set `raw.annotations = my_annotations`, which should convert it to the
> raw
> > object's time reference in `raw.info['meas_date']`. Check out the
> > Annotations tutorials -- such as this one
> > <
> https://mne.tools/dev/auto_tutorials/raw/plot_30_annotate_raw.html#creating-annotations-programmatically
> >
> > -- and if it's not clear from them how to do it, we should improve the
> > documentation.
> >
> > We do not allow modifying the `raw.times` attribute intentionally. A lot
> of
> > downstream code (e.g., epoching) would break, loudly or (worse) silently,
> > in unexpected and unpredictable if users could do this.
> >
> > Eric
> >
> >
> > On Mon, Nov 4, 2019 at 6:03 AM vahid.bokharaie at tuebingen.mpg.de <
> > vahid.bokharaie at tuebingen.mpg.de> wrote:
> >
> >>        External Email - Use Caution
> >>
> >> Hi Philip
> >> Thanks for your sharp response. It calarified the situation for me.
> >> And to answer to your question, for rat EEG, we record behavioural data
> in
> >> a go/no-go task, pupil diameters and EEG. I define Events based on
> >> behavioural and pupil size, and then should convert them into proper
> format
> >> to be read in mne. So it is important that time stamps match. Of course
> >> this is something that can be handled easily, but I could not believe
> such
> >> a simple feature is not incorporated into mne. Hence spent too much time
> >> trying to find the right function.
> >> Regards,
> >> Vahid
> >>
> >>
> >> -------- Original Message --------
> >> Subject: Re: [Mne_analysis] How to edit time attribute in a raw object
> >> From: Phillip Alday
> >> To: Discussion and support forum for the users of MNE Software ,Vahid
> >> Bokharaie
> >> CC:
> >>
> >>
> >> The time in the raw recordings (the Raw object) are assumed to be
> >> arbitrary and just a measure of time elapsed since the beginning of the
> >> recording, so there's not really a way to set or manipulate them. Why do
> >> you need absolute time here? Are you concatenating Raw objects?
> >>
> >> Best,
> >> Phillip
> >>
> >> On 4/11/19 10:55 am, Vahid Bokharaie wrote:
> >>>        External Email - Use Caution
> >>>
> >>> Hi all
> >>> I posted this question in stackoverflow but seems MNE community is not
> >>> active there, hence I searched for MNE mailing list and joined it.
> >>> I use MNE for analysis of both rat and human EEG recordings. The system
> >>> we have for rat EEG is from a company called NeuroNexus, and they have
> >>> their own Matlab script to convert the EEG recordings and the time
> >>> stamps into mat files. And then I import them in python and use MNE to
> >>> analyse and visualise them. This means I have to establish my EEG raw
> >>> objects from the scratch and save them to file, which I can do. But a
> >>> seemingly trivial thing that I have not managed to find out how to do
> is
> >>> to incorporate the time array into the EEG raw object. When I create
> and
> >>> save the EEG raw object, it automatically set the initial time to 0,
> but
> >>> my initial recording time is not 0 and I need to offset that. It is
> >>> important to correct this, because the time stamps of EEG and
> >>> behavioural data should match.
> >>> Simply typing |raw.times = new_array| leads to |AttributeError: can't
> >>> set attribute. ||This should be a very simple thing to do, but I have
> >>> not been able to find it although I have looked into the documentation.
> >>> So, I thought to ask it in here and if it is not really possible, then
> >>> dig into the source code to fix it myself. Thanks in advance.
> >>> Regards,
> >>> Vahid
> >>> |
> >>>
> >>> --
> >>>
> >>
> ---------------------------------------------------------------------------------------
> >>> Vahid S. Bokharaie, PhD
> >>> Senior Research Scientist
> >>> Max Planck Institute for Biological Cybernetics
> >>> Department of Physiology of Cognitive Processes
> >>> Max Planck Ring 8, 72076 Tuebingen, Germany
> >>> +49 (0)7071 - 601-1644
> >>> vahid.bokharaie at tuebingen.mpg.de
> >>> https://www.kyb.tuebingen.mpg.de/person/59086/84548
> >>>
> >>
> --------------------------------------------------------------------------------------
> >>>
> >>>
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